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Conserved domains on  [gi|86742444|ref|YP_482844|]
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PAS/PAC sensor protein [Frankia sp. CcI3]

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List of domain hits

Name Accession Description Interval E-value
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
44-148 3.36e-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. 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: 36.46  E-value: 3.36e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444  44 APIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPlgwERLRRVLATGEAILDEEIIGATPADPSNPRI 123
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDR---EELRERLENLLSGGEPVTLEVRLRRKDGSVI 77
                        90       100
                ....*....|....*....|....*.
gi 86742444 124 W-RASYYPLHDSTGARIAVGVTAVDV 148
Cdd:cd00130  78 WvLVSLTPIRDEGGEVIGLLGVVRDI 103
SpoIIE pfam07228
Stage II sporulation protein E (SpoIIE); This family contains a number of bacterial stage II ...
423-584 4.33e-40

Stage II sporulation protein E (SpoIIE); This family contains a number of bacterial stage II sporulation E proteins (EC:3.1.3.16). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments.


:

Pssm-ID: 254114  Cd Length: 192  Bit Score: 145.13  E-value: 4.33e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444   423 PAGRVALVIGDVMGRGLNAAAAMGQLRTAARTLARLDLPPAALLTELDAVTRSI---DTIASVAYVIQDPATSTLTVANG 499
Cdd:pfam07228   1 PDGRVALVIGDVMGHGLPAALLMGMLRTALRALALEGLDPAEVLERLNRALQRNlegERFATAVLAVYDPETGTLEYANA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444   500 GHLPPALRHPDGTADLLDDPHGIILGVTEQ-TFTETRHRFPPGSTLALYTDGLVESPTVDIGE-GCRRLLRILTETADLP 577
Cdd:pfam07228  81 GHPPPLLLRPDGGVVELLESPGLPLGVLPDaPYETAEFPLEPGDTLLLYTDGLTEARDPDGELfGLERLLALLAERHGLS 160

                  ....*....
gi 86742444   578 --TTADRLL 584
Cdd:pfam07228 161 peELLDALL 169
GAF super family cl17456
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
315-372 1.61e-04

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.


The actual alignment was detected with superfamily member smart00065:

Pssm-ID: 266697  Cd Length: 149  Bit Score: 41.21  E-value: 1.61e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 86742444    315 RHSHLRSAIIVPLLVGPHCLGTVGFA-VTAARPYREQDTQTATELGSRIATAIANAHAF 372
Cdd:smart00065  87 RYQGVRSFLAVPLVADGELVGVLALHnKKSPRPFTEEDEELLQALANQLAIALANAQLY 145
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
41-153 4.33e-16

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: 75.14  E-value: 4.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    41 FDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPLGWER-LRRVLATGEAILDEEIigatPADPS 119
Cdd:pfam08448   1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERaLRRALEGEEPIDFLEE----LLLNG 76
                          90       100       110
                  ....*....|....*....|....*....|....
gi 86742444   120 NPRIWRASYYPLHDSTGARIAVGVTAVDVTDERR 153
Cdd:pfam08448  77 EERHYELRLTPLRDPDGEVIGVLVISRDITERRR 110
 
Name Accession Description Interval E-value
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
44-148 3.36e-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. 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: 36.46  E-value: 3.36e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444  44 APIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPlgwERLRRVLATGEAILDEEIIGATPADPSNPRI 123
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDR---EELRERLENLLSGGEPVTLEVRLRRKDGSVI 77
                        90       100
                ....*....|....*....|....*.
gi 86742444 124 W-RASYYPLHDSTGARIAVGVTAVDV 148
Cdd:cd00130  78 WvLVSLTPIRDEGGEVIGLLGVVRDI 103
SpoIIE pfam07228
Stage II sporulation protein E (SpoIIE); This family contains a number of bacterial stage II ...
423-584 4.33e-40

Stage II sporulation protein E (SpoIIE); This family contains a number of bacterial stage II sporulation E proteins (EC:3.1.3.16). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments.


