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Conserved domains on  [gi|1278886390|gb|PJD73708|]
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pili assembly chaperone [Enterobacter kobei]

Protein Classification

PAS domain-containing methyl-accepting chemotaxis protein( domain architecture ID 14306470)

PAS domain-containing methyl-accepting chemotaxis protein (MCP) is a bacterial receptor that mediates chemotaxis to diverse signals, responding to changes in the concentration of attractants and repellents in the environment by altering swimming behavior

CATH:  3.30.450.20|1.10.287.950
Gene Ontology:  GO:0007165|GO:0006935
PubMed:  15009198|9382818|18165013|20738376
SCOP:  3000471|4003862

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PAS COG2202
PAS domain [Signal transduction mechanisms];
12-261 2.30e-27

PAS domain [Signal transduction mechanisms];


:

Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 109.73  E-value: 2.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  12 LQRSAISYDAICQNKP--VIEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSLvSSPEYSQFWQRLARGESFSG 89
Cdd:COG2202     6 LEESERRLRALVESSPdaIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPED-DDEFLELLRAALAGGGVWRG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  90 KYLRLAKGNRSVWLEASYIPVSDRRGRVIRVIKIAADISERVHS--ALEQ-----EAVVNAInrSMAIITFNPEGIVLEA 162
Cdd:COG2202    85 ELRNRRKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAeeALREseerlRLLVENA--PDGIFVLDLDGRILYV 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 163 NENFVNATGYKRDEIIGKHHRLFCAETLYKSDEyRHFWESLNQG-EFFSGLFPRLNRQGDPLWFRATYNPVFNSDGQLYk 241
Cdd:COG2202   163 NPAAEELLGYSPEELLGKSLLDLLHPEDRERLL-ELLRRLLEGGrESYELELRLKDGDGRWVWVEASAVPLRDGGEVIG- 240

                         250       260
                  ....*....|....*....|
gi 1278886390 242 IVKFATDVTAdvlRNQREQE 261
Cdd:COG2202   241 VLGIVRDITE---RKRAEEA 257
MCP_signal super family cl46910
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
 260-428 1.53e-24

Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.


The actual alignment was detected with superfamily member smart00283:

Pssm-ID: 481250 [Multi-domain]  Cd Length: 262  Bit Score: 101.98  E-value: 1.53e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  260 QEAAVHAWDMAV---QTRESAQNGANVIENSILMIDRIAQGMGAVSTDISRLNNQSESIDDMVETIRKFAMQTRLIALNA 336
Cdd:smart00283  35 EEVAANADEIAAtaqSAAEAAEEGREAVEDAITAMDQIREVVEEAVSAVEELEESSDEIGEIVSVIDDIADQTNLLALNA 114

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  337 AIEAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRN 416
Cdd:smart00283 115 AIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETNEAVAAMEESSSEVEEGVELVEETGDALEEIVDS 194

                          170
                   ....*....|..
gi 1278886390  417 AAGVETAVKDVA 428
Cdd:smart00283 195 VEEIADLVQEIA 206
 
Name Accession Description Interval E-value
PAS COG2202
PAS domain [Signal transduction mechanisms];
12-261 2.30e-27

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 109.73  E-value: 2.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  12 LQRSAISYDAICQNKP--VIEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSLvSSPEYSQFWQRLARGESFSG 89
Cdd:COG2202     6 LEESERRLRALVESSPdaIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPED-DDEFLELLRAALAGGGVWRG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  90 KYLRLAKGNRSVWLEASYIPVSDRRGRVIRVIKIAADISERVHS--ALEQ-----EAVVNAInrSMAIITFNPEGIVLEA 162
Cdd:COG2202    85 ELRNRRKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAeeALREseerlRLLVENA--PDGIFVLDLDGRILYV 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 163 NENFVNATGYKRDEIIGKHHRLFCAETLYKSDEyRHFWESLNQG-EFFSGLFPRLNRQGDPLWFRATYNPVFNSDGQLYk 241
Cdd:COG2202   163 NPAAEELLGYSPEELLGKSLLDLLHPEDRERLL-ELLRRLLEGGrESYELELRLKDGDGRWVWVEASAVPLRDGGEVIG- 240

                         250       260
                  ....*....|....*....|
gi 1278886390 242 IVKFATDVTAdvlRNQREQE 261
Cdd:COG2202   241 VLGIVRDITE---RKRAEEA 257
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
 260-428 1.53e-24

Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo reversible methylation in response to attractants or repellants during bacterial chemotaxis.


