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Conserved domains on  [gi|307151595|ref|YP_003886979|]
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PAS/PAC sensors-containing diguanylate cyclase/phosphodiesterase [Cyanothece sp. PCC 7822]

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List of domain hits

Name Accession Description Interval E-value
EAL cd01948
EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL ...
1159-1400 3.14e-112

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria.


:

Pssm-ID: 238923  Cd Length: 240  Bit Score: 354.54  E-value: 3.14e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1159 TNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEq 1238
Cdd:cd01948     1 ADLRRALERGEFELYYQPIVDLRTGRIVGYEALLRWRHPEGGLISPAEFIPLAEETGLIVELGRWVLEEACRQLARWQA- 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1239 fiGAENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGY 1318
Cdd:cd01948    80 --GGPDLRLSVNLSARQLRDPDFLDRLLELLAETGLPPRRLVLEITESALIDDLEEALATLRRLRALGVRIALDDFGTGY 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1319 SSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLE 1398
Cdd:cd01948   158 SSLSYLKRLPVDYLKIDRSFVRDIETDPEDRAIVRAIIALAHSLGLKVVAEGVETEEQLELLRELGCDYVQGYLFSRPLP 237

                  ..
gi 307151595 1399 SE 1400
Cdd:cd01948   238 AE 239
GGDEF cd01949
Diguanylate-cyclase (DGC) or GGDEF domain; Diguanylate-cyclase (DGC) or GGDEF domain: ...
982-1140 8.51e-61

Diguanylate-cyclase (DGC) or GGDEF domain; Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.


:

Pssm-ID: 143635  Cd Length: 158  Bit Score: 206.64  E-value: 8.51e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  982 LHDGLTGLPNRTLLLDRVEQAIKRKQQQpNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARFG 1061
Cdd:cd01949     1 YTDPLTGLPNRRAFEERLERLLARARRS-GRPLALLLIDIDHFKQINDTYGHAAGDEVLKEVAERLRSSLRESDLVARLG 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 307151595 1062 GDEFVILLEDLTIwTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIAMYRSKEAGRARY 1140
Cdd:cd01949    80 GDEFAILLPGTDL-EEAEALAERLREAIEEPFFIDGQEIRVTASIGIATYPEDGEDAEELLRRADEALYRAKRSGRNRV 157
PBPb cd00134
Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, ...
47-256 3.97e-28

Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.


:

Pssm-ID: 238078 [Multi-domain]  Cd Length: 218  Bit Score: 114.78  E-value: 3.97e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   47 FPPLYLVDRTGKPSGFAIDVMKEVAKlaQLKVRYEIKNT-WSEVQETLINGNADLIPN-LGITPARQTQMSFTAPVETDS 124
Cdd:cd00134     9 YPPFSFRDANGELTGFDVDLAKAIAK--ELGVKVKFVEVdWDGLITALKSGKVDLIAAgMTITPERAKQVDFSDPYYKSG 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  125 VSVFVRASNhQIKTVAHLAGHRVGVVKG-TVGYEIAKNRQNIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQAD 203
Cdd:cd00134    87 QVILVKKGS-PIKSVKDLKGKKVAVQKGsTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHP 165
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 307151595  204 VSNRIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:cd00134   166 PELKIVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 218
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
319-420 7.95e-13

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


:

Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 66.89  E-value: 7.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  319 SEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIASLTPENPMITHEHRVRLSSGEIRWNQW 398
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLV 81
                          90       100
                  ....*....|....*....|..
gi 307151595  399 TNRVIMDEKRNIIEFQAVGRDI 420
Cdd:cd00130    82 SLTPIRDEGGEVIGLLGVVRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
740-839 3.45e-07

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


:

Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 49.94  E-value: 3.45e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  740 PNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQ-INPHFNRSGQWRHRKANGEIIDVE 818
Cdd:cd00130     2 PDGVIVLDLD-GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENlLSGGEPVTLEVRLRRKDGSVIWVL 80
                          90       100
                  ....*....|....*....|...
gi 307151595  819 ITSHGLEYAGRKARLVLA--HDI 839
Cdd:cd00130    81 VSLTPIRDEGGEVIGLLGvvRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
863-967 1.14e-05

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


:

Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 45.32  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  863 APLPILIHAEDGEIVQVNHAWTELSGYHLDELSTIADWTEKAYGERKDIVRSVIDQLyeIDGKVEEGEFAITIKSGETRI 942
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLL--SGGEPVTLEVRLRRKDGSVIW 78
                          90       100
                  ....*....|....*....|....*
gi 307151595  943 WDFSSAPLGKLADGRRLIISMAIDI 967
Cdd:cd00130    79 VLVSLTPIRDEGGEVIGLLGVVRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
494-596 1.57e-04

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


:

Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 41.85  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  494 IWEWNLGTGELYCDPNWIRRLGYDPrEEAINIEWWrSKIDPETLSDHEAALENYLNGKTEYlALEYKIQTLEGEWLWIGG 573
Cdd:cd00130     5 VIVLDLDGRILYANPAAEQLLGYSP-EELIGKSLL-DLIHPEDREELRERLENLLSGGEPV-TLEVRLRRKDGSVIWVLV 81
                          90       100
                  ....*....|....*....|...
gi 307151595  574 RGKCIaYDQQRKPLKILGTHRDI 596
Cdd:cd00130    82 SLTPI-RDEGGEVIGLLGVVRDI 103
PAS_8 pfam13188
PAS domain;
611-675 3.93e-04

PAS domain;


:

Pssm-ID: 257556  Cd Length: 66  Bit Score: 40.29  E-value: 3.93e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 307151595   611 ELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGW-SLENRQKGDLLAEFEPESEYRQSVLNYIK 675
Cdd:pfam13188    1 ERLRALFENAPDGILVLDRGGRILYANPAALELLGYeELLGELLGELLDDLEALAEEALELLEELE 66
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3;
39-256 6.53e-41

Bacterial extracellular solute-binding proteins, family 3;


:

Pssm-ID: 249906 [Multi-domain]  Cd Length: 220  Bit Score: 152.04  E-value: 6.53e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    39 VTAVIPKYFPPLYLVDRTGKPSGFAIDVMKEVAKlaQLKVRYEIKNT-WSEVQETLINGNADLIPN-LGITPARQTQMSF 116
Cdd:pfam00497    1 LRVGTDADYPPFEYVDENGKLVGFDVDLAKAIAK--RLGVKVEFVPVsWDGLIPALQSGKIDVIIAgMTITPERKKQVDF 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   117 TAPVETDSVSVFVRASNHQ--IKTVAHLAGHRVGVVKGTVGYEIA-KNRQNIQLEVFDGIEYGVFELLAGHVDALIYSES 193
Cdd:pfam00497   79 SDPYYTSGQVLVVRKKDSDksIKSLADLKGKTVGVQKGTTAEDLLlLKKPGAKIVEYDDLAEALQALAAGRVDAVVADSP 158
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595   194 VLKEIVAQADVSNrIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:pfam00497  159 VLAYLIKKNPGLN-LVVVGEPLSGEPYGIAVRKGDPELLAALNKALAELKADGTLAKLYEKWF 220
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
753-974 1.38e-16

FOG: PAS/PAC domain [Signal transduction mechanisms]


:

Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 80.66  E-value: 1.38e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  753 FLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVpLLEQYILQINPHFNRSGQWRHRKANGEIIDVEITSHGL-EYAGRKA 831
Cdd:COG2202    11 IIYANEAAEELLGYSAEELLGLLLALHPEDRDR-LRELLRRLLAGEELLSEELRLVRKDGEERWVELSAAPLrDGEGRVL 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  832 RLVLAHDITERLKAEKALQESKERFHRAIVDAPLPILIHAEDGEIVQVNHAWTELSGYHLDELSTIADWTEKAYGERKDI 911
Cdd:COG2202    90 GLLGLRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERR 169
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595  912 VRSVIDQLYEIDGKVEEGEFAITIKSGETRIWDFSSAPLGKLADGRRLIISMAIDITERKQAE 974
Cdd:COG2202   170 ELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRDDGEIVGVVGIARDITERKQAE 232
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
623-846 1.18e-14

FOG: PAS/PAC domain [Signal transduction mechanisms]


:

Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 74.50  E-value: 1.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  623 MLAYFDQHYNLLWVNREWEKIWGWSLENRQKGDLLAEFEPESEYRQSVLNYIKSAQGKWRDFKILVRDGRIIDTSWANVK 702
Cdd:COG2202     1 LILVLDRDGRIIYANEAAEELLGYSAEELLGLLLALHPEDRDRLRELLRRLLAGEELLSEELRLVRKDGEERWVELSAAP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  703 LSDGTSIAIG----QDITERKRIEEILRESEEKYRLFFDANPNPLWVYDLETFaFLEVNQATIEHYGYTREEFLAMTIRD 778
Cdd:COG2202    81 LRDGEGRVLGllglRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGR-ILYANPAAEELLGYSPEEELGRGLSD 159
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595  779 IRPPEDVPL----LEQYILQINPHFNRSGQWRHRKANGEIIDVEITSHGLEYAGRKARLV-LAHDITERLKAE 846
Cdd:COG2202   160 LIHPEDEERreleLARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRDDGEIVGVVgIARDITERKQAE 232
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
307-430 2.49e-12

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


:

Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 65.77  E-value: 2.49e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   307 SESRYRGIVEDQSEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIAS-LTPENPMITHEHR 385
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERrLEGEREPVSEERR 80
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 307151595   386 VRLSSGEIRWNQWTNRvIMDEKRNIIEFQAVGRDITQLKQVEAAL 430
Cdd:TIGR00229   81 VRRKDGSEIWVEVSVS-PIRTNGGELGVVGIVRDITERKQAEEAL 124
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
494-722 3.49e-12

FOG: PAS/PAC domain [Signal transduction mechanisms]


:

Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 66.80  E-value: 3.49e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  494 IWEWNLGTGELYCDPNWIRRLGYDPrEEAINIEWWRSKIDPETLSDHEAALENYLngktEYLALEYKIQTLEGEWLWIGG 573
Cdd:COG2202     2 ILVLDRDGRIIYANEAAEELLGYSA-EELLGLLLALHPEDRDRLRELLRRLLAGE----ELLSEELRLVRKDGEERWVEL 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  574 RGKCIAyDQQRKPLKILGtHRDITETKQTQENLRQQQELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLENRQK 653
Cdd:COG2202    77 SAAPLR-DGEGRVLGLLG-LRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELG 154
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 307151595  654 GDLLAEFEPESEYRQSVLNYIKSAQGK----WRDFKILVRDGRIIDTSWANVKLSDGT-----SIAIGQDITERKRIE 722
Cdd:COG2202   155 RGLSDLIHPEDEERRELELARALAEGRggplEIEYRVRRKDGERVRWILSRISPVRDDgeivgVVGIARDITERKQAE 232
 
Name Accession Description Interval E-value
EAL cd01948
EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL ...
1159-1400 3.14e-112

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria.


Pssm-ID: 238923  Cd Length: 240  Bit Score: 354.54  E-value: 3.14e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1159 TNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEq 1238
Cdd:cd01948     1 ADLRRALERGEFELYYQPIVDLRTGRIVGYEALLRWRHPEGGLISPAEFIPLAEETGLIVELGRWVLEEACRQLARWQA- 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1239 fiGAENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGY 1318
Cdd:cd01948    80 --GGPDLRLSVNLSARQLRDPDFLDRLLELLAETGLPPRRLVLEITESALIDDLEEALATLRRLRALGVRIALDDFGTGY 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1319 SSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLE 1398
Cdd:cd01948   158 SSLSYLKRLPVDYLKIDRSFVRDIETDPEDRAIVRAIIALAHSLGLKVVAEGVETEEQLELLRELGCDYVQGYLFSRPLP 237

                  ..
gi 307151595 1399 SE 1400
Cdd:cd01948   238 AE 239
GGDEF cd01949
Diguanylate-cyclase (DGC) or GGDEF domain; Diguanylate-cyclase (DGC) or GGDEF domain: ...
982-1140 8.51e-61

Diguanylate-cyclase (DGC) or GGDEF domain; Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.


Pssm-ID: 143635  Cd Length: 158  Bit Score: 206.64  E-value: 8.51e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  982 LHDGLTGLPNRTLLLDRVEQAIKRKQQQpNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARFG 1061
Cdd:cd01949     1 YTDPLTGLPNRRAFEERLERLLARARRS-GRPLALLLIDIDHFKQINDTYGHAAGDEVLKEVAERLRSSLRESDLVARLG 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 307151595 1062 GDEFVILLEDLTIwTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIAMYRSKEAGRARY 1140
Cdd:cd01949    80 GDEFAILLPGTDL-EEAEALAERLREAIEEPFFIDGQEIRVTASIGIATYPEDGEDAEELLRRADEALYRAKRSGRNRV 157
PBPb cd00134
Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, ...
47-256 3.97e-28

Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.


Pssm-ID: 238078 [Multi-domain]  Cd Length: 218  Bit Score: 114.78  E-value: 3.97e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   47 FPPLYLVDRTGKPSGFAIDVMKEVAKlaQLKVRYEIKNT-WSEVQETLINGNADLIPN-LGITPARQTQMSFTAPVETDS 124
Cdd:cd00134     9 YPPFSFRDANGELTGFDVDLAKAIAK--ELGVKVKFVEVdWDGLITALKSGKVDLIAAgMTITPERAKQVDFSDPYYKSG 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  125 VSVFVRASNhQIKTVAHLAGHRVGVVKG-TVGYEIAKNRQNIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQAD 203
Cdd:cd00134    87 QVILVKKGS-PIKSVKDLKGKKVAVQKGsTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHP 165
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 307151595  204 VSNRIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:cd00134   166 PELKIVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 218
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
319-420 7.95e-13

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 66.89  E-value: 7.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  319 SEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIASLTPENPMITHEHRVRLSSGEIRWNQW 398
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLV 81
                          90       100
                  ....*....|....*....|..
gi 307151595  399 TNRVIMDEKRNIIEFQAVGRDI 420
Cdd:cd00130    82 SLTPIRDEGGEVIGLLGVVRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
740-839 3.45e-07

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 49.94  E-value: 3.45e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  740 PNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQ-INPHFNRSGQWRHRKANGEIIDVE 818
Cdd:cd00130     2 PDGVIVLDLD-GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENlLSGGEPVTLEVRLRRKDGSVIWVL 80
                          90       100
                  ....*....|....*....|...
gi 307151595  819 ITSHGLEYAGRKARLVLA--HDI 839
Cdd:cd00130    81 VSLTPIRDEGGEVIGLLGvvRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
863-967 1.14e-05

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 45.32  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  863 APLPILIHAEDGEIVQVNHAWTELSGYHLDELSTIADWTEKAYGERKDIVRSVIDQLyeIDGKVEEGEFAITIKSGETRI 942
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLL--SGGEPVTLEVRLRRKDGSVIW 78
                          90       100
                  ....*....|....*....|....*
gi 307151595  943 WDFSSAPLGKLADGRRLIISMAIDI 967
Cdd:cd00130    79 VLVSLTPIRDEGGEVIGLLGVVRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
494-596 1.57e-04

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 41.85  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  494 IWEWNLGTGELYCDPNWIRRLGYDPrEEAINIEWWrSKIDPETLSDHEAALENYLNGKTEYlALEYKIQTLEGEWLWIGG 573
Cdd:cd00130     5 VIVLDLDGRILYANPAAEQLLGYSP-EELIGKSLL-DLIHPEDREELRERLENLLSGGEPV-TLEVRLRRKDGSVIWVLV 81
                          90       100
                  ....*....|....*....|...
gi 307151595  574 RGKCIaYDQQRKPLKILGTHRDI 596
Cdd:cd00130    82 SLTPI-RDEGGEVIGLLGVVRDI 103
Rtn COG2200
c-di-GMP phosphodiesterase class I (EAL domain) [Signal transduction mechanisms]
1155-1408 1.01e-104

c-di-GMP phosphodiesterase class I (EAL domain) [Signal transduction mechanisms]


Pssm-ID: 225110  Cd Length: 256  Bit Score: 334.26  E-value: 1.01e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1155 LELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKA 1234
Cdd:COG2200     2 LQLERDLRQALENGEFSLYYQPIVDLATGRIVGYEALLRWRHPDGGLISPGEFIPLAEETGLIVELGRWVLEEACRQLRT 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1235 WQEQFigaeNLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDF 1314
Cdd:COG2200    82 WPRAG----PLRLAVNLSPVQLRSPGLVDLLLRLLARLGLPPHRLVLEITESALIDDLDTALALLRQLRELGVRIALDDF 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1315 GTGYSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFS 1394
Cdd:COG2200   158 GTGYSSLSYLKRLPPDILKIDRSFVRDLETDARDQAIVRAIVALAHKLGLTVVAEGVETEEQLDLLRELGCDYLQGYLFS 237
                         250
                  ....*....|....
gi 307151595 1395 KPLESEKIVSWLER 1408
Cdd:COG2200   238 RPLPADALDALLSS 251
EAL smart00052
Putative diguanylate phosphodiesterase; Putative diguanylate phosphodiesterase, present in a ...
1158-1400 9.38e-102

Putative diguanylate phosphodiesterase; Putative diguanylate phosphodiesterase, present in a variety of bacteria.