Pssm-ID: 254114  Cd Length: 192  Bit Score: 145.13  E-value: 4.33e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444   423 PAGRVALVIGDVMGRGLNAAAAMGQLRTAARTLARLDLPPAALLTELDAVTRSI---DTIASVAYVIQDPATSTLTVANG 499
Cdd:pfam07228   1 PDGRVALVIGDVMGHGLPAALLMGMLRTALRALALEGLDPAEVLERLNRALQRNlegERFATAVLAVYDPETGTLEYANA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444   500 GHLPPALRHPDGTADLLDDPHGIILGVTEQ-TFTETRHRFPPGSTLALYTDGLVESPTVDIGE-GCRRLLRILTETADLP 577
Cdd:pfam07228  81 GHPPPLLLRPDGGVVELLESPGLPLGVLPDaPYETAEFPLEPGDTLLLYTDGLTEARDPDGELfGLERLLALLAERHGLS 160

                  ....*....
gi 86742444   578 --TTADRLL 584
Cdd:pfam07228 161 peELLDALL 169
PP2C_SIG smart00331
Sigma factor PP2C-like phosphatases;
403-577 1.08e-30

Sigma factor PP2C-like phosphatases;


Pssm-ID: 214624  Cd Length: 193  Bit Score: 118.99  E-value: 1.08e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    403 YQPGTSGTEVGGDWFDVIPLPAGRVALVIGDVMGRGLNAAAAMGQLRTAARTLARLDLPPAALLTELDAVTRSI---DTI 479
Cdd:smart00331   7 AQYYEDATQVGGDFYDVVKLPEGRLLIAIADVMGKGLAAALAMSMARSALRTLLSEGISLSQILERLNRAIYENgedGMF 86
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    480 ASVAYVIQDPATSTLTVANGGHLPPAL-RHPDGTADLLDDPHGIILGVTEQTFTETRHRFPPGSTLALYTDGLVESPTVD 558
Cdd:smart00331  87 ATLFLALYDFAGGTLSYANAGHSPPYLlRADGGLVEDLDDLGAPLGLEPDVEVDVRELTLEPGDLLLLYTDGLTEARNPE 166
                          170
                   ....*....|....*....
gi 86742444    559 igegcrRLLRILTETADLP 577
Cdd:smart00331 167 ------RLEELLEELLGSP 179
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
315-372 1.61e-04

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500  Cd Length: 149  Bit Score: 41.21  E-value: 1.61e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 86742444    315 RHSHLRSAIIVPLLVGPHCLGTVGFA-VTAARPYREQDTQTATELGSRIATAIANAHAF 372
Cdd:smart00065  87 RYQGVRSFLAVPLVADGELVGVLALHnKKSPRPFTEEDEELLQALANQLAIALANAQLY 145
GAF_2 pfam13185
GAF domain;
311-367 2.44e-04

GAF domain;


Pssm-ID: 257553  Cd Length: 150  Bit Score: 40.65  E-value: 2.44e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 86742444   311 AALFRHSHLRSAIIVPLLVGPHCLGTVGFAVTAARPYREQDTQTATELGSRIATAIA 367
Cdd:pfam13185  94 GLPAGHEGLRSFLSVPLISGGRVIGVLALGSKEPGAFDEEDLELLELLAEQIAIAIE 150
PAS_8 pfam13188
PAS domain;
40-100 9.90e-04

PAS domain;


Pssm-ID: 257556  Cd Length: 66  Bit Score: 37.97  E-value: 9.90e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 86742444    40 VFDTAPIIFAVFDRGLRYRAVNQAAARASGLsaEEMIGGYGPEVLPGIDPLGWERLRRVLA 100
Cdd:pfam13188   6 LFENAPDGILVLDRGGRILYANPAALELLGY--EELLGELLGELLDDLEALAEEALELLEE 64
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
39-100 4.30e-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: 35.84  E-value: 4.30e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 86742444     39 RVFDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGID-PLGWERLRRVLA 100
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDrERVQEALQRLLS 67
FhlA COG2203
FOG: GAF domain [Signal transduction mechanisms]
314-379 7.17e-03

FOG: GAF domain [Signal transduction mechanisms]