Pssm-ID: 214599 [Multi-domain]  Cd Length: 262  Bit Score: 101.98  E-value: 1.53e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  260 QEAAVHAWDMAV---QTRESAQNGANVIENSILMIDRIAQGMGAVSTDISRLNNQSESIDDMVETIRKFAMQTRLIALNA 336
Cdd:smart00283  35 EEVAANADEIAAtaqSAAEAAEEGREAVEDAITAMDQIREVVEEAVSAVEELEESSDEIGEIVSVIDDIADQTNLLALNA 114

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  337 AIEAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRN 416
Cdd:smart00283 115 AIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETNEAVAAMEESSSEVEEGVELVEETGDALEEIVDS 194

                          170
                   ....*....|..
gi 1278886390  417 AAGVETAVKDVA 428
Cdd:smart00283 195 VEEIADLVQEIA 206
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
261-431 1.23e-23

Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 103.18  E-value: 1.23e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 261 EAAVHAWDMAVQTRESAQNGANVIENSILMIDRIAQGMGAVSTDISRLNNQSESIDDMVETIRKFAMQTRLIALNAAIEA 340
Cdd:COG0840   309 ENAQQAAELAEEASELAEEGGEVVEEAVEGIEEIRESVEETAETIEELGESSQEIGEIVDVIDDIAEQTNLLALNAAIEA 388

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 341 ARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRNAAGV 420
Cdd:COG0840   389 ARAGEAGRGFAVVADEVRKLAERSAEATKEIEELIEEIQSETEEAVEAMEEGSEEVEEGVELVEEAGEALEEIVEAVEEV 468

                         170
                  ....*....|.
gi 1278886390 421 ETAVKDVAISV 431
Cdd:COG0840   469 SDLIQEIAAAS 479
MCP_signal cd11386
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
 260-432 3.40e-21

Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.


Pssm-ID: 206779 [Multi-domain]  Cd Length: 200  Bit Score: 90.76  E-value: 3.40e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 260 QEAAVHAWDMAV---QTRESAQNGANVIENSILMIDRIAQGMGAVSTDISRLNNQSESIDDMVETIRKFAMQTRLIALNA 336
Cdd:cd11386     8 EEVAASADQVAEtsqQAAELAEKGREAAEDAINQMNQIDESVDEAVSAVEELEESSAEIGEIVEVIDDIAEQTNLLALNA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 337 AIEAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRN 416
Cdd:cd11386    88 AIEAARAGEAGRGFAVVADEVRKLAEESAEAAKEIEELIEEIQEQTEEAVEAMEETSEEVEEGVELVEETGRAFEEIVAS 167

                         170
                  ....*....|....*.
gi 1278886390 417 AAGVETAVKDVAISVK 432
Cdd:cd11386   168 VEEVADGIQEISAATQ 183
MCPsignal pfam00015
Methyl-accepting chemotaxis protein (MCP) signalling domain; This domain is thought to ...
 268-431 9.64e-20

Methyl-accepting chemotaxis protein (MCP) signalling domain; This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.


Pssm-ID: 333767 [Multi-domain]  Cd Length: 172  Bit Score: 85.95  E-value: 9.64e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 268 DMAVQTRESAQNGANVIENSILMIDRIAQgmgavstdisrlnnQSESIDDMVETIRKFAMQTRLIALNAAIEAARAGASG 347
Cdd:pfam00015   2 DLAQLASEEAQDGGKEVANVVGQMEQIAQ--------------SSKKISDIISVIDEIAFQTNLLALNAAIEAARAGEQG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 348 RSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRNAAGVETAVKDV 427
Cdd:pfam00015  68 RGFAVVADEVRKLAERSAQAAKEIEALIIEIQKQTNDSTASIESTRQRVEVGSTIVESTGEALKEIVDAVAEIADIVQEI 147


                  ....
gi 1278886390 428 AISV 431
Cdd:pfam00015 148 AAAS 151
PRK15041 PRK15041
methyl-accepting chemotaxis protein;
249-413 4.31e-14

methyl-accepting chemotaxis protein;


Pssm-ID: 185001 [Multi-domain]  Cd Length: 554  Bit Score: 74.22  E-value: 4.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 249 VTADVLRNQreqEAAVHAWDMAVQTRESAQNGANVIENsilmidrIAQGMGAVSTdisrlnnQSESIDDMVETIRKFAMQ 328
Cdd:PRK15041  312 LTATVKQNA---ENARQASHLALSASETAQRGGKVVDN-------VVQTMRDIST-------SSQKIADIISVIDGIAFQ 374

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 329 TRLIALNAAIEAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVvasnsqlakdvlcgIENSLMNTREGVTLMREAGE 408
Cdd:PRK15041  375 TNILALNAAVEAARAGEQGRGFAVVAGEVRNLAQRSAQAAREIKSL--------------IEDSVGKVDVGSTLVESAGE 440


                  ....*
gi 1278886390 409 VMTSI 413
Cdd:PRK15041  441 TMAEI 445
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 159-246 6.89e-13

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: 63.90  E-value: 6.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 159 VLEANENFVNATGYKRDEIIGK---HHRLFCAETLYKsdEYRHFWESLNQGEFFSGLFPRLNRQGDPLWFRATYNPVFNS 235
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgesWLDLVHPDDRER--VREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDE 78

                          90
                  ....*....|.
gi 1278886390 236 DGQLYKIVKFA 246
Cdd:pfam08447  79 NGKPVRVIGVA 89
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 147-249 8.77e-09

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: 53.02  E-value: 8.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 147 SMAIITFNPEGIVLEANENFVNATGYKRDEIIGKHHRLFCAEtlykSDEYRH---FWESLNQGEFFSGLFPRLNRQGDPL 223
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHP----EDREELrerLENLLSGGEPVTLEVRLRRKDGSVI 77

