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Conserved domains on  [gi|134104401]
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Chain B, Nitrogen fixation regulatory protein

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
nifL_nitrog super family cl31271
nitrogen fixation negative regulator NifL; NifL is a modulator of the nitrogen fixation ...
 2-120 6.41e-81

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]


The actual alignment was detected with superfamily member TIGR02938:

Pssm-ID: 131984 [Multi-domain]  Cd Length: 494  Bit Score: 245.58  E-value: 6.41e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401    2 LLPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLV 81
Cdd:TIGR02938   1 LPPEAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 134104401   82 NRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH 120
Cdd:TIGR02938  81 NRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELH 119
 
Name Accession Description Interval E-value
nifL_nitrog TIGR02938
nitrogen fixation negative regulator NifL; NifL is a modulator of the nitrogen fixation ...
 2-120 6.41e-81

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: 245.58  E-value: 6.41e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401    2 LLPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLV 81
Cdd:TIGR02938   1 LPPEAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 134104401   82 NRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH 120
Cdd:TIGR02938  81 NRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELH 119
PAS COG2202
PAS domain [Signal transduction mechanisms];
5-120 1.75e-28

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 103.95  E-value: 1.75e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRR 84
Cdd:COG2202   11 RRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRR 90

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 134104401  85 KDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH 120
Cdd:COG2202   91 KDGSLFWVELSISPVRDEDGEITGFVGIARDITERK 126
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 5-115 4.72e-26

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. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 93.64  E-value: 4.72e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401    5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVN-R 83
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFEVSfR 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 134104401   84 RKDKTLYLAELTVAPVLNEAGETIYYLGMHRD 115
Cdd:pfam00989  81 VPDGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 9-118 2.96e-17

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 76.03  E-value: 2.96e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   9 QTVEHAPIAISITDLKAN---ILYANRAFRTITGYGSEEVLGKNESILSN-GTTPRLVYQaLWGRLAQKKPWSGVLVNRR 84
Cdd:PRK13558 152 RALDEAPVGITIADATLPdepLIYINDAFERITGYSPDEVLGRNCRFLQGeDTNEERVAE-LREAIDEERPTSVELRNYR 230

                         90       100       110
                 ....*....|....*....|....*....|....
gi 134104401  85 KDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSE 118
Cdd:PRK13558 231 KDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTE 264
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 14-115 3.94e-11

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: 55.33  E-value: 3.94e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401  14 APIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAE 93
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                         90       100
                 ....*....|....*....|..
gi 134104401  94 LTVAPVLNEAGETIYYLGMHRD 115
Cdd:cd00130   81 VSLTPIRDEGGEVIGLLGVVRD 102
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 5-49 2.81e-08

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: 47.01  E-value: 2.81e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 134104401     5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKN 49
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKS 45
 
Name Accession Description Interval E-value
nifL_nitrog TIGR02938
nitrogen fixation negative regulator NifL; NifL is a modulator of the nitrogen fixation ...
 2-120 6.41e-81

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: 245.58  E-value: 6.41e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401    2 LLPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLV 81
Cdd:TIGR02938   1 LPPEAYRQTVDQAPLAISITDLKANILYANDAFTRITGYTKEEIIGKNESVLSNHTTPPEVYQALWGSLAEQKPWAGKLL 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 134104401   82 NRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH 120
Cdd:TIGR02938  81 NRRKDGELYLAELTVAPVLNEAGETTHFLGMHRDITELH 119
PAS COG2202
PAS domain [Signal transduction mechanisms];
5-120 1.75e-28

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 103.95  E-value: 1.75e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRR 84
Cdd:COG2202   11 RRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPEDDDEFLELLRAALAGGGVWRGELRNRR 90

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 134104401  85 KDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH 120
Cdd:COG2202   91 KDGSLFWVELSISPVRDEDGEITGFVGIARDITERK 126
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 5-115 4.72e-26