Pssm-ID: 225113  Cd Length: 175  Bit Score: 36.88  E-value: 7.17e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 86742444 314 FRHSHLRSAIIVPLLVGPHCLGTVGFA-VTAARPYREQDTQTATELGSRIATAIANAHAFDHQRTAA 379
Cdd:COG2203 109 LLEPPIRSYLGVPLIAQGELLGLLCVHdSEPRRQWSEEELELLEELAEQVAIAIERARLYEELQEAE 175
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
41-153 4.33e-16

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: 75.14  E-value: 4.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    41 FDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPLGWER-LRRVLATGEAILDEEIigatPADPS 119
Cdd:pfam08448   1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERaLRRALEGEEPIDFLEE----LLLNG 76
                          90       100       110
                  ....*....|....*....|....*....|....
gi 86742444   120 NPRIWRASYYPLHDSTGARIAVGVTAVDVTDERR 153
Cdd:pfam08448  77 EERHYELRLTPLRDPDGEVIGVLVISRDITERRR 110
RsbU COG2208
Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / ...
362-589 2.80e-28

Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]


Pssm-ID: 225118 [Multi-domain]  Cd Length: 367  Bit Score: 115.96  E-value: 2.80e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444 362 IATAIANAH---------AFDHQRTAALTLQRALLPRDIPTLDDLDLAWRYQPGTsgtEVGGDWFDVIPLPAGRVALVIG 432
Cdd:COG2208 105 RAVGLVSAHnelllleqnNISAELEVARQIQQNLLPKALPLFPGIDIEAILVPAS---EVGGDYYDFIQLGEKRLRIGIG 181
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444 433 DVMGRGLNAAAAMGQLRTAARTLARLDLP-PAALLTELDAV---TRSIDTIASVAYVIQDPATSTLTVANGGHLPPALRH 508
Cdd:COG2208 182 DVSGKGVPAALLMLMPKLALRLLLESGPLdPADVLETLNRVlkqNLEEDMFVTLFLGVYDLDSGELTYSNAGHEPALILS 261
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444 509 PDGTADL-----LDDPHGIILGVTEQTFTETrhrFPPGSTLALYTDGLVESPTVDiGE--GCRRLLRILTETADLPttAD 581
Cdd:COG2208 262 ADGEIEVedltaLGLPIGLLPDYQYEVASLQ---LEPGDLLVLYTDGVTEARNSD-GEffGLERLLKILGRLLGQP--AE 335

                ....*...
gi 86742444 582 RLLTLLNR 589
Cdd:COG2208 336 EILEAILE 343
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
29-155 3.65e-07

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 50.23  E-value: 3.65e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444  29 ARWEEALLCLRVFDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPLGW--ERLRRVLATGEAIL 106
Cdd:COG2202 106 ALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRelELARALAEGRGGPL 185
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 86742444 107 DEEIIGATPADpsNPRIWRASYYPLHDSTGARIAVGVTAVDVTDERRAQ 155
Cdd:COG2202 186 EIEYRVRRKDG--ERVRWILSRISPVRDDGEIVGVVGIARDITERKQAE 232
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
41-157 1.55e-05

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: 43.81  E-value: 1.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    41 FDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPgidPLGWERLRRVLatgEAILDEEIIG------AT 114
Cdd:TIGR00229   9 FESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIP---EEDREEVRERI---ERRLEGEREPvseerrVR 82
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 86742444   115 PADPSnpRIW-RASYYPLHDSTGARIAVGVtAVDVTDERRAQAE 157
Cdd:TIGR00229  83 RKDGS--EIWvEVSVSPIRTNGGELGVVGI-VRDITERKQAEEA 123
PRK11360 PRK11360
sensory histidine kinase AtoS; Provisional
59-155 5.01e-05

sensory histidine kinase AtoS; Provisional


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 44.96  E-value: 5.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444   59 AVNQAAARASGLSAEEMIGGYGPEVLPGIDPLGwERLRRVLATGEAILDEEIIgaTPADPSNPRIwRASYYPLHDSTGAR 138
Cdd:PRK11360 286 TMNPAAEVITGLQRHELVGKPYSELFPPNTPFA-SPLLDTLEHGTEHVDLEIS--FPGRDRTIEL-SVSTSLLHNTHGEM 361
                         90
                 ....*....|....*..
gi 86742444  139 IAVGVTAVDVTDERRAQ 155
Cdd:PRK11360 362 IGALVIFSDLTERKRLQ 378
 