Pssm-ID: 214491  Cd Length: 242  Bit Score: 325.33  E-value: 9.38e-102
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   1158 ETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQE 1237
Cdd:smart00052    1 ERELRQALENGQFLLYYQPIVSLRTGRLVGVEALIRWQHPEGGIISPDEFIPLAEETGLIVPLGRWVLEQACQQLAEWQA 80
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   1238 QFIgaENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTG 1317
Cdd:smart00052   81 QGP--PPLLISINLSARQLISPDLVPRVLELLEETGLPPQRLELEITESVLLDDDESAVATLQRLRELGVRIALDDFGTG 158
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   1318 YSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPL 1397
Cdd:smart00052  159 YSSLSYLKRLPVDLLKIDKSFVRDLQTDPEDEAIVQSIIELAQKLGLQVVAEGVETPEQLDLLRSLGCDYGQGYLFSRPL 238

                    ...
gi 307151595   1398 ESE 1400
Cdd:smart00052  239 PLD 241
EAL pfam00563
EAL domain; This domain is found in diverse bacterial signaling proteins. It is called EAL ...
1160-1396 3.43e-69

EAL domain; This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site.


Pssm-ID: 249961  Cd Length: 231  Bit Score: 233.43  E-value: 3.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  1160 NLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEqf 1239
Cdd:pfam00563    3 ALREALENGEFSLYFQPIVDLRTGKVLGYEALLRWQHPDGGLISPDEFLPLAERLGLIAELDRWVLEKALAQLAEWLN-- 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  1240 igaENLRVSVNLSGKQLQQPNLINRIDNiLTETGLEGKNLKLEITESmLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYS 1319
Cdd:pfam00563   81 ---PDLPLSVNLSPASLLDPSFLEALLA-LKQGGLPPSRLVLEITES-ALDEDLRLLEALARLRSLGFRLALDDFGTGYS 155
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 307151595  1320 SLSYLHYLPVDTLKIDRSFVSRMSQvGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKP 1396
Cdd:pfam00563  156 SLSLLSRLPPDYIKIDRSFIKDLSD-PESRALLRALIALARSLGIKVVAEGVETEEQLELLKELGIDYVQGYLFSKP 231
COG2199 COG2199
c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
963-1143 1.82e-57

c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]


Pssm-ID: 225109  Cd Length: 181  Bit Score: 198.06  E-value: 1.82e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  963 MAIDITERKQAEEQLRHSVLHDGLTGLPNRTLLLDRVEQAIkRKQQQPNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKT 1042
Cdd:COG2199     2 LLRLLTRLRKAEERLERLALHDPLTGLPNRRAFEERLERAL-ARARRHGEPLALLLLDLDHFKQINDTYGHAAGDEVLRE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1043 IADKLQRCVRPTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSE-L 1121
Cdd:COG2199    81 VARRLRSNLREGDLVARLGGDEFAVLLPGTSL-EEAARLAERIRAALEEPFFLGGEELRVTVSIGVALYPEDGSDDAElL 159
                         170       180
                  ....*....|....*....|..
gi 307151595 1122 VRNADIAMYRSKEAGRARYTMF 1143
Cdd:COG2199   160 LRRADLALYRAKRAGRNRVVVF 181
GGDEF pfam00990
GGDEF domain; This domain is found linked to a wide range of non-homologous domains in a ...
981-1137 2.45e-55

GGDEF domain; This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain and has diguanylate cyclase activity. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate.


Pssm-ID: 250276  Cd Length: 159  Bit Score: 191.30  E-value: 2.45e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   981 VLHDGLTGLPNRTLLLDRVEQAIKRkQQQPNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARF 1060
Cdd:pfam00990    1 AAHDPLTGLPNRRYFEEELEQELQR-ARRQQSPLALLLIDLDNFKRINDTYGHAVGDEVLQEVAQRLSSSLRRSDLVARL 79
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 307151595  1061 GGDEFVILLED--LTIWTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIAMYRSKEAGR 1137
Cdd:pfam00990   80 GGEEFAILLPDtsLEGAQELAERIRRLLAALAIPHTLSGLPLYVTISIGIAAYPNDGEDPEDLLKRADQALYQAKQQGR 158
GGDEF smart00267
diguanylate cyclase; Diguanylate cyclase, present in a variety of bacteria.
979-1143 3.19e-54

diguanylate cyclase; Diguanylate cyclase, present in a variety of bacteria.


Pssm-ID: 128563  Cd Length: 163  Bit Score: 188.22  E-value: 3.19e-54
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    979 HSVLHDGLTGLPNRTLLLDRVEQAIKRKQQQPNYlFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVA 1058
Cdd:smart00267    1 RLAFRDPLTGLPNRRYFEEELEQELQRAQRQGSP-FALLLIDLDNFKDINDTYGHAVGDELLQEVAQRLSSCLRPGDLLA 79
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   1059 RFGGDEFVILLEDLTIWtDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIAMYRSKEAGRA 1138
Cdd:smart00267   80 RLGGDEFALLLPETSLE-EAIALAERILQQLREPIIIHGIPLYLTISIGVAAYPNPGEDAEDLLKRADTALYQAKKAGRN 158

                    ....*
gi 307151595   1139 RYTMF 1143
Cdd:smart00267  159 QVAVY 163
GGDEF TIGR00254
diguanylate cyclase (GGDEF) domain; The GGDEF domain is named for the motif GG[DE]EF shared by ...
982-1144 2.42e-41

diguanylate cyclase (GGDEF) domain; The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus, and FixL, a heme-containing oxygen sensor protein [Regulatory functions, Small molecule interactions, Signal transduction, Other].


Pssm-ID: 232895  Cd Length: 165  Bit Score: 151.33  E-value: 2.42e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   982 LHDGLTGLPNRTLLLDRVEQAIKRKQQQpNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARFG 1061
Cdd:TIGR00254    3 VRDPLTGLYNRRYLEEMLDSELKRARRF-QRSFSVLMIDIDNFKKINDTLGHDVGDEVLREVARILQSSVRGSDVVGRYG 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  1062 GDEFVILLEDlTIWTDATKMAQRITEEFES-SFTLQEQEYFT-SASIGITFCSSPEQTPSELVRNADIAMYRSKEAGRAR 1139
Cdd:TIGR00254   82 GEEFVVILPG-TPLEDALSKAERLRDAINSkPIEVAGSETLTvTVSIGVACYPGHGLTLEELLKRADEALYQAKKAGRNR 160

                   ....*
gi 307151595  1140 YTMFD 1144
Cdd:TIGR00254  161 VVVAD 165
PRK11596 PRK11596
cyclic-di-GMP phosphodiesterase; Provisional
1174-1402 6.96e-14

cyclic-di-GMP phosphodiesterase; Provisional


Pssm-ID: 183222  Cd Length: 255  Bit Score: 72.34  E-value: 6.96e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1174 YQPIVSLMNRnLLGFEALVRWIHPEkgviSPANFI-PVAEETGLIIPLGEWVLRESCRQMKAWQEQFIGaENLRVSVNLS 1252
Cdd:PRK11596   34 FQPIYRTSGR-LMAIELLTAVTHPS----NPSQRLsPERYFAEITVSHRLDVVKEQLDLLAQWADFFVR-HGLLASVNID 107
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1253 GKQL----QQPNLINRIDNIltetglegKNLKLEITESMLMNNKEQVSELllqmkAKKIQVSIDDFGTG---YSSLSYLH 1325
Cdd:PRK11596  108 GPTLialrQQPAILRLIERL--------PWLRFELVEHIRLPKDSPFASM-----CEFGPLWLDDFGTGmanFSALSEVR 174
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 307151595 1326 YlpvDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLESEKI 1402
Cdd:PRK11596  175 Y---DYIKVARELFIMLRQSEEGRNLFSQLLHLMNRYCRGVIVEGVETPEEWRDVQRSPAFAAQGYFLSRPAPFETL 248
orph_peri_GRRM TIGR04262
extracellular substrate-binding orphan protein, GRRM family; This subfamily belongs to ...
49-188 5.47e-10

extracellular substrate-binding orphan protein, GRRM family; This subfamily belongs to bacterial extracellular solute-binding protein family 3 (pfam00497). In that family, most members are ABC transporter periplasmic substrate-binding proteins. However, members of the present subfamily are orphans in the sense of being adjacent to neither ABC transporter ATP-binding proteins or permease subunits. Instead, most members are encoded next to the two signature proteins of the proposed Glycine-Rich Repeat Modification (GRRM) system, a radical SAM/SPASM protein GrrM (TIGR04261) and the Gly-rich repeat protein itself GrrA (TIGR04260).


Pssm-ID: 211985  Cd Length: 257  Bit Score: 60.45  E-value: 5.47e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    49 PLYLVDRTGKpSGFAIDVMKEVAKLAQLKVRYEIK------NTWSEVQETLINGNADLIPNLGITPARQTQMSFTAPVET 122
Cdd:TIGR04262   13 PLYQKDDAGY-DGLSFDVLELIRDQLQAELGKPITiqfvvvNSVQEGLPKLRSGKADIACGVAFTWERQMFVDYSLPFAV 91
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 307151595   123 DSVSVFVRASNHqiKTVAHLAGHRVGVVKGTVGYEIAKNRQ-NIQLEVFDGIEYGVFELLAGHVDAL 188
Cdd:TIGR04262   92 SGIRLLAPKGND--GTPESLEGKTVGVVKDSVAAAVLANVVpKATLQPFATPAEALAALKAGKVDAL 156
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
730-794 1.03e-07

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 50.86  E-value: 1.03e-07
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 307151595    730 EKYRLFFDANPNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQ 794
Cdd:smart00091    1 ERLRAILESLPDGIFVLDLD-GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQR 64
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
309-373 1.25e-07

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 50.86  E-value: 1.25e-07
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 307151595    309 SRYRGIVEDQSEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIASL 373
Cdd:smart00091    1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRL 65
PAS_8 pfam13188
PAS domain;
611-675 3.93e-04

PAS domain;


Pssm-ID: 257556  Cd Length: 66  Bit Score: 40.29  E-value: 3.93e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 307151595   611 ELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGW-SLENRQKGDLLAEFEPESEYRQSVLNYIK 675
Cdd:pfam13188    1 ERLRALFENAPDGILVLDRGGRILYANPAALELLGYeELLGELLGELLDDLEALAEEALELLEELE 66
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
854-894 6.82e-03

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 36.61  E-value: 6.82e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 307151595    854 ERFHRAIVDAPLPILIHAEDGEIVQVNHAWTELSGYHLDEL 894
Cdd:smart00091    1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEEL 41
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3;
39-256 6.53e-41

Bacterial extracellular solute-binding proteins, family 3;


Pssm-ID: 249906 [Multi-domain]  Cd Length: 220  Bit Score: 152.04  E-value: 6.53e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    39 VTAVIPKYFPPLYLVDRTGKPSGFAIDVMKEVAKlaQLKVRYEIKNT-WSEVQETLINGNADLIPN-LGITPARQTQMSF 116
Cdd:pfam00497    1 LRVGTDADYPPFEYVDENGKLVGFDVDLAKAIAK--RLGVKVEFVPVsWDGLIPALQSGKIDVIIAgMTITPERKKQVDF 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   117 TAPVETDSVSVFVRASNHQ--IKTVAHLAGHRVGVVKGTVGYEIA-KNRQNIQLEVFDGIEYGVFELLAGHVDALIYSES 193
Cdd:pfam00497   79 SDPYYTSGQVLVVRKKDSDksIKSLADLKGKTVGVQKGTTAEDLLlLKKPGAKIVEYDDLAEALQALAAGRVDAVVADSP 158
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595   194 VLKEIVAQADVSNrIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:pfam00497  159 VLAYLIKKNPGLN-LVVVGEPLSGEPYGIAVRKGDPELLAALNKALAELKADGTLAKLYEKWF 220
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
753-974 1.38e-16

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 80.66  E-value: 1.38e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  753 FLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVpLLEQYILQINPHFNRSGQWRHRKANGEIIDVEITSHGL-EYAGRKA 831
Cdd:COG2202    11 IIYANEAAEELLGYSAEELLGLLLALHPEDRDR-LRELLRRLLAGEELLSEELRLVRKDGEERWVELSAAPLrDGEGRVL 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  832 RLVLAHDITERLKAEKALQESKERFHRAIVDAPLPILIHAEDGEIVQVNHAWTELSGYHLDELSTIADWTEKAYGERKDI 911
Cdd:COG2202    90 GLLGLRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERR 169
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595  912 VRSVIDQLYEIDGKVEEGEFAITIKSGETRIWDFSSAPLGKLADGRRLIISMAIDITERKQAE 974
Cdd:COG2202   170 ELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRDDGEIVGVVGIARDITERKQAE 232
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
623-846 1.18e-14

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 74.50  E-value: 1.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  623 MLAYFDQHYNLLWVNREWEKIWGWSLENRQKGDLLAEFEPESEYRQSVLNYIKSAQGKWRDFKILVRDGRIIDTSWANVK 702
Cdd:COG2202     1 LILVLDRDGRIIYANEAAEELLGYSAEELLGLLLALHPEDRDRLRELLRRLLAGEELLSEELRLVRKDGEERWVELSAAP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  703 LSDGTSIAIG----QDITERKRIEEILRESEEKYRLFFDANPNPLWVYDLETFaFLEVNQATIEHYGYTREEFLAMTIRD 778
Cdd:COG2202    81 LRDGEGRVLGllglRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGR-ILYANPAAEELLGYSPEEELGRGLSD 159
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595  779 IRPPEDVPL----LEQYILQINPHFNRSGQWRHRKANGEIIDVEITSHGLEYAGRKARLV-LAHDITERLKAE 846
Cdd:COG2202   160 LIHPEDEERreleLARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRDDGEIVGVVgIARDITERKQAE 232
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
307-430 2.49e-12

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 65.77  E-value: 2.49e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   307 SESRYRGIVEDQSEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIAS-LTPENPMITHEHR 385
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERrLEGEREPVSEERR 80
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 307151595   386 VRLSSGEIRWNQWTNRvIMDEKRNIIEFQAVGRDITQLKQVEAAL 430
Cdd:TIGR00229   81 VRRKDGSEIWVEVSVS-PIRTNGGELGVVGIVRDITERKQAEEAL 124
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
494-722 3.49e-12

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 66.80  E-value: 3.49e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  494 IWEWNLGTGELYCDPNWIRRLGYDPrEEAINIEWWRSKIDPETLSDHEAALENYLngktEYLALEYKIQTLEGEWLWIGG 573
Cdd:COG2202     2 ILVLDRDGRIIYANEAAEELLGYSA-EELLGLLLALHPEDRDRLRELLRRLLAGE----ELLSEELRLVRKDGEERWVEL 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  574 RGKCIAyDQQRKPLKILGtHRDITETKQTQENLRQQQELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLENRQK 653
Cdd:COG2202    77 SAAPLR-DGEGRVLGLLG-LRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELG 154
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 307151595  654 GDLLAEFEPESEYRQSVLNYIKSAQGK----WRDFKILVRDGRIIDTSWANVKLSDGT-----SIAIGQDITERKRIE 722
Cdd:COG2202   155 RGLSDLIHPEDEERRELELARALAEGRggplEIEYRVRRKDGERVRWILSRISPVRDDgeivgVVGIARDITERKQAE 232
PRK10060 PRK10060
RNase II stability modulator; Provisional
959-1408 5.07e-122

RNase II stability modulator; Provisional


Pssm-ID: 236645 [Multi-domain]  Cd Length: 663  Bit Score: 397.51  E-value: 5.07e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  959 LIISmAIDITERKQAEEQLRHSVLHDGLTGLPNRTLLLDRVEQAIkrkQQQPNYLFAILFIDLDRFKVVNDSLGHLVGDQ 1038
Cdd:PRK10060  216 LICS-GTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAI---NAADNNQVGIVYLDLDNFKKVNDAYGHMFGDQ 291
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1039 LLKTIADKLQRCVRPTDTVARFGGDEFVILLEDLTIWTdATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTP 1118
Cdd:PRK10060  292 LLQDVSLAILSCLEEDQTLARLGGDEFLVLASHTSQAA-LEAMASRILTRLRLPFRIGLIEVYTGCSIGIALAPEHGDDS 370
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1119 SELVRNADIAMYRSKEAGRARYTMFDPIMHTQATQLLELETNLRLALEREEFIVYYQPIVSLmNRNLLGFEALVRWIHPE 1198
Cdd:PRK10060  371 ESLIRSADTAMYTAKEGGRGQFCVFSPEMNQRVFEYLWLDTNLRKALENDQLVIHYQPKITW-RGEVRSLEALVRWQSPE 449
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1199 KGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEQFIgaeNLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKN 1278
Cdd:PRK10060  450 RGLIPPLEFISYAEESGLIVPLGRWVMLDVVRQVAKWRDKGI---NLRVAVNVSARQLADQTIFTALKQALQELNFEYCP 526
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1279 LKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITL 1358
Cdd:PRK10060  527 IDVELTESCLIENEELALSVIQQFSQLGAQVHLDDFGTGYSSLSQLARFPIDAIKLDQSFVRDIHKQPVSQSLVRAIVAV 606
                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|
gi 307151595 1359 AHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLESEKIVSWLER 1408
Cdd:PRK10060  607 AQALNLQVIAEGVETAKEDAFLTKNGVNERQGFLFAKPMPAVAFERWYKR 656
COG5001 COG5001
Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain ...
958-1400 6.18e-96

Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]