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. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 395786 [Multi-domain]  Cd Length: 113  Bit Score: 93.64  E-value: 4.72e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401    5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVN-R 83
Cdd:pfam00989   1 EDLRAILESLPDGIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEEDDAEVAELLRQALLQGEESRGFEVSfR 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 134104401   84 RKDKTLYLAELTVAPVLNEAGETIYYLGMHRD 115
Cdd:pfam00989  81 VPDGRPRHVEVRASPVRDAGGEILGFLGVLRD 112
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 5-120 7.30e-20

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: 272971 [Multi-domain]  Cd Length: 124  Bit Score: 78.10  E-value: 7.30e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401    5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVN-R 83
Cdd:TIGR00229   3 ERYRAIFESSPDAIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPEPVSEERRvR 82

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 134104401   84 RKDKTLYLAELTVAPVlNEAGETIYYLGMHRDTSELH 120
Cdd:TIGR00229  83 RKDGSEIWVEVSVSPI-RTNGGELGVVGIVRDITERK 118
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 9-118 2.96e-17

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 76.03  E-value: 2.96e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   9 QTVEHAPIAISITDLKAN---ILYANRAFRTITGYGSEEVLGKNESILSN-GTTPRLVYQaLWGRLAQKKPWSGVLVNRR 84
Cdd:PRK13558 152 RALDEAPVGITIADATLPdepLIYINDAFERITGYSPDEVLGRNCRFLQGeDTNEERVAE-LREAIDEERPTSVELRNYR 230

                         90       100       110
                 ....*....|....*....|....*....|....
gi 134104401  85 KDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSE 118
Cdd:PRK13558 231 KDGSTFWNQVDIAPIRDEDGTVTHYVGFQTDVTE 264
PRK13557 PRK13557
histidine kinase; Provisional
 5-117 8.96e-16

histidine kinase; Provisional


Pssm-ID: 237425 [Multi-domain]  Cd Length: 540  Bit Score: 71.63  E-value: 8.96e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   5 EIFRQTVEHAPIAISITDLKAN---ILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLV 81
Cdd:PRK13557  30 DIFFAAVETTRMPMIVTDPNQPdnpIVFANRAFLEMTGYAAEEIIGNNCRFLQGPETDRATVAEVRDAIAERREIATEIL 109

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 134104401  82 NRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTS 117
Cdd:PRK13557 110 NYRKDGSSFWNALFVSPVYNDAGDLVYFFGSQLDVS 145
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 26-118 4.57e-15

PAS domain; This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463873 [Multi-domain]  Cd Length: 93  Bit Score: 65.18  E-value: 4.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   26 NILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLaqKKPWSGVLVNRRKDKTLYLAELTVAPVLNEAGE 105
Cdd:pfam13426   3 RIIYVNDAALRLLGYTREELLGKSITDLFAEPEDSERLREALREG--KAVREFEVVLYRKDGEPFPVLVSLAPIRDDGGE 80

                          90
                  ....*....|...
gi 134104401  106 TIYYLGMHRDTSE 118
Cdd:pfam13426  81 LVGIIAILRDITE 93
PRK13559 PRK13559
hypothetical protein; Provisional
 6-120 8.20e-15

hypothetical protein; Provisional


Pssm-ID: 237427 [Multi-domain]  Cd Length: 361  Bit Score: 68.69  E-value: 8.20e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   6 IFRQTVEHAPIAISITDLKAN---ILYANRAFRTITGYGSEEVLGKNESILSN-GTTPRLVYQaLWGRLAQKKPWSGVLV 81
Cdd:PRK13559  44 LFEQAMEQTRMAMCITDPHQPdlpIVLANQAFLDLTGYAAEEVVGRNCRFLQGaATDPIAVAK-IRAAIAAEREIVVELL 122

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 134104401  82 NRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSELH 120
Cdd:PRK13559 123 NYRKDGEPFWNALHLGPVYGEDGRLLYFFGSQWDVTDIR 161
PAS COG2202
PAS domain [Signal transduction mechanisms];
5-118 1.91e-13