Name Accession Description Interval E-value
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
44-148 3.36e-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. 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: 36.46  E-value: 3.36e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444  44 APIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPlgwERLRRVLATGEAILDEEIIGATPADPSNPRI 123
Cdd:cd00130   1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDR---EELRERLENLLSGGEPVTLEVRLRRKDGSVI 77
                        90       100
                ....*....|....*....|....*.
gi 86742444 124 W-RASYYPLHDSTGARIAVGVTAVDV 148
Cdd:cd00130  78 WvLVSLTPIRDEGGEVIGLLGVVRDI 103
SpoIIE pfam07228
Stage II sporulation protein E (SpoIIE); This family contains a number of bacterial stage II ...
423-584 4.33e-40

Stage II sporulation protein E (SpoIIE); This family contains a number of bacterial stage II sporulation E proteins (EC:3.1.3.16). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments.


Pssm-ID: 254114  Cd Length: 192  Bit Score: 145.13  E-value: 4.33e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444   423 PAGRVALVIGDVMGRGLNAAAAMGQLRTAARTLARLDLPPAALLTELDAVTRSI---DTIASVAYVIQDPATSTLTVANG 499
Cdd:pfam07228   1 PDGRVALVIGDVMGHGLPAALLMGMLRTALRALALEGLDPAEVLERLNRALQRNlegERFATAVLAVYDPETGTLEYANA 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444   500 GHLPPALRHPDGTADLLDDPHGIILGVTEQ-TFTETRHRFPPGSTLALYTDGLVESPTVDIGE-GCRRLLRILTETADLP 577
Cdd:pfam07228  81 GHPPPLLLRPDGGVVELLESPGLPLGVLPDaPYETAEFPLEPGDTLLLYTDGLTEARDPDGELfGLERLLALLAERHGLS 160

                  ....*....
gi 86742444   578 --TTADRLL 584
Cdd:pfam07228 161 peELLDALL 169
PP2C_SIG smart00331
Sigma factor PP2C-like phosphatases;
403-577 1.08e-30

Sigma factor PP2C-like phosphatases;


Pssm-ID: 214624  Cd Length: 193  Bit Score: 118.99  E-value: 1.08e-30
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    403 YQPGTSGTEVGGDWFDVIPLPAGRVALVIGDVMGRGLNAAAAMGQLRTAARTLARLDLPPAALLTELDAVTRSI---DTI 479
Cdd:smart00331   7 AQYYEDATQVGGDFYDVVKLPEGRLLIAIADVMGKGLAAALAMSMARSALRTLLSEGISLSQILERLNRAIYENgedGMF 86
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    480 ASVAYVIQDPATSTLTVANGGHLPPAL-RHPDGTADLLDDPHGIILGVTEQTFTETRHRFPPGSTLALYTDGLVESPTVD 558
Cdd:smart00331  87 ATLFLALYDFAGGTLSYANAGHSPPYLlRADGGLVEDLDDLGAPLGLEPDVEVDVRELTLEPGDLLLLYTDGLTEARNPE 166
                          170
                   ....*....|....*....
gi 86742444    559 igegcrRLLRILTETADLP 577
Cdd:smart00331 167 ------RLEELLEELLGSP 179
GAF smart00065
Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these ...
315-372 1.61e-04

Domain present in phytochromes and cGMP-specific phosphodiesterases; Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.


Pssm-ID: 214500  Cd Length: 149  Bit Score: 41.21  E-value: 1.61e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 86742444    315 RHSHLRSAIIVPLLVGPHCLGTVGFA-VTAARPYREQDTQTATELGSRIATAIANAHAF 372
Cdd:smart00065  87 RYQGVRSFLAVPLVADGELVGVLALHnKKSPRPFTEEDEELLQALANQLAIALANAQLY 145
GAF_2 pfam13185
GAF domain;
311-367 2.44e-04

GAF domain;