Pssm-ID: 227334 [Multi-domain]  Cd Length: 663  Bit Score: 324.16  E-value: 6.18e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  958 RLIISMAIDITERKQAEEQLRHSVlhDGLTGLPNRTLLLDRVEQAIKRKQQQPNYlFAILFIDLDRFKVVNDSLGHLVGD 1037
Cdd:COG5001   207 QVTLTQRAEETRRLSDENDRLANL--DSLTGLPNRRRFFAELDARLAAARQSGRR-LVLGVIDLDGFKPVNDAFGHATGD 283
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1038 QLLKTIADKLQRCVRPTDTVARFGGDEFVILLEDLTIWTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQT 1117
Cdd:COG5001   284 RLLIEVGRRLKAFDGAPILAARLGGDEFALIIPALEDDALRVAGARALCESLQAPYDLRGVRVQVGASIGIAPFPSGADT 363
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1118 PSELVRNADIAMYRSKEAGRARYTMFDPIMHTQATQLLELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHP 1197
Cdd:COG5001   364 SEQLFERADYALYHAKQNGKGAAVLFDARHEAAIRDMAVVEQALRSADLEQELSVHFQPIVDIVSGKTIALEALARWHSP 443
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1198 EKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQeqfigaENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGK 1277
Cdd:COG5001   444 EIGPVPPDVFIGIAERSGQIVELTRLLLAKALREARAWP------MDVRVSINLSARDLASMENVRRLLAIVSESCIAPH 517
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1278 NLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIIT 1357
Cdd:COG5001   518 RLDFEITETAIVCDFDQARDALAALHELGVRTALDDFGTGYSSLSHLRALPLDKIKIDRSFVSDLEENPTSEDIVRTVLQ 597
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 307151595 1358 LAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLESE 1400
Cdd:COG5001   598 LGRNLRMECVVEGVETEAQRDRVAALGATVMQGYHYARPMPAE 640
PRK09776 PRK09776
putative diguanylate cyclase; Provisional
689-1396 1.03e-81

putative diguanylate cyclase; Provisional


Pssm-ID: 182070 [Multi-domain]  Cd Length: 1092  Bit Score: 291.58  E-value: 1.03e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  689 RDGriiDTSWANVKLS-----DGTS---IAIGQDITERKRIEEILRESEEKYRLFFDANPNPLWVYDLET---------F 751
Cdd:PRK09776  364 RDG---EVVWALLAVSlvrdtDGTPlyfIAQIEDINELKRTEQVNERLMERITLANEAGGIGIWEWDLKPniiswdkrmF 440
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  752 AFLEVNQATIEHYgytrEEFLAMTIrdirpPEDVPLLEQYI---LQINPHFN------RSGQWRHRKANGEIIdveitsh 822
Cdd:PRK09776  441 ELYEIPPHIKPTW----QVWYACLH-----PEDRQRVEKEIrdaLQGRSPFKlefrivVKDGVRHIRALANRV------- 504
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  823 gLEYAGRKARLV-LAHDITERLKAEKALQESKERFH---RAIVDAplpILIHAEDGEIVQVNHAWTELSGYHLDE----- 893
Cdd:PRK09776  505 -LNKDGEVERLLgINMDMTEVRQLNEALFQEKERLHitlDSIGEA---VVCTDMAMKVTFMNPVAEKMTGWTQEEalgvp 580
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  894 LSTIADWTEKAYGERKDIVRSVIDQLYeiDGKVEEGEFAITIKSGETRIWDfSSAPLgKLADGRRLIISMAI-DITERKQ 972
Cdd:PRK09776  581 LLTVLHITFGDNGPLMENIYSCLTSRS--AAYLEQDVVLHCRSGGSYDVHY-SITPL-STLDGENIGSVLVIqDVTESRK 656
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  973 AEEQLRHSVLHDGLTGLPNRT---LLLDRVEQAIKRKQQQpnylFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQR 1049
Cdd:PRK09776  657 MLRQLSYSASHDALTHLANRAsfeKQLRRLLQTVNSTHQR----HALVFIDLDRFKAVNDSAGHAAGDALLRELASLMLS 732
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1050 CVRPTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEFES-SFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIA 1128
Cdd:PRK09776  733 MLRSSDVLARLGGDEFGLLLPDCNV-ESARFIATRIISAINDyHFPWEGRVYRVGASAGITLIDANNHQASEVMSQADIA 811
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1129 MYRSKEAGRARYTMFDPiMHTQAT---QLLELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPA 1205
Cdd:PRK09776  812 CYAAKNAGRGRVTVYEP-QQAAAHsehRALSLAEQWRMIKENQLMMLAHGVASPRIPEARNHWLISLRLWDPEGEIIDEG 890
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1206 NFIPVAEETGLIIPLGEWVLRESCRQmkawQEQFIGAENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITE 1285
Cdd:PRK09776  891 AFRPAAEDPALMHALDRRVIHEFFRQ----AAKAVASKGLSIALPLSVAGLSSPTLLPFLLEQLENSPLPPRLLHLEITE 966
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1286 SMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSLSYLHYLPVDTLKIDRSFVSRM--SQVGEnfEIVEAIITLAHHLQ 1363
Cdd:PRK09776  967 TALLNHAESASRLVQKLRLAGCRVVLSDFGRGLSSFNYLKAFMADYLKLDGELVANLhgNLMDE--MLISIIQGHAQRLG 1044
                         730       740       750
                  ....*....|....*....|....*....|...
gi 307151595 1364 MDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKP 1396
Cdd:PRK09776 1045 MKTIAGPVELPLVLDTLSGIGVDLAYGYAIARP 1077
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
47-256 6.53e-33

Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 128.99  E-value: 6.53e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595     47 FPPLYLVDRTGKPSGFAIDVMKEVAKLAQLKVryEIKN-TWSEVQETLINGNADLIPN-LGITPARQTQMSFTAPVETDS 124
Cdd:smart00062   10 YPPFSFADEDGELTGFDVDLAKAIAKELGLKV--EFVEvSFDSLLTALKSGKIDVVAAgMTITPERAKQVDFSDPYYRSG 87
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    125 VSVFVRASNHqIKTVAHLAGHRVGVVKGTVGYEIAKNRQ-NIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQAD 203
Cdd:smart00062   88 QVILVRKDSP-IKSLEDLKGKKVAVVAGTTAEELLKKLYpEAKIVSYDSNAEALAALKAGRADAAVADAPLLAALVKQHG 166
                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|....
gi 307151595    204 VSnRIKILGEPLAE-IKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:smart00062  167 LP-ELKIVPDPLDTpEGYAIAVRKGDPELLDKINKALKELKADGTLKKISEKWF 219
3A0103s03R TIGR01096
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ...
14-256 2.86e-29

lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino acids, peptides and amines].


Pssm-ID: 233269 [Multi-domain]  Cd Length: 250  Bit Score: 119.00  E-value: 2.86e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    14 SLLLASQLFCLKGVAQDTDQVSLLEVTAVIPKYfPPLYLVDRTGKPSGFAIDVMKEVAKLAQLKVRYeIKNTWSEVQETL 93
Cdd:TIGR01096    2 SVLLAALVAGASSAATAAAAKEGSVRIGTETGY-PPFESKDANGKLVGFDVDLAKALCKRMKAKCKF-VEQNFDGLIPSL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    94 INGNADLI-PNLGITPARQTQMSFTAPVETDSVSVFVRASNHQIKTVAHLAGHRVGVVKGTVGYEIAKN--RQNIQLEVF 170
Cdd:TIGR01096   80 KAKKVDAImATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLDGKTVGVQSGTTHEQYLKDyfKPGVDIVEY 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   171 DGIEYGVFELLAGHVDALIYSESVLKEIVAQADVSNRIKILGEPLAEIKR-----AIALRKDNLLLLTRLDKAVNSFVGS 245
Cdd:TIGR01096  160 DSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYfgdgyGIGLRKGDTELKAAFNKALAAIRAD 239
                          250
                   ....*....|.
gi 307151595   246 PKYEQIYRKWY 256
Cdd:TIGR01096  240 GTYQKISKKWF 250
HisJ COG0834
ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino ...
1-260 1.71e-28

ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]


Pssm-ID: 223904 [Multi-domain]  Cd Length: 275  Bit Score: 117.41  E-value: 1.71e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    1 MKTIIKIVYLGFFSLLLASQLFCLKGVAQDTDQVSLleVTAVIPKYFPPL-YLVDRTGKPSGFAIDVMKEVAKLAQLKVR 79
Cdd:COG0834     1 MKKLKLLALAALLAALLLAACAAADLLDKIKARGKL--RVGTEATYAPPFeFLDAKGGKLVGFDVDLAKAIAKRLGGDKK 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   80 YEIKN-TWSEVQETLINGNADLIP-NLGITPARQTQMSFTAPVETDSVSVFVRA-SNHQIKTVAHLAGHRVGVVKGTVGY 156
Cdd:COG0834    79 VEFVPvAWDGLIPALKAGKVDIIIaGMTITPERKKKVDFSDPYYYSGQVLLVKKdSDIGIKSLEDLKGKKVGVQLGTTDE 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  157 EIAKNRQ---NIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQADVSNRIKILGEPLAEIKR-AIALRKDNLL-L 231
Cdd:COG0834   159 AEEKAKKpgpNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYlGIALRKGDDPeL 238
                         250       260
                  ....*....|....*....|....*....
gi 307151595  232 LTRLDKAVNSFVGSPKYEQIYRKWYGEPE 260
Cdd:COG0834   239 LEAVNKALKELKADGTLQKISDKWFGPDD 267
PRK11260 PRK11260
cystine transporter subunit; Provisional
47-257 3.33e-19

cystine transporter subunit; Provisional


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 89.01  E-value: 3.33e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   47 FPPLYLVDRTGKPSGFAIDVMKEVAKlaQLKVRYEIKNT-WSEVQETLINGNADLIPN-LGITPARQTQMSFTAPVETDS 124
Cdd:PRK11260   51 YPPFSFQGEDGKLTGFEVEFAEALAK--HLGVKASLKPTkWDGMLASLDSKRIDVVINqVTISDERKKKYDFSTPYTVSG 128
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  125 VSVFVRASNH-QIKTVAHLAGHRVGVVKGTvGYE--IAKNRQNIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQ 201
Cdd:PRK11260  129 IQALVKKGNEgTIKTAADLKGKKVGVGLGT-NYEqwLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKK 207
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 307151595  202 AdvSNRIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWYG 257
Cdd:PRK11260  208 T--NDTLAVAGEAFSRQESGVALRKGNPDLLKAVNQAIAEMQKDGTLKALSEKWFG 261
PRK09776 PRK09776
putative diguanylate cyclase; Provisional
302-649 1.18e-16

putative diguanylate cyclase; Provisional


Pssm-ID: 182070 [Multi-domain]  Cd Length: 1092  Bit Score: 84.72  E-value: 1.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  302 AALRASESRYRGIVEDQSEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSED----QPQVAQNIASLTPEN 377
Cdd:PRK09776  276 KHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDlnkdLQQVEKLLSGEINSY 355
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  378 PMithEHRVRLSSGEIRWNQWTNRVIMDEKRNIIEFQAVGRDITQLKQVEAALRQLNEeleqrveqrtaelaaeirerqe 457
Cdd:PRK09776  356 SM---EKRYYRRDGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLME---------------------- 410
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  458 ietaliksqakyeqlveklskseeRLQLALEGSGDTIWEWNLGTGELycdpNWIRRL----GYDPrEEAINIEWWRSKID 533
Cdd:PRK09776  411 ------------------------RITLANEAGGIGIWEWDLKPNII----SWDKRMfelyEIPP-HIKPTWQVWYACLH 461
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  534 PETLSDHEAALENYLNGKTEYlALEYKIQTLEG-EWLwiggrgKCIA---YDQQRKPLKILGTHRDITETKQTQENLRQQ 609
Cdd:PRK09776  462 PEDRQRVEKEIRDALQGRSPF-KLEFRIVVKDGvRHI------RALAnrvLNKDGEVERLLGINMDMTEVRQLNEALFQE 534
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 307151595  610 QELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLE 649
Cdd:PRK09776  535 KERLHITLDSIGEAVVCTDMAMKVTFMNPVAEKMTGWTQE 574
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
728-849 6.46e-15

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 73.47  E-value: 6.46e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   728 SEEKYRLFFDANPNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQI---NPHFNRSGQ 804
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLE-GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRlegEREPVSEER 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 307151595   805 WRHRKaNGEIIDVEITSHGLEYAGRKARLVL-AHDITERLKAEKAL 849
Cdd:TIGR00229   80 RVRRK-DGSEIWVEVSVSPIRTNGGELGVVGiVRDITERKQAEEAL 124
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
504-593 5.26e-12

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 254805 [Multi-domain]  Cd Length: 90  Bit Score: 64.32  E-value: 5.26e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   504 LYCDPNWIRRLGYDPREEAINIEWWRSKIDPETLSDHEAALENYLNGKTEYLALEYKIQTLEGEWLWIGGRGKcIAYDQQ 583
Cdd:pfam08447    2 IYWSPRFEEILGYTPEELKSSYEGWLDLVHPEDRERVRRALQELLLKKGEPYSGEYRIRRKDGSYRWVEARGR-PIRDEN 80
                           90
                   ....*....|
gi 307151595   584 RKPLKILGTH 593
Cdd:pfam08447   81 GKPVRVIGVA 90
PAS_9 pfam13426
PAS domain;
327-422 1.63e-10

PAS domain;


Pssm-ID: 257751 [Multi-domain]  Cd Length: 104  Bit Score: 60.09  E-value: 1.63e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   327 PGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIASLTPENPMITHEHRVRLSSGEIRWNQWTNRVIMDE 406
Cdd:pfam13426    9 PEGRIVYANPAALRLLGYTREELLGKSIRDLFGPGTDEEAVARLREALRNGGEVEVELELRRKDGEPFPVLVSASPVRDE 88
                           90
                   ....*....|....*.
gi 307151595   407 KRNIIEFQAVGRDITQ 422
Cdd:pfam13426   89 DGEVVGIVGILRDITE 104
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
321-603 8.21e-10

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 59.48  E-value: 8.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  321 FICRYRPGGTLTFVNQAYCRYFQKTPAAVLDntFWDLIYSEDQPQVAQNIASLTPENPMITHEHRVRLSSGEIRWNQWTN 400
Cdd:COG2202     1 LILVLDRDGRIIYANEAAEELLGYSAEELLG--LLLALHPEDRDRLRELLRRLLAGEELLSEELRLVRKDGEERWVELSA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  401 RVIMDEKRNIIEFQAVgRDITQLKQVEAALRQlneeleqrveqrtaelaaeirerqeietaliksqakyeqlveklskSE 480
Cdd:COG2202    79 APLRDGEGRVLGLLGL-RDITERKRAEEALRE----------------------------------------------SE 111
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  481 ERLQLALEGSGDTIWEWNLGTGELYCDPNWIRRLGYdPREEAINIEWWRSKIDPETLSDHEAALENYLNGKTEYLALEYK 560
Cdd:COG2202   112 ERLRALLEASPDGIWVLDEDGRILYANPAAEELLGY-SPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEIEYR 190
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 307151595  561 IQTLEGE-WLWIGGRGKCIayDQQRKPLKILGTHRDITETKQTQ 603
Cdd:COG2202   191 VRRKDGErVRWILSRISPV--RDDGEIVGVVGIARDITERKQAE 232
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
609-725 1.07e-09

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 58.06  E-value: 1.07e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   609 QQELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLEnRQKGDLLAEFEPEsEYRQSVLNYIKSA-----QGKWRD 683
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAE-ELIGRNVLELIPE-EDREEVRERIERRlegerEPVSEE 78
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 307151595   684 FKILVRDGRIIdtsWANVKLS----DGT---SIAIGQDITERKRIEEIL 725
Cdd:TIGR00229   79 RRVRRKDGSEI---WVEVSVSpirtNGGelgVVGIVRDITERKQAEEAL 124
PAS_9 pfam13426
PAS domain;
740-841 2.94e-08

PAS domain;


Pssm-ID: 257751 [Multi-domain]  Cd Length: 104  Bit Score: 53.16  E-value: 2.94e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   740 PNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQ-INPHFNRSGQWRHRKANGEIIDVE 818
Cdd:pfam13426    1 PDGILVLDPE-GRIVYANPAALRLLGYTREELLGKSIRDLFGPGTDEEAVARLREaLRNGGEVEVELELRRKDGEPFPVL 79
                           90       100
                   ....*....|....*....|....*
gi 307151595   819 ITSHGLEYAGRKARLVLA--HDITE 841
Cdd:pfam13426   80 VSASPVRDEDGEVVGIVGilRDITE 104
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
479-606 8.05e-07

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 49.20  E-value: 8.05e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   479 SEERLQLALEGSGDTIWEWNLGTGELYCDPNWIRRLGYDpREEAINIEWWrSKIDPETLSDHEAALENYLNGKTEYLALE 558
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYS-AEELIGRNVL-ELIPEEDREEVRERIERRLEGEREPVSEE 78
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 307151595   559 YKIQTLEGEWLWIGGRGKCIayDQQRKPLKILGTHRDITETKQTQENL 606
Cdd:TIGR00229   79 RRVRRKDGSEIWVEVSVSPI--RTNGGELGVVGIVRDITERKQAEEAL 124
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
617-720 1.50e-03

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 254806 [Multi-domain]  Cd Length: 110  Bit Score: 38.55  E-value: 1.50e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   617 VEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLEnRQKGDLLAEFEPEsEYRQSVLNYI-KSAQGKWR----DFKILVRDG 691
Cdd:pfam08448    1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPE-ELLGKTLAELLPP-EDAARLERALrRALEGEEPidflEELLLNGEE 78
                           90       100       110
                   ....*....|....*....|....*....|..
gi 307151595   692 RIIDTSWANVKLSDGTSIA---IGQDITERKR 720
Cdd:pfam08448   79 RHYELRLTPLRDPDGEVIGvlvISRDITERRR 110
CALCOCO1 pfam07888
Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are ...
414-484 1.53e-03

Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region.


Pssm-ID: 116500 [Multi-domain]  Cd Length: 546  Bit Score: 41.51  E-value: 1.53e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 307151595   414 QAVGRDITQLKQVEAALRQLNEELEQRVEQRTAELAAEIRERQEIetaliksQAKYEQLVEKLSKSEERLQ 484
Cdd:pfam07888  237 QENDRVLEGTQDIEAELERMKGELKQRLKKMTIQRRDEETERIDL-------QLENEQLHEDLRTLQERLE 300
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
399-488 1.90e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins].