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 64.28  E-value: 1.91e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVyQALWGRLAQKKPWSGVLVNRR 84
Cdd:COG2202  137 ERLRLLVENAPDGIFVLDLDGRILYVNPAAEELLGYSPEELLGKSLLDLLHPEDRERL-LELLRRLLEGGRESYELELRL 215

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 134104401  85 KDKTLYLAELTVAPVLNEAGETI-YYLGMHRDTSE 118
Cdd:COG2202  216 KDGDGRWVWVEASAVPLRDGGEViGVLGIVRDITE 250
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
3-118 3.01e-13

Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 64.48  E-value: 3.01e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   3 LPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKN-ESILSNgttPRLVYQALWGRLAQKKP-WSGVL 80
Cdd:COG3852    5 SEELLRAILDSLPDAVIVLDADGRITYVNPAAERLLGLSAEELLGRPlAELFPE---DSPLRELLERALAEGQPvTEREV 81

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 134104401  81 VNRRKDKTLYLAELTVAPVLNEAGETiYYLGMHRDTSE 118
Cdd:COG3852   82 TLRRKDGEERPVDVSVSPLRDAEGEG-GVLLVLRDITE 118
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 1-120 2.86e-12

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 61.71  E-value: 2.86e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   1 ELLPEIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVyqalwgrLAQKKPWSGVL 80
Cdd:COG3829    7 KELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEVIGKNVTELIPNSPLLEV-------LKTGKPVTGVI 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 134104401  81 VNRRKDKTLYLAelTVAPVLnEAGETIYYLGMHRDTSELH 120
Cdd:COG3829   80 QKTGGKGKTVIV--TAIPIF-EDGEVIGAVETFRDITELK 116
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 7-119 9.53e-12

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 60.37  E-value: 9.53e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   7 FRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILsngttPRLVYQALWGRLAQKKPWSGVLVN---- 82
Cdd:COG5809  143 FRLIFNHSPDGIIVTDLDGRIIYANPAACKLLGISIEELIGKSILEL-----IHSDDQENVAAFISQLLKDGGIAQgevr 217

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 134104401  83 -RRKDKTLYLAELTVAPvLNEAGETIYYLGMHRDTSEL 119
Cdd:COG5809  218 fWTKDGRWRLLEASGAP-IKKNGEVDGIVIIFRDITER 254
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 14-115 3.94e-11

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: 55.33  E-value: 3.94e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401  14 APIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAE 93
Cdd:cd00130    1 LPDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPEDREELRERLENLLSGGEPVTLEVRLRRKDGSVIWVL 80

                         90       100
                 ....*....|....*....|..
gi 134104401  94 LTVAPVLNEAGETIYYLGMHRD 115
Cdd:cd00130   81 VSLTPIRDEGGEVIGLLGVVRD 102
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 11-120 9.25e-11

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. This domain is associated to signalling systems and works as a signal sensor domain. It recognizes differently substituted aromatic hydrocarbons, oxygen, different dodecanoic acids, autoinducers, 3,5-dimethyl-pyrazin-2-ol and N-alanyl-aminoacetone (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 312075 [Multi-domain]  Cd Length: 110  Bit Score: 54.34  E-value: 9.25e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   11 VEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKN-ESILSNGTTPRLvyQALWGR-LAQKKPWSGVLVNRRKDKT 88
Cdd:pfam08448   1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTlAELLPPEDAARL--ERALRRaLEGEEPIDFLEELLLNGEE 78

                          90       100       110
                  ....*....|....*....|....*....|..
gi 134104401   89 LYLaELTVAPVLNEAGETIYYLGMHRDTSELH 120
Cdd:pfam08448  79 RHY-ELRLTPLRDPDGEVIGVLVISRDITERR 109
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 27-111 6.72e-10

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: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 51.57  E-value: 6.72e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   27 ILYANRAFRTITGYGSEEVLGKNESILS--NGTTPRLVYQALWGRLAQKKPWSGVLVNRRKDKTLYLAELTVAPVLNEAG 104
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKGESWLDlvHPDDRERVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDENG 80