Pssm-ID: 257553  Cd Length: 150  Bit Score: 40.65  E-value: 2.44e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 86742444   311 AALFRHSHLRSAIIVPLLVGPHCLGTVGFAVTAARPYREQDTQTATELGSRIATAIA 367
Cdd:pfam13185  94 GLPAGHEGLRSFLSVPLISGGRVIGVLALGSKEPGAFDEEDLELLELLAEQIAIAIE 150
PAS_8 pfam13188
PAS domain;
40-100 9.90e-04

PAS domain;


Pssm-ID: 257556  Cd Length: 66  Bit Score: 37.97  E-value: 9.90e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 86742444    40 VFDTAPIIFAVFDRGLRYRAVNQAAARASGLsaEEMIGGYGPEVLPGIDPLGWERLRRVLA 100
Cdd:pfam13188   6 LFENAPDGILVLDRGGRILYANPAALELLGY--EELLGELLGELLDDLEALAEEALELLEE 64
GAF pfam01590
GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl ...
308-366 3.52e-03

GAF domain; This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyse ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalysed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.


Pssm-ID: 250726  Cd Length: 146  Bit Score: 37.18  E-value: 3.52e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 86742444   308 SSVAALFRHSHLRSAIIVPLLVGPHCLGTVGFAVTAARPYREQDTQTATELGSRIATAI 366
Cdd:pfam01590  88 SDLPHFLRGLGIRSCLAVPLKGGGELIGVLVLHSTSPRAFTEEELELLQALADQVAIAL 146
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
39-100 4.30e-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: 35.84  E-value: 4.30e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 86742444     39 RVFDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGID-PLGWERLRRVLA 100
Cdd:smart00091   5 AILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKSLLELIHPEDrERVQEALQRLLS 67
FhlA COG2203
FOG: GAF domain [Signal transduction mechanisms]
314-379 7.17e-03

FOG: GAF domain [Signal transduction mechanisms]


Pssm-ID: 225113  Cd Length: 175  Bit Score: 36.88  E-value: 7.17e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 86742444 314 FRHSHLRSAIIVPLLVGPHCLGTVGFA-VTAARPYREQDTQTATELGSRIATAIANAHAFDHQRTAA 379
Cdd:COG2203 109 LLEPPIRSYLGVPLIAQGELLGLLCVHdSEPRRQWSEEELELLEELAEQVAIAIERARLYEELQEAE 175
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
41-153 4.33e-16

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: 75.14  E-value: 4.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    41 FDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPLGWER-LRRVLATGEAILDEEIigatPADPS 119
Cdd:pfam08448   1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDAARLERaLRRALEGEEPIDFLEE----LLLNG 76
                          90       100       110
                  ....*....|....*....|....*....|....
gi 86742444   120 NPRIWRASYYPLHDSTGARIAVGVTAVDVTDERR 153
Cdd:pfam08448  77 EERHYELRLTPLRDPDGEVIGVLVISRDITERRR 110
RsbU COG2208
Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / ...
362-589 2.80e-28

Serine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms / Transcription]


Pssm-ID: 225118 [Multi-domain]  Cd Length: 367  Bit Score: 115.96  E-value: 2.80e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444 362 IATAIANAH---------AFDHQRTAALTLQRALLPRDIPTLDDLDLAWRYQPGTsgtEVGGDWFDVIPLPAGRVALVIG 432
Cdd:COG2208 105 RAVGLVSAHnelllleqnNISAELEVARQIQQNLLPKALPLFPGIDIEAILVPAS---EVGGDYYDFIQLGEKRLRIGIG 181
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444 433 DVMGRGLNAAAAMGQLRTAARTLARLDLP-PAALLTELDAV---TRSIDTIASVAYVIQDPATSTLTVANGGHLPPALRH 508
Cdd:COG2208 182 DVSGKGVPAALLMLMPKLALRLLLESGPLdPADVLETLNRVlkqNLEEDMFVTLFLGVYDLDSGELTYSNAGHEPALILS 261
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444 509 PDGTADL-----LDDPHGIILGVTEQTFTETrhrFPPGSTLALYTDGLVESPTVDiGE--GCRRLLRILTETADLPttAD 581
Cdd:COG2208 262 ADGEIEVedltaLGLPIGLLPDYQYEVASLQ---LEPGDLLVLYTDGVTEARNSD-GEffGLERLLKILGRLLGQP--AE 335