Pssm-ID: 233757 [Multi-domain]  Cd Length: 1179  Bit Score: 41.20  E-value: 1.90e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   399 TNRVIMDEKRNI-----IEFQAVGRDITQLKQVEAALRQLNEELEQRVEQRTAELAAEIRERQEIETALIKSQAKYEQLV 473
Cdd:TIGR02168  800 ALREALDELRAEltllnEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALL 879
                           90
                   ....*....|....*
gi 307151595   474 EKLSKSEERLQLALE 488
Cdd:TIGR02168  880 NERASLEEALALLRS 894
 
Name Accession Description Interval E-value
EAL cd01948
EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL ...
1159-1400 3.14e-112

EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria.


Pssm-ID: 238923  Cd Length: 240  Bit Score: 354.54  E-value: 3.14e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1159 TNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEq 1238
Cdd:cd01948     1 ADLRRALERGEFELYYQPIVDLRTGRIVGYEALLRWRHPEGGLISPAEFIPLAEETGLIVELGRWVLEEACRQLARWQA- 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1239 fiGAENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGY 1318
Cdd:cd01948    80 --GGPDLRLSVNLSARQLRDPDFLDRLLELLAETGLPPRRLVLEITESALIDDLEEALATLRRLRALGVRIALDDFGTGY 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1319 SSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLE 1398
Cdd:cd01948   158 SSLSYLKRLPVDYLKIDRSFVRDIETDPEDRAIVRAIIALAHSLGLKVVAEGVETEEQLELLRELGCDYVQGYLFSRPLP 237

                  ..
gi 307151595 1399 SE 1400
Cdd:cd01948   238 AE 239
GGDEF cd01949
Diguanylate-cyclase (DGC) or GGDEF domain; Diguanylate-cyclase (DGC) or GGDEF domain: ...
982-1140 8.51e-61

Diguanylate-cyclase (DGC) or GGDEF domain; Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.


Pssm-ID: 143635  Cd Length: 158  Bit Score: 206.64  E-value: 8.51e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  982 LHDGLTGLPNRTLLLDRVEQAIKRKQQQpNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARFG 1061
Cdd:cd01949     1 YTDPLTGLPNRRAFEERLERLLARARRS-GRPLALLLIDIDHFKQINDTYGHAAGDEVLKEVAERLRSSLRESDLVARLG 79
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 307151595 1062 GDEFVILLEDLTIwTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIAMYRSKEAGRARY 1140
Cdd:cd01949    80 GDEFAILLPGTDL-EEAEALAERLREAIEEPFFIDGQEIRVTASIGIATYPEDGEDAEELLRRADEALYRAKRSGRNRV 157
PBPb cd00134
Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, ...
47-256 3.97e-28

Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.


Pssm-ID: 238078 [Multi-domain]  Cd Length: 218  Bit Score: 114.78  E-value: 3.97e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   47 FPPLYLVDRTGKPSGFAIDVMKEVAKlaQLKVRYEIKNT-WSEVQETLINGNADLIPN-LGITPARQTQMSFTAPVETDS 124
Cdd:cd00134     9 YPPFSFRDANGELTGFDVDLAKAIAK--ELGVKVKFVEVdWDGLITALKSGKVDLIAAgMTITPERAKQVDFSDPYYKSG 86
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  125 VSVFVRASNhQIKTVAHLAGHRVGVVKG-TVGYEIAKNRQNIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQAD 203
Cdd:cd00134    87 QVILVKKGS-PIKSVKDLKGKKVAVQKGsTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKHP 165
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 307151595  204 VSNRIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:cd00134   166 PELKIVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 218
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
319-420 7.95e-13

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 66.89  E-value: 7.95e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  319 SEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIASLTPENPMITHEHRVRLSSGEIRWNQW 398
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVLV 81
                          90       100
                  ....*....|....*....|..
gi 307151595  399 TNRVIMDEKRNIIEFQAVGRDI 420
Cdd:cd00130    82 SLTPIRDEGGEVIGLLGVVRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
740-839 3.45e-07

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 49.94  E-value: 3.45e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  740 PNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQ-INPHFNRSGQWRHRKANGEIIDVE 818
Cdd:cd00130     2 PDGVIVLDLD-GRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENlLSGGEPVTLEVRLRRKDGSVIWVL 80
                          90       100
                  ....*....|....*....|...
gi 307151595  819 ITSHGLEYAGRKARLVLA--HDI 839
Cdd:cd00130    81 VSLTPIRDEGGEVIGLLGvvRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
863-967 1.14e-05

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 45.32  E-value: 1.14e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  863 APLPILIHAEDGEIVQVNHAWTELSGYHLDELSTIADWTEKAYGERKDIVRSVIDQLyeIDGKVEEGEFAITIKSGETRI 942
Cdd:cd00130     1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLL--SGGEPVTLEVRLRRKDGSVIW 78
                          90       100
                  ....*....|....*....|....*
gi 307151595  943 WDFSSAPLGKLADGRRLIISMAIDI 967
Cdd:cd00130    79 VLVSLTPIRDEGGEVIGLLGVVRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
494-596 1.57e-04

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.


Pssm-ID: 238075 [Multi-domain]  Cd Length: 103  Bit Score: 41.85  E-value: 1.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  494 IWEWNLGTGELYCDPNWIRRLGYDPrEEAINIEWWrSKIDPETLSDHEAALENYLNGKTEYlALEYKIQTLEGEWLWIGG 573
Cdd:cd00130     5 VIVLDLDGRILYANPAAEQLLGYSP-EELIGKSLL-DLIHPEDREELRERLENLLSGGEPV-TLEVRLRRKDGSVIWVLV 81
                          90       100
                  ....*....|....*....|...
gi 307151595  574 RGKCIaYDQQRKPLKILGTHRDI 596
Cdd:cd00130    82 SLTPI-RDEGGEVIGLLGVVRDI 103
Rtn COG2200
c-di-GMP phosphodiesterase class I (EAL domain) [Signal transduction mechanisms]
1155-1408 1.01e-104

c-di-GMP phosphodiesterase class I (EAL domain) [Signal transduction mechanisms]


Pssm-ID: 225110  Cd Length: 256  Bit Score: 334.26  E-value: 1.01e-104
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1155 LELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKA 1234
Cdd:COG2200     2 LQLERDLRQALENGEFSLYYQPIVDLATGRIVGYEALLRWRHPDGGLISPGEFIPLAEETGLIVELGRWVLEEACRQLRT 81
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1235 WQEQFigaeNLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDF 1314
Cdd:COG2200    82 WPRAG----PLRLAVNLSPVQLRSPGLVDLLLRLLARLGLPPHRLVLEITESALIDDLDTALALLRQLRELGVRIALDDF 157
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1315 GTGYSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFS 1394
Cdd:COG2200   158 GTGYSSLSYLKRLPPDILKIDRSFVRDLETDARDQAIVRAIVALAHKLGLTVVAEGVETEEQLDLLRELGCDYLQGYLFS 237
                         250
                  ....*....|....
gi 307151595 1395 KPLESEKIVSWLER 1408
Cdd:COG2200   238 RPLPADALDALLSS 251
EAL smart00052
Putative diguanylate phosphodiesterase; Putative diguanylate phosphodiesterase, present in a ...
1158-1400 9.38e-102

Putative diguanylate phosphodiesterase; Putative diguanylate phosphodiesterase, present in a variety of bacteria.


Pssm-ID: 214491  Cd Length: 242  Bit Score: 325.33  E-value: 9.38e-102
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   1158 ETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQE 1237
Cdd:smart00052    1 ERELRQALENGQFLLYYQPIVSLRTGRLVGVEALIRWQHPEGGIISPDEFIPLAEETGLIVPLGRWVLEQACQQLAEWQA 80
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   1238 QFIgaENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTG 1317
Cdd:smart00052   81 QGP--PPLLISINLSARQLISPDLVPRVLELLEETGLPPQRLELEITESVLLDDDESAVATLQRLRELGVRIALDDFGTG 158
                           170       180       190       200       210       220       230       240
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   1318 YSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPL 1397
Cdd:smart00052  159 YSSLSYLKRLPVDLLKIDKSFVRDLQTDPEDEAIVQSIIELAQKLGLQVVAEGVETPEQLDLLRSLGCDYGQGYLFSRPL 238

                    ...
gi 307151595   1398 ESE 1400
Cdd:smart00052  239 PLD 241
EAL pfam00563
EAL domain; This domain is found in diverse bacterial signaling proteins. It is called EAL ...
1160-1396 3.43e-69

EAL domain; This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site.


Pssm-ID: 249961  Cd Length: 231  Bit Score: 233.43  E-value: 3.43e-69
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  1160 NLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEqf 1239
Cdd:pfam00563    3 ALREALENGEFSLYFQPIVDLRTGKVLGYEALLRWQHPDGGLISPDEFLPLAERLGLIAELDRWVLEKALAQLAEWLN-- 80
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  1240 igaENLRVSVNLSGKQLQQPNLINRIDNiLTETGLEGKNLKLEITESmLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYS 1319
Cdd:pfam00563   81 ---PDLPLSVNLSPASLLDPSFLEALLA-LKQGGLPPSRLVLEITES-ALDEDLRLLEALARLRSLGFRLALDDFGTGYS 155
                          170       180       190       200       210       220       230
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 307151595  1320 SLSYLHYLPVDTLKIDRSFVSRMSQvGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKP 1396
Cdd:pfam00563  156 SLSLLSRLPPDYIKIDRSFIKDLSD-PESRALLRALIALARSLGIKVVAEGVETEEQLELLKELGIDYVQGYLFSKP 231
COG2199 COG2199
c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
963-1143 1.82e-57

c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]


Pssm-ID: 225109  Cd Length: 181  Bit Score: 198.06  E-value: 1.82e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  963 MAIDITERKQAEEQLRHSVLHDGLTGLPNRTLLLDRVEQAIkRKQQQPNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKT 1042
Cdd:COG2199     2 LLRLLTRLRKAEERLERLALHDPLTGLPNRRAFEERLERAL-ARARRHGEPLALLLLDLDHFKQINDTYGHAAGDEVLRE 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1043 IADKLQRCVRPTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSE-L 1121
Cdd:COG2199    81 VARRLRSNLREGDLVARLGGDEFAVLLPGTSL-EEAARLAERIRAALEEPFFLGGEELRVTVSIGVALYPEDGSDDAElL 159
                         170       180
                  ....*....|....*....|..
gi 307151595 1122 VRNADIAMYRSKEAGRARYTMF 1143
Cdd:COG2199   160 LRRADLALYRAKRAGRNRVVVF 181
GGDEF pfam00990
GGDEF domain; This domain is found linked to a wide range of non-homologous domains in a ...
981-1137 2.45e-55

GGDEF domain; This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain and has diguanylate cyclase activity. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate.


Pssm-ID: 250276  Cd Length: 159  Bit Score: 191.30  E-value: 2.45e-55
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   981 VLHDGLTGLPNRTLLLDRVEQAIKRkQQQPNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARF 1060
Cdd:pfam00990    1 AAHDPLTGLPNRRYFEEELEQELQR-ARRQQSPLALLLIDLDNFKRINDTYGHAVGDEVLQEVAQRLSSSLRRSDLVARL 79
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 307151595  1061 GGDEFVILLED--LTIWTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIAMYRSKEAGR 1137
Cdd:pfam00990   80 GGEEFAILLPDtsLEGAQELAERIRRLLAALAIPHTLSGLPLYVTISIGIAAYPNDGEDPEDLLKRADQALYQAKQQGR 158
GGDEF smart00267
diguanylate cyclase; Diguanylate cyclase, present in a variety of bacteria.
979-1143 3.19e-54

diguanylate cyclase; Diguanylate cyclase, present in a variety of bacteria.


Pssm-ID: 128563  Cd Length: 163  Bit Score: 188.22  E-value: 3.19e-54
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    979 HSVLHDGLTGLPNRTLLLDRVEQAIKRKQQQPNYlFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVA 1058
Cdd:smart00267    1 RLAFRDPLTGLPNRRYFEEELEQELQRAQRQGSP-FALLLIDLDNFKDINDTYGHAVGDELLQEVAQRLSSCLRPGDLLA 79
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   1059 RFGGDEFVILLEDLTIWtDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIAMYRSKEAGRA 1138
Cdd:smart00267   80 RLGGDEFALLLPETSLE-EAIALAERILQQLREPIIIHGIPLYLTISIGVAAYPNPGEDAEDLLKRADTALYQAKKAGRN 158

                    ....*
gi 307151595   1139 RYTMF 1143
Cdd:smart00267  159 QVAVY 163
GGDEF TIGR00254
diguanylate cyclase (GGDEF) domain; The GGDEF domain is named for the motif GG[DE]EF shared by ...
982-1144 2.42e-41

diguanylate cyclase (GGDEF) domain; The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus, and FixL, a heme-containing oxygen sensor protein [Regulatory functions, Small molecule interactions, Signal transduction, Other].


Pssm-ID: 232895  Cd Length: 165  Bit Score: 151.33  E-value: 2.42e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   982 LHDGLTGLPNRTLLLDRVEQAIKRKQQQpNYLFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARFG 1061
Cdd:TIGR00254    3 VRDPLTGLYNRRYLEEMLDSELKRARRF-QRSFSVLMIDIDNFKKINDTLGHDVGDEVLREVARILQSSVRGSDVVGRYG 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  1062 GDEFVILLEDlTIWTDATKMAQRITEEFES-SFTLQEQEYFT-SASIGITFCSSPEQTPSELVRNADIAMYRSKEAGRAR 1139
Cdd:TIGR00254   82 GEEFVVILPG-TPLEDALSKAERLRDAINSkPIEVAGSETLTvTVSIGVACYPGHGLTLEELLKRADEALYQAKKAGRNR 160

                   ....*
gi 307151595  1140 YTMFD 1144
Cdd:TIGR00254  161 VVVAD 165
PRK11596 PRK11596
cyclic-di-GMP phosphodiesterase; Provisional
1174-1402 6.96e-14

cyclic-di-GMP phosphodiesterase; Provisional


Pssm-ID: 183222  Cd Length: 255  Bit Score: 72.34  E-value: 6.96e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1174 YQPIVSLMNRnLLGFEALVRWIHPEkgviSPANFI-PVAEETGLIIPLGEWVLRESCRQMKAWQEQFIGaENLRVSVNLS 1252
Cdd:PRK11596   34 FQPIYRTSGR-LMAIELLTAVTHPS----NPSQRLsPERYFAEITVSHRLDVVKEQLDLLAQWADFFVR-HGLLASVNID 107
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1253 GKQL----QQPNLINRIDNIltetglegKNLKLEITESMLMNNKEQVSELllqmkAKKIQVSIDDFGTG---YSSLSYLH 1325
Cdd:PRK11596  108 GPTLialrQQPAILRLIERL--------PWLRFELVEHIRLPKDSPFASM-----CEFGPLWLDDFGTGmanFSALSEVR 174
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 307151595 1326 YlpvDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLESEKI 1402
Cdd:PRK11596  175 Y---DYIKVARELFIMLRQSEEGRNLFSQLLHLMNRYCRGVIVEGVETPEEWRDVQRSPAFAAQGYFLSRPAPFETL 248
orph_peri_GRRM TIGR04262
extracellular substrate-binding orphan protein, GRRM family; This subfamily belongs to ...
49-188 5.47e-10

extracellular substrate-binding orphan protein, GRRM family; This subfamily belongs to bacterial extracellular solute-binding protein family 3 (pfam00497). In that family, most members are ABC transporter periplasmic substrate-binding proteins. However, members of the present subfamily are orphans in the sense of being adjacent to neither ABC transporter ATP-binding proteins or permease subunits. Instead, most members are encoded next to the two signature proteins of the proposed Glycine-Rich Repeat Modification (GRRM) system, a radical SAM/SPASM protein GrrM (TIGR04261) and the Gly-rich repeat protein itself GrrA (TIGR04260).


Pssm-ID: 211985  Cd Length: 257  Bit Score: 60.45  E-value: 5.47e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    49 PLYLVDRTGKpSGFAIDVMKEVAKLAQLKVRYEIK------NTWSEVQETLINGNADLIPNLGITPARQTQMSFTAPVET 122
Cdd:TIGR04262   13 PLYQKDDAGY-DGLSFDVLELIRDQLQAELGKPITiqfvvvNSVQEGLPKLRSGKADIACGVAFTWERQMFVDYSLPFAV 91
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 307151595   123 DSVSVFVRASNHqiKTVAHLAGHRVGVVKGTVGYEIAKNRQ-NIQLEVFDGIEYGVFELLAGHVDAL 188
Cdd:TIGR04262   92 SGIRLLAPKGND--GTPESLEGKTVGVVKDSVAAAVLANVVpKATLQPFATPAEALAALKAGKVDAL 156
Nucleotidyl_cyc_III cd07556
Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse ...
1016-1108 4.93e-09

Class III nucleotidyl cyclases; Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways.


Pssm-ID: 143637  Cd Length: 133  Bit Score: 56.21  E-value: 4.93e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1016 ILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQR-CVRPTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEFESsft 1094
Cdd:cd07556     4 ILFADIVGFTSLADALGPDEGDELLNELAGRFDSlIRRSGDLKIKTIGDEFMVVSGLDHP-AAAVAFAEDMREAVSA--- 79
                          90
                  ....*....|....*
gi 307151595 1095 LQEQEY-FTSASIGI 1108
Cdd:cd07556    80 LNQSEGnPVRVRIGI 94
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
730-794 1.03e-07

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 50.86  E-value: 1.03e-07
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 307151595    730 EKYRLFFDANPNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQ 794
Cdd:smart00091    1 ERLRAILESLPDGIFVLDLD-GRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQR 64
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
309-373 1.25e-07

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 50.86  E-value: 1.25e-07
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 307151595    309 SRYRGIVEDQSEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIASL 373
Cdd:smart00091    1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDRERVQEALQRL 65
PAS_8 pfam13188
PAS domain;
611-675 3.93e-04

PAS domain;


Pssm-ID: 257556  Cd Length: 66  Bit Score: 40.29  E-value: 3.93e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 307151595   611 ELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGW-SLENRQKGDLLAEFEPESEYRQSVLNYIK 675
Cdd:pfam13188    1 ERLRALFENAPDGILVLDRGGRILYANPAALELLGYeELLGELLGELLDDLEALAEEALELLEELE 66
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
381-423 1.45e-03

Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold.