                  ....*..
gi 134104401  105 ETIYYLG 111
Cdd:pfam08447  81 KPVRVIG 87
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 5-119 1.01e-09

Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444511 [Multi-domain]  Cd Length: 489  Bit Score: 54.60  E-value: 1.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401   5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRlVYQALWGRLAQKKPWSGVLVNRR 84
Cdd:COG5809   15 QRFRSLFENAPDAILILDLEGKILKVNPAAERIFGYTEDELLGTNILDFLHPDDEK-ELREILKLLKEGESRDELEFELR 93

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 134104401  85 -KDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSEL 119
Cdd:COG5809   94 hKNGKRLEFSSKLSPIFDQNGDIEGMLAISRDITER 129
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 11-119 2.39e-08

Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 50.50  E-value: 2.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401  11 VEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALWGRLAQKKPwSGVLVNRR-KDKTL 89
Cdd:COG5805  163 IENSPDLICVIDTDGRILFINESIERLFGAPREELIGKNLLELLHPCDKEEFKERIESITEVWQE-FIIEREIItKDGRI 241

                         90       100       110
                 ....*....|....*....|....*....|
gi 134104401  90 YLAELTVAPVLNEAGETIYYLGMHRDTSEL 119
Cdd:COG5805  242 RYFEAVIVPLIDTDGSVKGILVILRDITEK 271
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 5-49 2.81e-08

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: 47.01  E-value: 2.81e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 134104401     5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKN 49
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGKS 45
PAS_8 pfam13188
PAS domain; PAS domains are involved in many signalling proteins where they are used as a ...
 5-44 3.93e-07

PAS domain; PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. This domain recognizes oxygen and CO (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 463802 [Multi-domain]  Cd Length: 65  Bit Score: 44.08  E-value: 3.93e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 134104401    5 EIFRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEE 44
Cdd:pfam13188   1 ERLRALFESSPDGILVLDEGGRIIYVNPAALELLGYELLG 40
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 11-112 3.11e-06

Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 444507 [Multi-domain]  Cd Length: 496  Bit Score: 44.34  E-value: 3.11e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 134104401  11 VEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKNESILSNGTTPRLVYQALwGRLAQKKPWSGVLVNRRKDKTLY 90
Cdd:COG5805   40 LENLPDAIIAVNREGKVIYINPAMEKLLGYTSEEIIGKTIFDFLEKEYHYRVKTRI-ERLQKGYDVVMIEQIYCKDGELI 118

                         90       100
                 ....*....|....*....|..
gi 134104401  91 LAELTVAPVLNEAGETIYYLGM 112
Cdd:COG5805  119 YVEVKLFPIYNQNGQAAILALR 140
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 77-119 3.65e-06

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: 41.01  E-value: 3.65e-06
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 134104401    77 SGVLVNRRKDKTLYLAELTVAPVLNEAGETIYYLGMHRDTSEL 119
Cdd:smart00086   1 TVEYRLRRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 7-66 1.23e-03

Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms];


Pssm-ID: 444024 [Multi-domain]  Cd Length: 422  Bit Score: 36.86  E-value: 1.23e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 134104401   7 FRQTVEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKN-ESILSNGTTPRLVYQAL 66
Cdd:COG5000   92 LETILENLPAGVIVLDADGRITLANPAAERLLGIPLEELIGKPlEELLPELDLAELLREAL 152
PRK11359 PRK11359
cyclic-di-GMP phosphodiesterase; Provisional
 11-69 4.98e-03

cyclic-di-GMP phosphodiesterase; Provisional


Pssm-ID: 183097 [Multi-domain]  Cd Length: 799  Bit Score: 35.52  E-value: 4.98e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 134104401  11 VEHAPIAISITDLKANILYANRAFRTITGYGSEEVLGKN-ESILSNGTTP----RLVYQALWGR 69
Cdd:PRK11359 142 VDHLDRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQpDTLLNIPEFPadnrIRLQQLLWKT 205
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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