                ....*...
gi 86742444 582 RLLTLLNR 589
Cdd:COG2208 336 EILEAILE 343
AtoS COG2202
FOG: PAS/PAC domain [Signal transduction mechanisms]
29-155 3.65e-07

FOG: PAS/PAC domain [Signal transduction mechanisms]


Pssm-ID: 225112 [Multi-domain]  Cd Length: 232  Bit Score: 50.23  E-value: 3.65e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444  29 ARWEEALLCLRVFDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPLGW--ERLRRVLATGEAIL 106
Cdd:COG2202 106 ALRESEERLRALLEASPDGIWVLDEDGRILYANPAAEELLGYSPEEELGRGLSDLIHPEDEERRelELARALAEGRGGPL 185
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 86742444 107 DEEIIGATPADpsNPRIWRASYYPLHDSTGARIAVGVTAVDVTDERRAQ 155
Cdd:COG2202 186 EIEYRVRRKDG--ERVRWILSRISPVRDDGEIVGVVGIARDITERKQAE 232
PAS_9 pfam13426
PAS domain;
45-150 5.18e-07

PAS domain;


Pssm-ID: 257751 [Multi-domain]  Cd Length: 104  Bit Score: 48.15  E-value: 5.18e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    45 PIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVL-PGIDPLGWERLRRVLATGEAIlDEEIIGATpadPSNPRI 123
Cdd:pfam13426   1 PDGILVLDPEGRIVYANPAALRLLGYTREELLGKSIRDLFgPGTDEEAVARLREALRNGGEV-EVELELRR---KDGEPF 76
                          90       100
                  ....*....|....*....|....*...
gi 86742444   124 W-RASYYPLHDSTGARIAVGVTAVDVTD 150
Cdd:pfam13426  77 PvLVSASPVRDEDGEVVGIVGILRDITE 104
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
41-157 1.55e-05

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: 43.81  E-value: 1.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    41 FDTAPIIFAVFDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPgidPLGWERLRRVLatgEAILDEEIIG------AT 114
Cdd:TIGR00229   9 FESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIP---EEDREEVRERI---ERRLEGEREPvseerrVR 82
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 86742444   115 PADPSnpRIW-RASYYPLHDSTGARIAVGVtAVDVTDERRAQAE 157
Cdd:TIGR00229  83 RKDGS--EIWvEVSVSPIRTNGGELGVVGI-VRDITERKQAEEA 123
PRK11360 PRK11360
sensory histidine kinase AtoS; Provisional
59-155 5.01e-05

sensory histidine kinase AtoS; Provisional


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 44.96  E-value: 5.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444   59 AVNQAAARASGLSAEEMIGGYGPEVLPGIDPLGwERLRRVLATGEAILDEEIIgaTPADPSNPRIwRASYYPLHDSTGAR 138
Cdd:PRK11360 286 TMNPAAEVITGLQRHELVGKPYSELFPPNTPFA-SPLLDTLEHGTEHVDLEIS--FPGRDRTIEL-SVSTSLLHNTHGEM 361
                         90
                 ....*....|....*..
gi 86742444  139 IAVGVTAVDVTDERRAQ 155
Cdd:PRK11360 362 IGALVIFSDLTERKRLQ 378
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
39-148 1.33e-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: 250275 [Multi-domain]  Cd Length: 111  Bit Score: 37.76  E-value: 1.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 86742444    39 RVFDTAP-IIFAVfDRGLRYRAVNQAAARASGLSAEEMIGGYGPEVLPGIDPLGWERLRRVLATGEAILDEEIIgaTPAD 117
Cdd:pfam00989   5 AILESLPdGIFVV-DEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAVAELLRQALLQGEESRGFEVS--FRVR 81
                          90       100       110
                  ....*....|....*....|....*....|.
gi 86742444   118 PSNPRIWRASYYPLHDSTGaRIAVGVTAVDV 148
Cdd:pfam00989  82 DGRPRHVEVRASPVRDAGG-EIGFLGVLRDI 111
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.11
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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