Pssm-ID: 197509  Cd Length: 43  Bit Score: 38.32  E-value: 1.45e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|...
gi 307151595    381 THEHRVRLSSGEIRWNQWTNRVIMDEKRNIIEFQAVGRDITQL 423
Cdd:smart00086    1 TVEYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
854-894 6.82e-03

PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels.


Pssm-ID: 214512  Cd Length: 67  Bit Score: 36.61  E-value: 6.82e-03
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|.
gi 307151595    854 ERFHRAIVDAPLPILIHAEDGEIVQVNHAWTELSGYHLDEL 894
Cdd:smart00091    1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEEL 41
SBP_bac_3 pfam00497
Bacterial extracellular solute-binding proteins, family 3;
39-256 6.53e-41

Bacterial extracellular solute-binding proteins, family 3;


Pssm-ID: 249906 [Multi-domain]  Cd Length: 220  Bit Score: 152.04  E-value: 6.53e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    39 VTAVIPKYFPPLYLVDRTGKPSGFAIDVMKEVAKlaQLKVRYEIKNT-WSEVQETLINGNADLIPN-LGITPARQTQMSF 116
Cdd:pfam00497    1 LRVGTDADYPPFEYVDENGKLVGFDVDLAKAIAK--RLGVKVEFVPVsWDGLIPALQSGKIDVIIAgMTITPERKKQVDF 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   117 TAPVETDSVSVFVRASNHQ--IKTVAHLAGHRVGVVKGTVGYEIA-KNRQNIQLEVFDGIEYGVFELLAGHVDALIYSES 193
Cdd:pfam00497   79 SDPYYTSGQVLVVRKKDSDksIKSLADLKGKTVGVQKGTTAEDLLlLKKPGAKIVEYDDLAEALQALAAGRVDAVVADSP 158
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595   194 VLKEIVAQADVSNrIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:pfam00497  159 VLAYLIKKNPGLN-LVVVGEPLSGEPYGIAVRKGDPELLAALNKALAELKADGTLAKLYEKWF 220
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
753-974 1.38e-16

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 80.66  E-value: 1.38e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  753 FLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVpLLEQYILQINPHFNRSGQWRHRKANGEIIDVEITSHGL-EYAGRKA 831
Cdd:COG2202    11 IIYANEAAEELLGYSAEELLGLLLALHPEDRDR-LRELLRRLLAGEELLSEELRLVRKDGEERWVELSAAPLrDGEGRVL 89
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  832 RLVLAHDITERLKAEKALQESKERFHRAIVDAPLPILIHAEDGEIVQVNHAWTELSGYHLDELSTIADWTEKAYGERKDI 911
Cdd:COG2202    90 GLLGLRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERR 169
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595  912 VRSVIDQLYEIDGKVEEGEFAITIKSGETRIWDFSSAPLGKLADGRRLIISMAIDITERKQAE 974
Cdd:COG2202   170 ELELARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRDDGEIVGVVGIARDITERKQAE 232
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
623-846 1.18e-14

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 74.50  E-value: 1.18e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  623 MLAYFDQHYNLLWVNREWEKIWGWSLENRQKGDLLAEFEPESEYRQSVLNYIKSAQGKWRDFKILVRDGRIIDTSWANVK 702
Cdd:COG2202     1 LILVLDRDGRIIYANEAAEELLGYSAEELLGLLLALHPEDRDRLRELLRRLLAGEELLSEELRLVRKDGEERWVELSAAP 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  703 LSDGTSIAIG----QDITERKRIEEILRESEEKYRLFFDANPNPLWVYDLETFaFLEVNQATIEHYGYTREEFLAMTIRD 778
Cdd:COG2202    81 LRDGEGRVLGllglRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGR-ILYANPAAEELLGYSPEEELGRGLSD 159
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 307151595  779 IRPPEDVPL----LEQYILQINPHFNRSGQWRHRKANGEIIDVEITSHGLEYAGRKARLV-LAHDITERLKAE 846
Cdd:COG2202   160 LIHPEDEERreleLARALAEGRGGPLEIEYRVRRKDGERVRWILSRISPVRDDGEIVGVVgIARDITERKQAE 232
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
307-430 2.49e-12

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 65.77  E-value: 2.49e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   307 SESRYRGIVEDQSEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIAS-LTPENPMITHEHR 385
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERrLEGEREPVSEERR 80
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*
gi 307151595   386 VRLSSGEIRWNQWTNRvIMDEKRNIIEFQAVGRDITQLKQVEAAL 430
Cdd:TIGR00229   81 VRRKDGSEIWVEVSVS-PIRTNGGELGVVGIVRDITERKQAEEAL 124
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
494-722 3.49e-12

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 66.80  E-value: 3.49e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  494 IWEWNLGTGELYCDPNWIRRLGYDPrEEAINIEWWRSKIDPETLSDHEAALENYLngktEYLALEYKIQTLEGEWLWIGG 573
Cdd:COG2202     2 ILVLDRDGRIIYANEAAEELLGYSA-EELLGLLLALHPEDRDRLRELLRRLLAGE----ELLSEELRLVRKDGEERWVEL 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  574 RGKCIAyDQQRKPLKILGtHRDITETKQTQENLRQQQELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLENRQK 653
Cdd:COG2202    77 SAAPLR-DGEGRVLGLLG-LRDITERKRAEEALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELG 154
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 307151595  654 GDLLAEFEPESEYRQSVLNYIKSAQGK----WRDFKILVRDGRIIDTSWANVKLSDGT-----SIAIGQDITERKRIE 722
Cdd:COG2202   155 RGLSDLIHPEDEERRELELARALAEGRggplEIEYRVRRKDGERVRWILSRISPVRDDgeivgVVGIARDITERKQAE 232
PRK10060 PRK10060
RNase II stability modulator; Provisional
959-1408 5.07e-122

RNase II stability modulator; Provisional


Pssm-ID: 236645 [Multi-domain]  Cd Length: 663  Bit Score: 397.51  E-value: 5.07e-122
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  959 LIISmAIDITERKQAEEQLRHSVLHDGLTGLPNRTLLLDRVEQAIkrkQQQPNYLFAILFIDLDRFKVVNDSLGHLVGDQ 1038
Cdd:PRK10060  216 LICS-GTDITEERRAQERLRILANTDSITGLPNRNAIQELIDHAI---NAADNNQVGIVYLDLDNFKKVNDAYGHMFGDQ 291
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1039 LLKTIADKLQRCVRPTDTVARFGGDEFVILLEDLTIWTdATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTP 1118
Cdd:PRK10060  292 LLQDVSLAILSCLEEDQTLARLGGDEFLVLASHTSQAA-LEAMASRILTRLRLPFRIGLIEVYTGCSIGIALAPEHGDDS 370
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1119 SELVRNADIAMYRSKEAGRARYTMFDPIMHTQATQLLELETNLRLALEREEFIVYYQPIVSLmNRNLLGFEALVRWIHPE 1198
Cdd:PRK10060  371 ESLIRSADTAMYTAKEGGRGQFCVFSPEMNQRVFEYLWLDTNLRKALENDQLVIHYQPKITW-RGEVRSLEALVRWQSPE 449
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1199 KGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEQFIgaeNLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKN 1278
Cdd:PRK10060  450 RGLIPPLEFISYAEESGLIVPLGRWVMLDVVRQVAKWRDKGI---NLRVAVNVSARQLADQTIFTALKQALQELNFEYCP 526
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1279 LKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITL 1358
Cdd:PRK10060  527 IDVELTESCLIENEELALSVIQQFSQLGAQVHLDDFGTGYSSLSQLARFPIDAIKLDQSFVRDIHKQPVSQSLVRAIVAV 606
                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|
gi 307151595 1359 AHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLESEKIVSWLER 1408
Cdd:PRK10060  607 AQALNLQVIAEGVETAKEDAFLTKNGVNERQGFLFAKPMPAVAFERWYKR 656
PRK11359 PRK11359
cyclic-di-GMP phosphodiesterase; Provisional
923-1407 2.76e-97

cyclic-di-GMP phosphodiesterase; Provisional


Pssm-ID: 183097 [Multi-domain]  Cd Length: 799  Bit Score: 331.73  E-value: 2.76e-97
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  923 DGKVEeGEFAI-TIKSGETriwdfsSAPLGKLADGRRLIISMAIDITERKQAEEQLrhsVLHDGLTGLPNRTLLLDRVEQ 1001
Cdd:PRK11359  327 DGAPA-GTLQIkTSSGAET------SAFIERVADISQHLAALALEQEKSRQHIEQL---IQFDPLTGLPNRNNLHNYLDD 396
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1002 AIKrKQQQPnylfAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARFGGDEFVILLEDLTIwTDATKM 1081
Cdd:PRK11359  397 LVD-KAVSP----VVYLIGVDHFQDVIDSLGYAWADQALLEVVNRFREKLKPDQYLCRIEGTQFVLVSLENDV-SNITQI 470
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1082 AQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQtpSELVRNADIAMYRSKEAGRARYTMFDPIMHTQATQLLELETNL 1161
Cdd:PRK11359  471 ADELRNVVSKPIMIDDKPFPLTLSIGISYDVGKNR--DYLLSTAHNAMDYIRKNGGNGWQFFSPAMNEMVKERLVLGAAL 548
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1162 RLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEQfiG 1241
Cdd:PRK11359  549 KEAISNNQLKLVYQPQIFAETGELYGIEALARWHDPLHGHVPPSRFIPLAEEIGEIENIGRWVIAEACRQLAEWRSQ--N 626
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1242 AENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSL 1321
Cdd:PRK11359  627 IHIPALSVNLSALHFRSNQLPNQVSDAMQAWGIDGHQLTVEITESMMMEHDTEIFKRIQILRDMGVGLSVDDFGTGFSGL 706
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1322 SYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLESEK 1401
Cdd:PRK11359  707 SRLVSLPVTEIKIDKSFVDRCLTEKRILALLEAITSIGQSLNLTVVAEGVETKEQFEMLRKIHCRVIQGYFFSRPLPAEE 786

                  ....*.
gi 307151595 1402 IVSWLE 1407
Cdd:PRK11359  787 IPGWMS 792
COG5001 COG5001
Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain ...
958-1400 6.18e-96

Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]


Pssm-ID: 227334 [Multi-domain]  Cd Length: 663  Bit Score: 324.16  E-value: 6.18e-96
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  958 RLIISMAIDITERKQAEEQLRHSVlhDGLTGLPNRTLLLDRVEQAIKRKQQQPNYlFAILFIDLDRFKVVNDSLGHLVGD 1037
Cdd:COG5001   207 QVTLTQRAEETRRLSDENDRLANL--DSLTGLPNRRRFFAELDARLAAARQSGRR-LVLGVIDLDGFKPVNDAFGHATGD 283
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1038 QLLKTIADKLQRCVRPTDTVARFGGDEFVILLEDLTIWTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQT 1117
Cdd:COG5001   284 RLLIEVGRRLKAFDGAPILAARLGGDEFALIIPALEDDALRVAGARALCESLQAPYDLRGVRVQVGASIGIAPFPSGADT 363
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1118 PSELVRNADIAMYRSKEAGRARYTMFDPIMHTQATQLLELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHP 1197
Cdd:COG5001   364 SEQLFERADYALYHAKQNGKGAAVLFDARHEAAIRDMAVVEQALRSADLEQELSVHFQPIVDIVSGKTIALEALARWHSP 443
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1198 EKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQeqfigaENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGK 1277
Cdd:COG5001   444 EIGPVPPDVFIGIAERSGQIVELTRLLLAKALREARAWP------MDVRVSINLSARDLASMENVRRLLAIVSESCIAPH 517
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1278 NLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIIT 1357
Cdd:COG5001   518 RLDFEITETAIVCDFDQARDALAALHELGVRTALDDFGTGYSSLSHLRALPLDKIKIDRSFVSDLEENPTSEDIVRTVLQ 597
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|...
gi 307151595 1358 LAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLESE 1400
Cdd:COG5001   598 LGRNLRMECVVEGVETEAQRDRVAALGATVMQGYHYARPMPAE 640
PRK09776 PRK09776
putative diguanylate cyclase; Provisional
689-1396 1.03e-81

putative diguanylate cyclase; Provisional


Pssm-ID: 182070 [Multi-domain]  Cd Length: 1092  Bit Score: 291.58  E-value: 1.03e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  689 RDGriiDTSWANVKLS-----DGTS---IAIGQDITERKRIEEILRESEEKYRLFFDANPNPLWVYDLET---------F 751
Cdd:PRK09776  364 RDG---EVVWALLAVSlvrdtDGTPlyfIAQIEDINELKRTEQVNERLMERITLANEAGGIGIWEWDLKPniiswdkrmF 440
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  752 AFLEVNQATIEHYgytrEEFLAMTIrdirpPEDVPLLEQYI---LQINPHFN------RSGQWRHRKANGEIIdveitsh 822
Cdd:PRK09776  441 ELYEIPPHIKPTW----QVWYACLH-----PEDRQRVEKEIrdaLQGRSPFKlefrivVKDGVRHIRALANRV------- 504
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  823 gLEYAGRKARLV-LAHDITERLKAEKALQESKERFH---RAIVDAplpILIHAEDGEIVQVNHAWTELSGYHLDE----- 893
Cdd:PRK09776  505 -LNKDGEVERLLgINMDMTEVRQLNEALFQEKERLHitlDSIGEA---VVCTDMAMKVTFMNPVAEKMTGWTQEEalgvp 580
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  894 LSTIADWTEKAYGERKDIVRSVIDQLYeiDGKVEEGEFAITIKSGETRIWDfSSAPLgKLADGRRLIISMAI-DITERKQ 972
Cdd:PRK09776  581 LLTVLHITFGDNGPLMENIYSCLTSRS--AAYLEQDVVLHCRSGGSYDVHY-SITPL-STLDGENIGSVLVIqDVTESRK 656
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  973 AEEQLRHSVLHDGLTGLPNRT---LLLDRVEQAIKRKQQQpnylFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQR 1049
Cdd:PRK09776  657 MLRQLSYSASHDALTHLANRAsfeKQLRRLLQTVNSTHQR----HALVFIDLDRFKAVNDSAGHAAGDALLRELASLMLS 732
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1050 CVRPTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEFES-SFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIA 1128
Cdd:PRK09776  733 MLRSSDVLARLGGDEFGLLLPDCNV-ESARFIATRIISAINDyHFPWEGRVYRVGASAGITLIDANNHQASEVMSQADIA 811
                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1129 MYRSKEAGRARYTMFDPiMHTQAT---QLLELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPA 1205
Cdd:PRK09776  812 CYAAKNAGRGRVTVYEP-QQAAAHsehRALSLAEQWRMIKENQLMMLAHGVASPRIPEARNHWLISLRLWDPEGEIIDEG 890
                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1206 NFIPVAEETGLIIPLGEWVLRESCRQmkawQEQFIGAENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITE 1285
Cdd:PRK09776  891 AFRPAAEDPALMHALDRRVIHEFFRQ----AAKAVASKGLSIALPLSVAGLSSPTLLPFLLEQLENSPLPPRLLHLEITE 966
                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1286 SMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSLSYLHYLPVDTLKIDRSFVSRM--SQVGEnfEIVEAIITLAHHLQ 1363
Cdd:PRK09776  967 TALLNHAESASRLVQKLRLAGCRVVLSDFGRGLSSFNYLKAFMADYLKLDGELVANLhgNLMDE--MLISIIQGHAQRLG 1044
                         730       740       750
                  ....*....|....*....|....*....|...
gi 307151595 1364 MDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKP 1396
Cdd:PRK09776 1045 MKTIAGPVELPLVLDTLSGIGVDLAYGYAIARP 1077
PRK13561 PRK13561
putative diguanylate cyclase; Provisional
971-1397 9.07e-79

putative diguanylate cyclase; Provisional


Pssm-ID: 184143 [Multi-domain]  Cd Length: 651  Bit Score: 274.67  E-value: 9.07e-79
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  971 KQAEEQLRHSvLHDGLTGLPNRTLLLDRVEQAIKRKQQqpnylFAILFIdldRFKVVNDSLGHLVGDQ---LLKTIADKL 1047
Cdd:PRK13561  222 RQYEEQSRNA-TRFPVSDLPNKALLMALLEQVVARKQT-----TALMII---TCETLRDTAGVLKEAQreiLLLTLVEKL 292
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1048 QRCVRPTDTVARFGGDEFVILLEDLTIWTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSpEQTPSELVRNADI 1127
Cdd:PRK13561  293 KSVLSPRMVLAQISGYDFAIIANGVKEPWHAITLGQQVLTIINERLPIQRIQLRPSCSIGIAMFYG-DLTAEQLYSRAIS 371
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1128 AMYRSKEAGRARYTMFDPIMHTQATQLLELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANF 1207
Cdd:PRK13561  372 AAFTARRKGKNQIQFFDPQQMEAAQKRLTEESDILNALENHQFAIWLQPQVEMRSGKLVSAEALLRMQQPDGSWDLPEGL 451
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1208 IPVAEETGLIIPLGEWVLRESCRQMKAWQEQFIgaeNLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESM 1287
Cdd:PRK13561  452 IDRIESCGLMVTVGHWVLEESCRLLAAWQERGI---MLPLSVNLSALQLMHPNMVADMLELLTRYRIQPGTLILEVTESR 528
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1288 LMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSLSYLHY---LPVDTLKIDRSFVSRMSqvgENFEIVEAIITLAHHLQM 1364
Cdd:PRK13561  529 RIDDPHAAVAILRPLRNAGVRVALDDFGMGYAGLRQLQHmksLPIDVLKIDKMFVDGLP---EDDSMVAAIIMLAQSLNL 605
                         410       420       430
                  ....*....|....*....|....*....|...
gi 307151595 1365 DVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPL 1397
Cdd:PRK13561  606 QVIAEGVETEAQRDWLLKAGVGIAQGFLFARAL 638
PRK11829 PRK11829
biofilm formation regulator HmsP; Provisional
987-1397 6.39e-78

biofilm formation regulator HmsP; Provisional


Pssm-ID: 183329 [Multi-domain]  Cd Length: 660  Bit Score: 272.59  E-value: 6.39e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  987 TGLPNRTLLLDRVEQAIKRKQQQPNylFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARFGGDEFV 1066
Cdd:PRK11829  238 TELPNRSLFISLLEKEIASSTRTDH--FHLLVIGIETLQEVSGAMSEAQHQQLLLTIVQRIEQCIDDSDLLAQLSKTEFA 315
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1067 ILLEDLTIWTDATKMAQRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSELVRNADIAMYRSKEAGRARYTMFDPI 1146
Cdd:PRK11829  316 VLARGTRRSFPAMQLARRIMSQVTQPLFFDEITLRPSASIGITRYQAQQDTAESMMRNASTAMMAAHHEGRNQIMVFEPH 395
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1147 MHTQATQLLELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLR 1226
Cdd:PRK11829  396 LIEKTHKRLTQENDLLQAIENHDFTLFLQPQWDMKRQQVIGAEALLRWCQPDGSYVLPSGFVHFAEEEGMMVPLGNWVLE 475
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1227 ESCRQMKAWQEQFIgaeNLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKEQVSELLLQMKAKK 1306
Cdd:PRK11829  476 EACRILADWKARGV---SLPLSVNISGLQVQNKQFLPHLKTLISHYHIDPQQLLLEITETAQIQDLDEALRLLRELQGLG 552
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1307 IQVSIDDFGTGYSSLSYLHY---LPVDTLKIDRSFVsrmSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQL 1383
Cdd:PRK11829  553 LLIALDDFGIGYSSLRYLNHlksLPIHMIKLDKSFV---KNLPEDDAIARIISCVSDVLKVRVMAEGVETEEQRQWLLEH 629
                         410
                  ....*....|....
gi 307151595 1384 GCEFGQGYFFSKPL 1397
Cdd:PRK11829  630 GIQCGQGFLFSPPL 643
COG4943 COG4943
Predicted signal transduction protein containing sensor and EAL domains [Signal transduction ...
1154-1409 4.00e-67

Predicted signal transduction protein containing sensor and EAL domains [Signal transduction mechanisms]


Pssm-ID: 227279 [Multi-domain]  Cd Length: 524  Bit Score: 237.33  E-value: 4.00e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1154 LLELETNLRLALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMK 1233
Cdd:COG4943   266 YLSPRRRLQRAIERRELCVHYQPIVDLATGKCVGAEALARWPQEDGTVVSPDVFIPLAEESGMIEQITDYVIRNVFRDLG 345
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1234 AWQEQfigAENLRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMLMNNKeQVSELLLQMKAKKIQVSIDD 1313
Cdd:COG4943   346 DLLRQ---HRDLHVSINLSASDLASPRLIDRLNRKLAQYQVRPQQIALELTERTFADPK-KMTPIILRLREAGHEIYIDD 421
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1314 FGTGYSSLSYLHYLPVDTLKIDRSFVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFF 1393
Cdd:COG4943   422 FGTGYSNLHYLQSLPVDALKIDKSFVDTLGTDSASHLIAPHIIEMAKSLGLKIVAEGVETEEQVDWLRKRGVHYGQGWLF 501
                         250
                  ....*....|....*.
gi 307151595 1394 SKPLESEKIVSWLERL 1409
Cdd:COG4943   502 SKALPAQAFLDWAEQQ 517
PRK10551 PRK10551
phage resistance protein; Provisional
1163-1406 1.86e-44

phage resistance protein; Provisional


Pssm-ID: 182541 [Multi-domain]  Cd Length: 518  Bit Score: 170.17  E-value: 1.86e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1163 LALEREEFIVYYQPIVSLMNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEQF-IG 1241
Cdd:PRK10551  270 TGIKRGQFYVEYQPVVDTQTLRVTGLEALLRWRHPTAGEIPPDAFINYAEAQKLIVPLTQHLFELIARDAAELQKVLpVG 349
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1242 AenlRVSVNLSGKQLQQPNLINRIDNILTETGLEGKNLKLEITESMlMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSL 1321
Cdd:PRK10551  350 A---KLGINISPAHLHSDSFKADVQRLLASLPADHFQIVLEITERD-MVQEEEATKLFAWLHSQGIEIAIDDFGTGHSAL 425
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1322 SYLHYLPVDTLKIDRSFVsrmSQVGENF---EIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLE 1398
Cdd:PRK10551  426 IYLERFTLDYLKIDRGFI---QAIGTETvtsPVLDAVLTLAKRLNMLTVAEGVETPEQARWLRERGVNFLQGYWISRPLP 502

                  ....*...
gi 307151595 1399 SEKIVSWL 1406
Cdd:PRK10551  503 LEDFVRWL 510
PleD COG3706
Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal ...
969-1140 2.42e-39

Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]


Pssm-ID: 226229 [Multi-domain]  Cd Length: 435  Bit Score: 153.25  E-value: 2.42e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  969 ERKQAEEQLR-------HSVLHDGLTGLPNRTLLLDRVEQAIKRKQQQpNYLFAILFIDLDRFKVVNDSLGHLVGDQLLK 1041
Cdd:COG3706   251 RRKRYERQLReslerlqELALVDGLTGLFNRRYFDEHLADLWKRALRE-GRPLSLLMLDIDDFKEINDTYGHDVGDEVLR 329
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1042 TIADKLQRCVRPTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEFESS-FTLQEQEY--FTSASIGITFCSSPEQTP 1118
Cdd:COG3706   330 QVARRLRQTVRGLDLVARYGGEEFAVVLPDTDL-EAAIAIAERIRQKINELpFVHELSREplEVTISIGVAEGKPGEDSI 408
                         170       180
                  ....*....|....*....|..
gi 307151595 1119 SELVRNADIAMYRSKEAGRARY 1140
Cdd:COG3706   409 EELLKRADKALYKAKASGRNRV 430
PRK09894 PRK09894
diguanylate cyclase; Provisional
984-1145 4.56e-34

diguanylate cyclase; Provisional


Pssm-ID: 182133 [Multi-domain]  Cd Length: 296  Bit Score: 134.42  E-value: 4.56e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  984 DGLTGLPNRTLLLDRVEQAIKRKQQQPnylFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVRPTDTVARFGGD 1063
Cdd:PRK09894  132 DVLTGLPGRRVLDESFDHQLRNREPQN---LYLALLDIDRFKLVNDTYGHLIGDVVLRTLATYLASWTRDYETVYRYGGE 208
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1064 EFVILLEDLTIwTDATKMAQRITEEF-ESSFTLQEQEYFTSASIGITFcSSPEQTPSELVRNADIAMYRSKEAGRARyTM 1142
Cdd:PRK09894  209 EFIICLKAATD-EEACRAGERIRQLIaNHAITHSDGRINITATFGVSR-AFPEETLDVVIGRADRAMYEGKQTGRNR-VM 285

                  ...
gi 307151595 1143 FDP 1145
Cdd:PRK09894  286 FID 288
pleD PRK09581
response regulator PleD; Reviewed
970-1139 1.31e-33

response regulator PleD; Reviewed


Pssm-ID: 236577 [Multi-domain]  Cd Length: 457  Bit Score: 136.18  E-value: 1.31e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  970 RKQAEEQLRHSVLH-------DGLTGLPNR----TLLLDRVEQAIKRKQQqpnylFAILFIDLDRFKVVNDSLGHLVGDQ 1038
Cdd:PRK09581  274 RKRYQDALRNNLEQsiemavtDGLTGLHNRryfdMHLKNLIERANERGKP-----LSLMMIDIDHFKKVNDTYGHDAGDE 348
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1039 LLKTIADKLQRCVRPTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEFESS-FTLQEQEYFTS--ASIGITFCSSPE 1115
Cdd:PRK09581  349 VLREFAKRLRNNIRGTDLIARYGGEEFVVVMPDTDI-EDAIAVAERIRRKIAEEpFIISDGKERLNvtVSIGVAELRPSG 427
                         170       180
                  ....*....|....*....|....
gi 307151595 1116 QTPSELVRNADIAMYRSKEAGRAR 1139
Cdd:PRK09581  428 DTIEALIKRADKALYEAKNTGRNR 451
PBPb smart00062
Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in ...
47-256 6.53e-33

Bacterial periplasmic substrate-binding proteins; bacterial proteins, eukaryotic ones are in PBPe


Pssm-ID: 214497 [Multi-domain]  Cd Length: 219  Bit Score: 128.99  E-value: 6.53e-33
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595     47 FPPLYLVDRTGKPSGFAIDVMKEVAKLAQLKVryEIKN-TWSEVQETLINGNADLIPN-LGITPARQTQMSFTAPVETDS 124
Cdd:smart00062   10 YPPFSFADEDGELTGFDVDLAKAIAKELGLKV--EFVEvSFDSLLTALKSGKIDVVAAgMTITPERAKQVDFSDPYYRSG 87
                            90       100       110       120       130       140       150       160
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    125 VSVFVRASNHqIKTVAHLAGHRVGVVKGTVGYEIAKNRQ-NIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQAD 203
Cdd:smart00062   88 QVILVRKDSP-IKSLEDLKGKKVAVVAGTTAEELLKKLYpEAKIVSYDSNAEALAALKAGRADAAVADAPLLAALVKQHG 166
                           170       180       190       200       210
                    ....*....|....*....|....*....|....*....|....*....|....
gi 307151595    204 VSnRIKILGEPLAE-IKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:smart00062  167 LP-ELKIVPDPLDTpEGYAIAVRKGDPELLDKINKALKELKADGTLKKISEKWF 219
3A0103s03R TIGR01096
lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino ...
14-256 2.86e-29

lysine-arginine-ornithine-binding periplasmic protein; [Transport and binding proteins, Amino acids, peptides and amines].


Pssm-ID: 233269 [Multi-domain]  Cd Length: 250  Bit Score: 119.00  E-value: 2.86e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    14 SLLLASQLFCLKGVAQDTDQVSLLEVTAVIPKYfPPLYLVDRTGKPSGFAIDVMKEVAKLAQLKVRYeIKNTWSEVQETL 93
Cdd:TIGR01096    2 SVLLAALVAGASSAATAAAAKEGSVRIGTETGY-PPFESKDANGKLVGFDVDLAKALCKRMKAKCKF-VEQNFDGLIPSL 79
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    94 INGNADLI-PNLGITPARQTQMSFTAPVETDSVSVFVRASNHQIKTVAHLAGHRVGVVKGTVGYEIAKN--RQNIQLEVF 170
Cdd:TIGR01096   80 KAKKVDAImATMSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLDGKTVGVQSGTTHEQYLKDyfKPGVDIVEY 159
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   171 DGIEYGVFELLAGHVDALIYSESVLKEIVAQADVSNRIKILGEPLAEIKR-----AIALRKDNLLLLTRLDKAVNSFVGS 245
Cdd:TIGR01096  160 DSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPNGKDFKFVGPSVTDEKYfgdgyGIGLRKGDTELKAAFNKALAAIRAD 239
                          250
                   ....*....|.
gi 307151595   246 PKYEQIYRKWY 256
Cdd:TIGR01096  240 GTYQKISKKWF 250
HisJ COG0834
ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino ...
1-260 1.71e-28

ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]


Pssm-ID: 223904 [Multi-domain]  Cd Length: 275  Bit Score: 117.41  E-value: 1.71e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    1 MKTIIKIVYLGFFSLLLASQLFCLKGVAQDTDQVSLleVTAVIPKYFPPL-YLVDRTGKPSGFAIDVMKEVAKLAQLKVR 79
Cdd:COG0834     1 MKKLKLLALAALLAALLLAACAAADLLDKIKARGKL--RVGTEATYAPPFeFLDAKGGKLVGFDVDLAKAIAKRLGGDKK 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   80 YEIKN-TWSEVQETLINGNADLIP-NLGITPARQTQMSFTAPVETDSVSVFVRA-SNHQIKTVAHLAGHRVGVVKGTVGY 156
Cdd:COG0834    79 VEFVPvAWDGLIPALKAGKVDIIIaGMTITPERKKKVDFSDPYYYSGQVLLVKKdSDIGIKSLEDLKGKKVGVQLGTTDE 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  157 EIAKNRQ---NIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQADVSNRIKILGEPLAEIKR-AIALRKDNLL-L 231
Cdd:COG0834   159 AEEKAKKpgpNAKIVAYDSNAEALLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYlGIALRKGDDPeL 238
                         250       260
                  ....*....|....*....|....*....
gi 307151595  232 LTRLDKAVNSFVGSPKYEQIYRKWYGEPE 260
Cdd:COG0834   239 LEAVNKALKELKADGTLQKISDKWFGPDD 267
PRK15426 PRK15426
putative diguanylate cyclase YedQ; Provisional
975-1139 5.72e-21

putative diguanylate cyclase YedQ; Provisional


Pssm-ID: 237964 [Multi-domain]  Cd Length: 570  Bit Score: 97.39  E-value: 5.72e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  975 EQLRHSVLHDGLTGLPNRTLLLDRVEQAIKR--KQQQPnylFAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQRCVR 1052
Cdd:PRK15426  392 SSLQWQAWHDPLTRLYNRGALFEKARALAKRcqRDQQP---FSVIQLDLDHFKSINDRFGHQAGDRVLSHAAGLISSSLR 468
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1053 PTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEfessftLQEQEYFT--------SASIGITfCSSPE--QTPSELV 1122
Cdd:PRK15426  469 AQDVAGRVGGEEFCVVLPGASL-AEAAQVAERIRLR------INEKEILVaksttiriSASLGVS-SAEEDgdYDFEQLQ 540
                         170
                  ....*....|....*..
gi 307151595 1123 RNADIAMYRSKEAGRAR 1139
Cdd:PRK15426  541 SLADRRLYLAKQAGRNR 557
PRK11260 PRK11260
cystine transporter subunit; Provisional
47-257 3.33e-19

cystine transporter subunit; Provisional


Pssm-ID: 183061 [Multi-domain]  Cd Length: 266  Bit Score: 89.01  E-value: 3.33e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   47 FPPLYLVDRTGKPSGFAIDVMKEVAKlaQLKVRYEIKNT-WSEVQETLINGNADLIPN-LGITPARQTQMSFTAPVETDS 124
Cdd:PRK11260   51 YPPFSFQGEDGKLTGFEVEFAEALAK--HLGVKASLKPTkWDGMLASLDSKRIDVVINqVTISDERKKKYDFSTPYTVSG 128
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  125 VSVFVRASNH-QIKTVAHLAGHRVGVVKGTvGYE--IAKNRQNIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQ 201
Cdd:PRK11260  129 IQALVKKGNEgTIKTAADLKGKKVGVGLGT-NYEqwLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKK 207
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 307151595  202 AdvSNRIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWYG 257
Cdd:PRK11260  208 T--NDTLAVAGEAFSRQESGVALRKGNPDLLKAVNQAIAEMQKDGTLKALSEKWFG 261
PRK11059 PRK11059
regulatory protein CsrD; Provisional
961-1398 3.22e-18

regulatory protein CsrD; Provisional


Pssm-ID: 236833 [Multi-domain]  Cd Length: 640  Bit Score: 89.15  E-value: 3.22e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  961 ISMAID--ITERKQAEEQ-------LRHSVLHDGLTGLPNRtLLLDRVEQAIKRKQQQPNYLFAILFIDLDRFKVVNDSL 1031
Cdd:PRK11059  199 ASRALDhlLSELQDAREErsrfdtfIRSNAFQDAKTGLGNR-LFFDNQLATLLEDQEMVGAHGVVMLIRLPDFDLLQEEW 277
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1032 GHLVGDQLL----KTIADKLQRcvRPTDTVARFGGDEFVILLEDLTIwTDATKMAQRITEEFES--SFTLQEQEYFTSas 1105
Cdd:PRK11059  278 GESQVEELLfeliNLLSTFVMR--YPGALLARYSRSDFAVLLPHRSL-KEADSLASQLLKAVDAlpPPKMLDRDDFLH-- 352
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1106 IGITFCSSpEQTPSELVRNADIAMYRSKEAGRARYTMFDpimhtqATQLLEL-------ETNLRLALEREEFIVYYQPIV 1178
Cdd:PRK11059  353 IGICAYRS-GQSTEQVMEEAEMALRSAQLQGGNGWFVYD------KAQLPEKgrgsvrwRTLLEQTLVRGGPRLYQQPAV 425
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1179 SLmNRNLLGFEALVRWIHPEKGVISPANFIPVAEETGLIIPLGEWVLRESCRQMKAWQEqfigaENLrvSVNLSGKQLQQ 1258
Cdd:PRK11059  426 TR-DGKVHHRELFCRIRDGQGELLSAELFMPMVQQLGLSEQYDRQVIERVLPLLRYWPE-----ENL--SINLSVDSLLS 497
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1259 PNLINRIDNILTETG-LEGKNLKLEITESMLMNNKEQVSELLLQMKAKKIQVSIDDFGTGYSSLSYLHYLPVDTLKIDRS 1337
Cdd:PRK11059  498 RAFQRWLRDTLLQCPrSQRKRLIFELAEADVCQHISRLRPVLRMLRGLGCRLAVDQAGLTVVSTSYIKELNVELIKLHPS 577
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 307151595 1338 FVSRMSQVGENFEIVEAIITLAHHLQMDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKPLE 1398
Cdd:PRK11059  578 LVRNIHKRTENQLFVRSLVGACAGTETQVFATGVESREEWQTLQELGVSGGQGDFFAESQP 638
adrA PRK10245
diguanylate cyclase AdrA; Provisional
968-1139 3.88e-17

diguanylate cyclase AdrA; Provisional


Pssm-ID: 182329 [Multi-domain]  Cd Length: 366  Bit Score: 83.72  E-value: 3.88e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  968 TERKQAEEQLRHSVL--HDGLTGLPNR----TLLldRVEQAIKRKQQQPNylfAILFIDLDRFKVVNDSLGHLVGDQLLK 1041
Cdd:PRK10245  190 TATKLAEHKRRLQVMstRDGMTGVYNRrhweTLL--RNEFDNCRRHHRDA---TLLIIDIDHFKSINDTWGHDVGDEAIV 264
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1042 TIADKLQRCVRPTDTVARFGGDEFVILLEDLTIWTDATKMAqRITEEFESSFTLQEQEYFTSASIGITFCSSPEQTPSEL 1121
Cdd:PRK10245  265 ALTRQLQITLRGSDVIGRFGGDEFAVIMSGTPAESAITAMS-RVHEGLNTLRLPNAPQVTLRISVGVAPLNPQMSHYREW 343
                         170
                  ....*....|....*...
gi 307151595 1122 VRNADIAMYRSKEAGRAR 1139
Cdd:PRK10245  344 LKSADLALYKAKNAGRNR 361
PRK09776 PRK09776
putative diguanylate cyclase; Provisional
302-649 1.18e-16

putative diguanylate cyclase; Provisional


Pssm-ID: 182070 [Multi-domain]  Cd Length: 1092  Bit Score: 84.72  E-value: 1.18e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  302 AALRASESRYRGIVEDQSEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSED----QPQVAQNIASLTPEN 377
Cdd:PRK09776  276 KHISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLTFQQLTWPEDlnkdLQQVEKLLSGEINSY 355
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  378 PMithEHRVRLSSGEIRWNQWTNRVIMDEKRNIIEFQAVGRDITQLKQVEAALRQLNEeleqrveqrtaelaaeirerqe 457
Cdd:PRK09776  356 SM---EKRYYRRDGEVVWALLAVSLVRDTDGTPLYFIAQIEDINELKRTEQVNERLME---------------------- 410
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  458 ietaliksqakyeqlveklskseeRLQLALEGSGDTIWEWNLGTGELycdpNWIRRL----GYDPrEEAINIEWWRSKID 533
Cdd:PRK09776  411 ------------------------RITLANEAGGIGIWEWDLKPNII----SWDKRMfelyEIPP-HIKPTWQVWYACLH 461
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  534 PETLSDHEAALENYLNGKTEYlALEYKIQTLEG-EWLwiggrgKCIA---YDQQRKPLKILGTHRDITETKQTQENLRQQ 609
Cdd:PRK09776  462 PEDRQRVEKEIRDALQGRSPF-KLEFRIVVKDGvRHI------RALAnrvLNKDGEVERLLGINMDMTEVRQLNEALFQE 534
                         330       340       350       360
                  ....*....|....*....|....*....|....*....|
gi 307151595  610 QELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLE 649
Cdd:PRK09776  535 KERLHITLDSIGEAVVCTDMAMKVTFMNPVAEKMTGWTQE 574
glnH PRK09495
glutamine ABC transporter periplasmic protein; Reviewed
1-259 2.41e-16

glutamine ABC transporter periplasmic protein; Reviewed


Pssm-ID: 236540 [Multi-domain]  Cd Length: 247  Bit Score: 79.79  E-value: 2.41e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    1 MKTIIKIvylgffSLLLASQLFCLKGVAQDTDQVSLLEvTAVIPKYFpplylvDRTGKPSGFAIDVMKEVAKlaQLKVRY 80
Cdd:PRK09495    1 MKSVLKV------SLAALTLAFAVSSHAADKKLVVATD-TAFVPFEF------KQGDKYVGFDIDLWAAIAK--ELKLDY 65
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   81 EIKNT-WSEVQETLINGNADL-IPNLGITPARQTQMSFTAPVETDSVSVFVRASNHQIKTVAHLAGHRVGVVKGTVGYEI 158
Cdd:PRK09495   66 TLKPMdFSGIIPALQTKNVDLaLAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDIKSVKDLDGKVVAVKSGTGSVDY 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  159 AK-NRQNIQLEVFDGIEYGVFELLAGHVDALIYSESVLKEIVAQADvSNRIKILGEPLAEIKRAIALRKDNlLLLTRLDK 237
Cdd:PRK09495  146 AKaNIKTKDLRQFPNIDNAYLELGTGRADAVLHDTPNILYFIKTAG-NGQFKAVGDSLEAQQYGIAFPKGS-ELREKVNG 223
                         250       260
                  ....*....|....*....|...
gi 307151595  238 AVNSFVGSPKYEQIYRKWYG-EP 259
Cdd:PRK09495  224 ALKTLKENGTYAEIYKKWFGtEP 246
PRK09966 PRK09966
putative inner membrane diguanylate cyclase; Provisional
970-1133 3.35e-16

putative inner membrane diguanylate cyclase; Provisional


Pssm-ID: 182171 [Multi-domain]  Cd Length: 407  Bit Score: 81.21  E-value: 3.35e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  970 RKQAEE-QLRHSVLHDGLTGLPNRTLLLDRVEQAIKRKQQQPNYlfAILFIDLDRFKVVNDSLGHLVGDQLLKTIADKLQ 1048
Cdd:PRK09966  236 RLQAKNaQLLRTALHDPLTGLANRAAFRSGINTLMNNSDARKTS--ALLFLDGDNFKYINDTWGHATGDRVLIEIAKRLA 313
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1049 RCVRPTDTVARFGGDEFVILLEDLTIWTDATKMAQRITEEFESSFTLQEQeYFTSASIGITFCSSPEQTPSELVRN-ADI 1127
Cdd:PRK09966  314 EFGGLRHKAYRLGGDEFAMVLYDVQSESEVQQICSALTQIFNLPFDLHNG-HQTTMTLSIGYAMTIEHASAEKLQElADH 392

                  ....*.
gi 307151595 1128 AMYRSK 1133
Cdd:PRK09966  393 NMYQAK 398
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
728-849 6.46e-15

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 73.47  E-value: 6.46e-15
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   728 SEEKYRLFFDANPNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQI---NPHFNRSGQ 804
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLE-GNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRlegEREPVSEER 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 307151595   805 WRHRKaNGEIIDVEITSHGLEYAGRKARLVL-AHDITERLKAEKAL 849
Cdd:TIGR00229   80 RVRRK-DGSEIWVEVSVSPIRTNGGELGVVGiVRDITERKQAEEAL 124
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
504-593 5.26e-12

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 254805 [Multi-domain]  Cd Length: 90  Bit Score: 64.32  E-value: 5.26e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   504 LYCDPNWIRRLGYDPREEAINIEWWRSKIDPETLSDHEAALENYLNGKTEYLALEYKIQTLEGEWLWIGGRGKcIAYDQQ 583
Cdd:pfam08447    2 IYWSPRFEEILGYTPEELKSSYEGWLDLVHPEDRERVRRALQELLLKKGEPYSGEYRIRRKDGSYRWVEARGR-PIRDEN 80
                           90
                   ....*....|
gi 307151595   584 RKPLKILGTH 593
Cdd:pfam08447   81 GKPVRVIGVA 90
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
853-977 1.08e-11

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 63.84  E-value: 1.08e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   853 KERFHRAIVD-APLPILIHAEDGEIVQVNHAWTELSGYHLDELSTIADWTEKAYGERkDIVRSVIDQLYEIDGKVEEGEF 931
Cdd:TIGR00229    1 SEERYRAIFEsSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDR-EEVRERIERRLEGEREPVSEER 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 307151595   932 AITIKSGETRIWDFSSAPLgKLADGRRLIISMAIDITERKQAEEQL 977
Cdd:TIGR00229   80 RVRRKDGSEIWVEVSVSPI-RTNGGELGVVGIVRDITERKQAEEAL 124
PRK13560 PRK13560
hypothetical protein; Provisional
591-1008 5.18e-11

hypothetical protein; Provisional


Pssm-ID: 106506 [Multi-domain]  Cd Length: 807  Bit Score: 65.85  E-value: 5.18e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  591 GTHRDITETKQTQENLRQQQELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLEnRQKGDLLAEFEPesEYRQSV 670
Cdd:PRK13560  184 GFAEDITERKRAEERIDEALHFLQQLLDNIADPAFWKDEDAKVFGCNDAACLACGFRRE-EIIGMSIHDFAP--AQPADD 260
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  671 LNYIKSAQGKWRDFKIL-----VRDGRI--IDTSWANVKLSD------GTSIAIgQDITERKRIEEILRESEEKYRLFFD 737
Cdd:PRK13560  261 YQEADAAKFDADGSQIIeaefqNKDGRTrpVDVIFNHAEFDDkenhcaGLVGAI-TDISGRRAAERELLEKEDMLRAIIE 339
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  738 ANPNPLWVYDLETFAFLEVNQATIEHYGYT----------------REEFLAMTIR----DIRPPEDVPLLEQYILQINP 797
Cdd:PRK13560  340 AAPIAAIGLDADGNICFVNNNAAERMLGWSaaevmgkplpgmdpelNEEFWCGDFQewypDGRPMAFDACPMAKTIKGGK 419
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  798 HFNRSGQWRHRKANGEiIDVEITSHGLEYA-GR-KARLVLAHDITERLKAEKALQESkerfHRAIVDAPLPIL-IHAEDG 874
Cdd:PRK13560  420 IFDGQEVLIEREDDGP-ADCSAYAEPLHDAdGNiIGAIALLVDITERKQVEEQLLLA----NLIVENSPLVLFrWKAEEG 494
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  875 -EIVQVNHAWTELsGYHLDELST---------IADWTEKAYGERKDIVRSVIDQLyeidgkveEGEFAITIKSGETRiWD 944
Cdd:PRK13560  495 wPVELVSKNITQF-GYEPDEFISgkrmfaaiiHPADLEQVAAEVAEFAAQGVDRF--------EQEYRILGKGGAVC-WI 564
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 307151595  945 FSSAPLGKLADGRrliIS----MAIDITERKQAEEQLRHSvlhdgltgLPNRTLLLDRVEQAIKRKQQ 1008
Cdd:PRK13560  565 DDQSAAERDEEGQ---IShfegIVIDISERKHAEEKIKAA--------LTEKEVLLKEIHHRVKNNLQ 621
PRK15437 PRK15437
histidine ABC transporter substrate-binding protein HisJ; Provisional
44-256 7.17e-11

histidine ABC transporter substrate-binding protein HisJ; Provisional


Pssm-ID: 185334 [Multi-domain]  Cd Length: 259  Bit Score: 63.13  E-value: 7.17e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   44 PKYfPPLYLVDRTGKPSGFAIDVMKEVAKLAQLKVRYeIKNTWSEVQETLINGNADLI-PNLGITPARQTQMSFTAPV-E 121
Cdd:PRK15437   34 PTY-APFESKNSQGELVGFDIDLAKELCKRINTQCTF-VENPLDALIPSLKAKKIDAImSSLSITEKRQQEIAFTDKLyA 111
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  122 TDSVSVFVRASNHQiKTVAHLAGHRVGVVKGTVgYEIAKNR----QNIQLEVFDGIEYGVFELLAGHVDA-----LIYSE 192
Cdd:PRK15437  112 ADSRLVVAKNSDIQ-PTVESLKGKRVGVLQGTT-QETFGNEhwapKGIEIVSYQGQDNIYSDLTAGRIDAafqdeVAASE 189
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 307151595  193 SVLKEIVAQADVSNRIKILGEPLAEIKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:PRK15437  190 GFLKQPVGKDYKFGGPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLAKKYF 253
PAS_9 pfam13426
PAS domain;
327-422 1.63e-10

PAS domain;


Pssm-ID: 257751 [Multi-domain]  Cd Length: 104  Bit Score: 60.09  E-value: 1.63e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   327 PGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIASLTPENPMITHEHRVRLSSGEIRWNQWTNRVIMDE 406
Cdd:pfam13426    9 PEGRIVYANPAALRLLGYTREELLGKSIRDLFGPGTDEEAVARLREALRNGGEVEVELELRRKDGEPFPVLVSASPVRDE 88
                           90
                   ....*....|....*.
gi 307151595   407 KRNIIEFQAVGRDITQ 422
Cdd:pfam13426   89 DGEVVGIVGILRDITE 104
PRK15007 PRK15007
putative ABC transporter arginine-biding protein; Provisional
47-256 4.19e-10

putative ABC transporter arginine-biding protein; Provisional


Pssm-ID: 184969 [Multi-domain]  Cd Length: 243  Bit Score: 60.43  E-value: 4.19e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   47 FPPLYLVDRTGKPSGFAIDVMKEVAKlaqlkvryEIKNTWsevqeTLINGNAD-LIPNL------------GITPARQTQ 113
Cdd:PRK15007   31 YPPFESIDANNQIVGFDVDLAQALCK--------EIDATC-----TFSNQAFDsLIPSLkfrrveavmagmDITPEREKQ 97
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  114 MSFTAPVeTDSVSVFVrASNHQIKTVAHLAGHRVGVVKGTVGYE-IAKNRQNIQLEVFDGIEYGVFELLAGHVDALIYSE 192
Cdd:PRK15007   98 VLFTTPY-YDNSALFV-GQQGKYTSVDQLKGKKVGVQNGTTHQKfIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGDT 175
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 307151595  193 SVLKEIVAQADvsnRIKILGEPLAE-----IKRAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:PRK15007  176 AVVTEWLKDNP---KLAAVGDKVTDkdyfgTGLGIAVRQGNTELQQKLNTALEKVKKDGTYETIYNKWF 241
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
321-603 8.21e-10

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 59.48  E-value: 8.21e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  321 FICRYRPGGTLTFVNQAYCRYFQKTPAAVLDntFWDLIYSEDQPQVAQNIASLTPENPMITHEHRVRLSSGEIRWNQWTN 400
Cdd:COG2202     1 LILVLDRDGRIIYANEAAEELLGYSAEELLG--LLLALHPEDRDRLRELLRRLLAGEELLSEELRLVRKDGEERWVELSA 78
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  401 RVIMDEKRNIIEFQAVgRDITQLKQVEAALRQlneeleqrveqrtaelaaeirerqeietaliksqakyeqlveklskSE 480
Cdd:COG2202    79 APLRDGEGRVLGLLGL-RDITERKRAEEALRE----------------------------------------------SE 111
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  481 ERLQLALEGSGDTIWEWNLGTGELYCDPNWIRRLGYdPREEAINIEWWRSKIDPETLSDHEAALENYLNGKTEYLALEYK 560
Cdd:COG2202   112 ERLRALLEASPDGIWVLDEDGRILYANPAAEELLGY-SPEEELGRGLSDLIHPEDEERRELELARALAEGRGGPLEIEYR 190
                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 307151595  561 IQTLEGE-WLWIGGRGKCIayDQQRKPLKILGTHRDITETKQTQ 603
Cdd:COG2202   191 VRRKDGErVRWILSRISPV--RDDGEIVGVVGIARDITERKQAE 232
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
609-725 1.07e-09

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 58.06  E-value: 1.07e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   609 QQELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLEnRQKGDLLAEFEPEsEYRQSVLNYIKSA-----QGKWRD 683
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAE-ELIGRNVLELIPE-EDREEVRERIERRlegerEPVSEE 78
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*....
gi 307151595   684 FKILVRDGRIIdtsWANVKLS----DGT---SIAIGQDITERKRIEEIL 725
Cdd:TIGR00229   79 RRVRRKDGSEI---WVEVSVSpirtNGGelgVVGIVRDITERKQAEEAL 124
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
249-427 3.85e-09

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 57.55  E-value: 3.85e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  249 EQIYRKWYGEPENFWTVGRLFWLMSGLLITTILLMSLWRYISLRPFYRLQQIEAALRASESRYRGIVEDQSEFICRYRPG 328
Cdd:COG2202    52 LAGEELLSEELRLVRKDGEERWVELSAAPLRDGEGRVLGLLGLRDITERKRAEEALRESEERLRALLEASPDGIWVLDED 131
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  329 GTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQN--IASLTPENPMITHEHRVRLSSGE-IRWNQWTNRVIMD 405
Cdd:COG2202   132 GRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRELElaRALAEGRGGPLEIEYRVRRKDGErVRWILSRISPVRD 211
                         170       180
                  ....*....|....*....|..
gi 307151595  406 EkRNIIEFQAVGRDITQLKQVE 427
Cdd:COG2202   212 D-GEIVGVVGIARDITERKQAE 232
PAS_9 pfam13426
PAS domain;
740-841 2.94e-08

PAS domain;


Pssm-ID: 257751 [Multi-domain]  Cd Length: 104  Bit Score: 53.16  E-value: 2.94e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   740 PNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYILQ-INPHFNRSGQWRHRKANGEIIDVE 818
Cdd:pfam13426    1 PDGILVLDPE-GRIVYANPAALRLLGYTREELLGKSIRDLFGPGTDEEAVARLREaLRNGGEVEVELELRRKDGEPFPVL 79
                           90       100
                   ....*....|....*....|....*
gi 307151595   819 ITSHGLEYAGRKARLVLA--HDITE 841
Cdd:pfam13426   80 VSASPVRDEDGEVVGIVGilRDITE 104
PRK15010 PRK15010
ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
47-256 1.81e-07

ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional


Pssm-ID: 184972 [Multi-domain]  Cd Length: 260  Bit Score: 52.70  E-value: 1.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   47 FPPLYLVDRTGKPSGFAIDVMKEVAKlaqlkvRYEIKNTW--SEVQETLINGNAD----LIPNLGITPARQTQMSFTAPV 120
Cdd:PRK15010   36 YAPFSSKDAKGDFVGFDIDLGNEMCK------RMQVKCTWvaSDFDALIPSLKAKkidaIISSLSITDKRQQEIAFSDKL 109
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  121 -ETDSVSVFVRASNHQiKTVAHLAGHRVGVVKGTVGYEIAKNR---QNIQLEVFDGIEYGVFELLAGHVDALIYSESVLK 196
Cdd:PRK15010  110 yAADSRLIAAKGSPIQ-PTLDSLKGKHVGVLQGSTQEAYANETwrsKGVDVVAYANQDLVYSDLAAGRLDAALQDEVAAS 188
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 307151595  197 EIVAQADVSNRIKILGEPLAEIK-----RAIALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKWY 256
Cdd:PRK15010  189 EGFLKQPAGKDFAFAGPSVKDKKyfgdgTGVGLRKDDAELTAAFNKALGELRQDGTYDKMAKKYF 253
PRK11917 PRK11917
bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
2-255 2.02e-07

bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed


Pssm-ID: 183381 [Multi-domain]  Cd Length: 259  Bit Score: 52.62  E-value: 2.02e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    2 KTIIKIVYLGFFSLLLASQLFCLKGVAQDTDqvSLLEVTAVIPKYFPPLYLVDR-TGKPSGFAIDVMKEVAK--LAQLKV 78
Cdd:PRK11917    5 KSLLKLAVFALGACVAFSNANAAEGKLESIK--SKGQLIVGVKNDVPHYALLDQaTGEIKGFEIDVAKLLAKsiLGDDKK 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   79 RYEIKNTWSEVQETLINGNAD-LIPNLGITPARQTQMSFTAPVETDSVSVFVRaSNHQIKTVAHLAGHRVGVVK-GTVGY 156
Cdd:PRK11917   83 IKLVAVNAKTRGPLLDNGSVDaVIATFTITPERKRIYNFSEPYYQDAIGLLVL-KEKNYKSLADMKGANIGVAQaATTKK 161
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  157 EIAKNRQNIQLEV-FDgiEYGVFELLAGHVDA-LIYSESVLKEIVAqADVSNRIKILGEPLAEIKRAIALRKDNllllTR 234
Cdd:PRK11917  162 AIGEAAKKIGIDVkFS--EFPDYPSIKAALDAkRVDAFSVDKSILL-GYVDDKSEILPDSFEPQSYGIVTKKDD----PA 234
                         250       260
                  ....*....|....*....|...
gi 307151595  235 LDKAVNSFVGSPKYE--QIYRKW 255
Cdd:PRK11917  235 FAKYVDDFVKEHKNEidALAKKW 257
PRK10859 PRK10859
membrane-bound lytic transglycosylase F; Provisional
1-153 7.73e-07

membrane-bound lytic transglycosylase F; Provisional


Pssm-ID: 236778 [Multi-domain]  Cd Length: 482  Bit Score: 51.80  E-value: 7.73e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    1 MKTI-IKIVYLGFFSLLLASQLFC---LKGVAQDT-DQVSLLEVTAVIPKYFPPLYLVDRTGkPSGFAIDVMKEVAKlaQ 75
Cdd:PRK10859    1 MKRLkINYLFIGLLALLLAAALWPsipWFSKEENQlEQIQERGELRVGTINSPLTYYIGNDG-PTGFEYELAKRFAD--Y 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   76 LKVRYEIK--NTWSEVQETLINGNADLI-PNLGITPARQTQMSFTAPVETDSVSVFVRASNHQIKTVAHLAGHRVGVVKG 152
Cdd:PRK10859   78 LGVKLEIKvrDNISQLFDALDKGKADLAaAGLTYTPERLKQFRFGPPYYSVSQQLVYRKGQPRPRSLGDLKGGTLTVAAG 157

                  .
gi 307151595  153 T 153
Cdd:PRK10859  158 S 158
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
479-606 8.05e-07

PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator [Regulatory functions, Small molecule interactions].


Pssm-ID: 232884 [Multi-domain]  Cd Length: 124  Bit Score: 49.20  E-value: 8.05e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   479 SEERLQLALEGSGDTIWEWNLGTGELYCDPNWIRRLGYDpREEAINIEWWrSKIDPETLSDHEAALENYLNGKTEYLALE 558
Cdd:TIGR00229    1 SEERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYS-AEELIGRNVL-ELIPEEDREEVRERIERRLEGEREPVSEE 78
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*...
gi 307151595   559 YKIQTLEGEWLWIGGRGKCIayDQQRKPLKILGTHRDITETKQTQENL 606
Cdd:TIGR00229   79 RRVRRKDGSEIWVEVSVSPI--RTNGGELGVVGIVRDITERKQAEEAL 124
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
730-839 2.16e-06

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 250275 [Multi-domain]  Cd Length: 111  Bit Score: 47.78  E-value: 2.16e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   730 EKYRLFFDANPNPLWVYDLETFaFLEVNQATIEHYGYTREEFLAMTIRDIRPPED---VPLLEQYILQINPhfNRSGQWR 806
Cdd:pfam00989    1 EDLRAILESLPDGIFVVDEDGR-ILYVNAAAEELLGLSREEVIGKSLLDLIPEEDdavAELLRQALLQGEE--SRGFEVS 77
                           90       100       110
                   ....*....|....*....|....*....|....
gi 307151595   807 HRKANGEIIDVEIT-SHGLEYAGRKARLVLAHDI 839
Cdd:pfam00989   78 FRVRDGRPRHVEVRaSPVRDAGGEIGFLGVLRDI 111
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
327-425 8.63e-06

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 254806 [Multi-domain]  Cd Length: 110  Bit Score: 45.87  E-value: 8.63e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   327 PGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSEDQPQVAQNIASLTPENPMItHEHRVRLSSGEIRWNQWTNRVIMDE 406
Cdd:pfam08448   13 PDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERALRRALEGEEPI-DFLEELLLNGEERHYELRLTPLRDP 91
                           90
                   ....*....|....*....
gi 307151595   407 KRNIIEFQAVGRDITQLKQ 425
Cdd:pfam08448   92 DGEVIGVLVISRDITERRR 110
COG4191 COG4191
Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal ...
422-466 9.17e-06

Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]


Pssm-ID: 226654 [Multi-domain]  Cd Length: 603  Bit Score: 48.85  E-value: 9.17e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 307151595  422 QLKQVEAALRQLNEELEQRVEQRTAEL-------AAEIRERQEIETALIKSQ 466
Cdd:COG4191   321 RARLRLAELQEARAELERRVEERTADLtranarlQAEIAEREQAEAALRRAQ 372
COG3434 COG3434
Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal ...
1288-1396 1.11e-05

Predicted signal transduction protein containing EAL and modified HD-GYP domains [Signal transduction mechanisms]


Pssm-ID: 225968 [Multi-domain]  Cd Length: 407  Bit Score: 48.17  E-value: 1.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595 1288 LMNNKEQVSELLLQ---MKAKKIQVSIDDFgTGYSSLSYLHYLP-VDTLKIDRSFVSRMsqvgenfEIVEAIITLAHhLQ 1363
Cdd:COG3434    90 ILEDCPPTEKLLSAikeLKQKGYLLALDDF-IFSNVSEWKPLLPlSDIVKIDFKRVTFD-------KARLFDRDLGY-IN 160
                          90       100       110
                  ....*....|....*....|....*....|...
gi 307151595 1364 MDVVAEGVETEQHLRQLQQLGCEFGQGYFFSKP 1396
Cdd:COG3434   161 KKFLAEKVETEEEFEQAKKAGFDLFQGYFFSKP 193
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
854-967 1.94e-05

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 250275 [Multi-domain]  Cd Length: 111  Bit Score: 44.70  E-value: 1.94e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   854 ERFHRAIVDAPLPILIHAEDGEIVQVNHAWTELSGYHLDEL---STIADWTEKaygerKDIVRSVIDQLYEIDGKVEEGE 930
Cdd:pfam00989    1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVigkSLLDLIPEE-----DDAVAELLRQALLQGEESRGFE 75
                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 307151595   931 FAITIKSGETRIWDFSSAPLGKlADGRRLIISMAIDI 967
Cdd:pfam00989   76 VSFRVRDGRPRHVEVRASPVRD-AGGEIGFLGVLRDI 111
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
332-416 2.02e-05

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 254805 [Multi-domain]  Cd Length: 90  Bit Score: 44.29  E-value: 2.02e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   332 TFVNQAYCRYFQKTPAAVLDN--TFWDLIYSEDQPQVAQNI-ASLTPENPMITHEHRVRLSSGEIRWNQWTNRVIMDEKR 408
Cdd:pfam08447    2 IYWSPRFEEILGYTPEELKSSyeGWLDLVHPEDRERVRRALqELLLKKGEPYSGEYRIRRKDGSYRWVEARGRPIRDENG 81

                   ....*...
gi 307151595   409 NIIEFQAV 416
Cdd:pfam08447   82 KPVRVIGV 89
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
736-842 4.41e-05

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 254806 [Multi-domain]  Cd Length: 110  Bit Score: 43.56  E-value: 4.41e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   736 FDANPNPLWVYDLEtFAFLEVNQATIEHYGYTREEFLAMTIRDIRPPEDVPLLEQYI-----------LQINPHFNRSGQ 804
Cdd:pfam08448    1 LDSLPDALAVLDPD-GRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERALrralegeepidFLEELLLNGEER 79
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 307151595   805 W------RHRKANGEIIDVeitshgleyagrkarLVLAHDITER 842
Cdd:pfam08448   80 HyelrltPLRDPDGEVIGV---------------LVISRDITER 108
PAS_9 pfam13426
PAS domain;
864-969 5.55e-05

PAS domain;


Pssm-ID: 257751 [Multi-domain]  Cd Length: 104  Bit Score: 43.14  E-value: 5.55e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   864 PLPILIHAEDGEIVQVNHAWTELSGYHLDEL--STIADWTekAYGERKDIVRSVIDQLyeIDGKVEEGEFAITIKSGETR 941
Cdd:pfam13426    1 PDGILVLDPEGRIVYANPAALRLLGYTREELlgKSIRDLF--GPGTDEEAVARLREAL--RNGGEVEVELELRRKDGEPF 76
                           90       100
                   ....*....|....*....|....*...
gi 307151595   942 IWDFSSAPLGKLADGRRLIISMAIDITE 969
Cdd:pfam13426   77 PVLVSASPVRDEDGEVVGIVGILRDITE 104
ectoine_ehuB TIGR02995
ectoine/hydroxyectoine ABC transporter solute-binding protein; Members of this family are the ...
48-257 1.33e-04

ectoine/hydroxyectoine ABC transporter solute-binding protein; Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes [Transport and binding proteins, Amino acids, peptides and amines].


Pssm-ID: 132040 [Multi-domain]  Cd Length: 275  Bit Score: 44.14  E-value: 1.33e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595    48 PPLYLVDRTGKPSGFAIDVMKEVAKLAQLKVRYEIKNTWSEVQETLINGNADLI-PNLGITPARQTQMSFTAPVETDSVS 126
Cdd:TIGR02995   43 PPFTYVGADGKVSGAAPDVARAIFKRLGIADVNASITEYGALIPGLQAGRFDAIaAGLFIKPERCKQVAFTQPILCDAEA 122
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   127 VFVRASN-HQIKTVAHLAGH---RVGVVKGTVGYEIAKN----RQNIqLEVFDGIEyGVFELLAGHVDALIYSESVLKEI 198
Cdd:TIGR02995  123 LLVKKGNpKGLKSYKDIAKNpdaKIAAPGGGTEEKLAREagvkREQI-IVVPDGQS-GLKMVQDGRADAYSLTVLTINDL 200
                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 307151595   199 VAQADVSNRikilgEPLAEIKRA-------IALRKDNLLLLTRLDKAVNSFVGSPKYEQIYRKwYG 257
Cdd:TIGR02995  201 ASKAGDPNV-----EVLAPFKDApvryyggAAFRPEDKELRDAFNVELAKLKESGEFAKIIAP-YG 260
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
310-420 1.79e-04

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 250275 [Multi-domain]  Cd Length: 111  Bit Score: 41.62  E-value: 1.79e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595   310 RYRGIVEDQSEFICRYRPGGTLTFVNQAYCRYFQKTPAAVLDNTFWDLIYSED---QPQVAQNIASLTPENpmiTHEHRV 386
Cdd:pfam00989    2 DLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDdavAELLRQALLQGEESR---GFEVSF 78
                           90       100       110
                   ....*....|....*....|....*....|....
gi 307151595   387 RLSSGEIRWNQWTNRVIMDEKRNiIEFQAVGRDI 420
Cdd:pfam00989   79 RVRDGRPRHVEVRASPVRDAGGE-IGFLGVLRDI 111
PRK13560 PRK13560
hypothetical protein; Provisional
298-489 2.75e-04

hypothetical protein; Provisional


Pssm-ID: 106506 [Multi-domain]  Cd Length: 807  Bit Score: 43.89  E-value: 2.75e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  298 QQIEAALRASESryrgIVEDQSEFICRYR--PGGTLTFVNQAYCRyFQKTPAAVLDNT--FWDLIYSEDQPQVAQNIASL 373
Cdd:PRK13560  466 KQVEEQLLLANL----IVENSPLVLFRWKaeEGWPVELVSKNITQ-FGYEPDEFISGKrmFAAIIHPADLEQVAAEVAEF 540
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  374 TPEN-PMITHEHRVRLSSGEIRWNQWTNRVIMDEKRNIIEFQAVGRDITQLKQVEAALRQ-------LNEELEQRVEQRT 445
Cdd:PRK13560  541 AAQGvDRFEQEYRILGKGGAVCWIDDQSAAERDEEGQISHFEGIVIDISERKHAEEKIKAaltekevLLKEIHHRVKNNL 620
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 307151595  446 A------ELAAEIRERQEIETALIKSQAKYEQLV---EKLSKSEERLQLALEG 489
Cdd:PRK13560  621 QiissllDLQAEKLHDEEAKCAFAESQDRICAMAlahEKLYQSEDLADIDFLD 673
RocR COG3829
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains ...
575-730 3.26e-04

Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]


Pssm-ID: 226350 [Multi-domain]  Cd Length: 560  Bit Score: 43.45  E-value: 3.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  575 GKCIAYDQQRKPLKILGTHRDITETKQ-TQENLRQQQELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKIWGWSLEnRQK 653
Cdd:COG3829    80 VGKTPVDEQGRVVGVLEVFLDISEALElIEENLRQLRQRLEAILDSIDDGLLVVDEDGIIIYYNKAYAKLLGLSPE-EVL 158
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  654 GDLLAEFEPESE--YRQSVLNYIKsaqgKWRDFKILVRDGRIIDTSWAnVKLSDGT--SIAIGQDITERKRIEEILRESE 729
Cdd:COG3829   159 GKHLLDVVSAGEdsTLLEVLRTGK----PIRDVVQTYNGNKIIVNVAP-VYADGQLigVVGISKDVSELERLTRELEESE 233

                  .
gi 307151595  730 E 730
Cdd:COG3829   234 G 234
nifL_nitrog TIGR02938
nitrogen fixation negative regulator NifL; NifL is a modulator of the nitrogen fixation ...
590-643 3.53e-04

nitrogen fixation negative regulator NifL; NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes [Central intermediary metabolism, Nitrogen fixation, Regulatory functions, Protein interactions].


Pssm-ID: 131984 [Multi-domain]  Cd Length: 494  Bit Score: 43.35  E-value: 3.53e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 307151595   590 LGTHRDITETKQTQENLRQQQELLKTIVEQIPVMLAYFDQHYNLLWVNREWEKI 643
Cdd:TIGR02938  109 LGMHRDITELHRLEQVVANQKLLIESVVDAAPVAFVLLDPTGRVILDNQEYKKL 162
PRK09776 PRK09776
putative diguanylate cyclase; Provisional
839-978 4.89e-04

putative diguanylate cyclase; Provisional


Pssm-ID: 182070 [Multi-domain]  Cd Length: 1092  Bit Score: 43.12  E-value: 4.89e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 307151595  839 ITERLKAEKA-LQESKERFHRAIVDAPLPILIHAEDGEIVQVNHAWTELSGYHLDELSTIAdWTEKAYGERKDIVRSVID 917
Cdd:PRK09776  267 VMYAFRAERKhISESETRFRNAMEYSAIGMALVGTEGQWLQVNKALCQFLGYSQEELRGLT-FQQLTWPEDLNKDLQQVE 345
                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 307151595  918 QLY--EIDGKVEEGEFaiTIKSGETRiWDFSSAPLGKLADGRRL-IISMAIDITERKQAEEQLR 978
Cdd:PRK09776  346 KLLsgEINSYSMEKRY--YRRDGEVV-WALLAVSLVRDTDGTPLyFIAQIEDINELKRTEQVNE 406
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
753-820 4.90e-04

PAS fold; The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya.


Pssm-ID: 254805 [Multi-domain]  Cd Length: 90  Bit Score: 40.06  E-value: 4.90e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 307151595   753 FLEVNQATIEHYGYTREEFLA--MTIRDIRPPEDVPL----LEQYILQINPHFnrSGQWRHRKANGEIIDVEIT 820
Cdd:pfam08447    1 IIYWSPRFEEILGYTPEELKSsyEGWLDLVHPEDRERvrraLQELLLKKGEPY--SGEYRIRRKDGSYRWVEAR 72