                          90       100
                  ....*....|....*....|....*.
gi 1278886390 224 WFRATYNPVFNSDGQLYKIVKFATDV 249
Cdd:cd00130    78 WVLVSLTPIRDEGGEVIGLLGVVRDI 103
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 105-261 1.05e-07

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 54.07  E-value: 1.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 105 ASYIPVSDRrgrvirvikiaaDISERVHSALEQEAVVNAINRSMAIITFN-----------------PEGIVLE------ 161
Cdd:PRK13558  103 AAYVPAVSD------------DATAAIAERIESAVPEHSRDTEARMPISDltvesdrrlkeraldeaPVGITIAdatlpd 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 162 -----ANENFVNATGYKRDEIIGKHHRLFCAEtlyKSDEYR--HFWESLNQGEFFSGLFPRLNRQGDPLWFRATYNPVFN 234
Cdd:PRK13558  171 epliyINDAFERITGYSPDEVLGRNCRFLQGE---DTNEERvaELREAIDEERPTSVELRNYRKDGSTFWNQVDIAPIRD 247

                         170       180       190
                  ....*....|....*....|....*....|
gi 1278886390 235 SDGQLYKIVKFATDVTADV---LRNQREQE 261
Cdd:PRK13558  248 EDGTVTHYVGFQTDVTERKeaeLALQRERR 277
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 19-131 1.06e-06

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: 47.29  E-value: 1.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  19 YDAICQNKPV--IEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSLvSSPEYSQFWQRLARGESFSGKYLRLA- 95
Cdd:TIGR00229   5 YRAIFESSPDaiIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEED-REEVRERIERRLEGEPEPVSEERRVRr 83

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1278886390  96 KGNRSVWLEASYIPVSdRRGRVIRVIKIAADISERV 131
Cdd:TIGR00229  84 KDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERK 118
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 138-181 1.40e-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: 36.99  E-value: 1.40e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1278886390  138 EAVVNAINrsMAIITFNPEGIVLEANENFVNATGYKRDEIIGKH 181
Cdd:smart00091   4 RAILESLP--DGIFVLDLDGRILYANPAAEELLGYSPEELIGKS 45
 
Name Accession Description Interval E-value
PAS COG2202
PAS domain [Signal transduction mechanisms];
12-261 2.30e-27

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 109.73  E-value: 2.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  12 LQRSAISYDAICQNKP--VIEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSLvSSPEYSQFWQRLARGESFSG 89
Cdd:COG2202     6 LEESERRLRALVESSPdaIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPPED-DDEFLELLRAALAGGGVWRG 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  90 KYLRLAKGNRSVWLEASYIPVSDRRGRVIRVIKIAADISERVHS--ALEQ-----EAVVNAInrSMAIITFNPEGIVLEA 162
Cdd:COG2202    85 ELRNRRKDGSLFWVELSISPVRDEDGEITGFVGIARDITERKRAeeALREseerlRLLVENA--PDGIFVLDLDGRILYV 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 163 NENFVNATGYKRDEIIGKHHRLFCAETLYKSDEyRHFWESLNQG-EFFSGLFPRLNRQGDPLWFRATYNPVFNSDGQLYk 241
Cdd:COG2202   163 NPAAEELLGYSPEELLGKSLLDLLHPEDRERLL-ELLRRLLEGGrESYELELRLKDGDGRWVWVEASAVPLRDGGEVIG- 240

                         250       260
                  ....*....|....*....|
gi 1278886390 242 IVKFATDVTAdvlRNQREQE 261
Cdd:COG2202   241 VLGIVRDITE---RKRAEEA 257
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
 260-428 1.53e-24

Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo reversible methylation in response to attractants or repellants during bacterial chemotaxis.


Pssm-ID: 214599 [Multi-domain]  Cd Length: 262  Bit Score: 101.98  E-value: 1.53e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  260 QEAAVHAWDMAV---QTRESAQNGANVIENSILMIDRIAQGMGAVSTDISRLNNQSESIDDMVETIRKFAMQTRLIALNA 336
Cdd:smart00283  35 EEVAANADEIAAtaqSAAEAAEEGREAVEDAITAMDQIREVVEEAVSAVEELEESSDEIGEIVSVIDDIADQTNLLALNA 114

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  337 AIEAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRN 416
Cdd:smart00283 115 AIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETNEAVAAMEESSSEVEEGVELVEETGDALEEIVDS 194

                          170
                   ....*....|..
gi 1278886390  417 AAGVETAVKDVA 428
Cdd:smart00283 195 VEEIADLVQEIA 206
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
261-431 1.23e-23

Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 103.18  E-value: 1.23e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 261 EAAVHAWDMAVQTRESAQNGANVIENSILMIDRIAQGMGAVSTDISRLNNQSESIDDMVETIRKFAMQTRLIALNAAIEA 340
Cdd:COG0840   309 ENAQQAAELAEEASELAEEGGEVVEEAVEGIEEIRESVEETAETIEELGESSQEIGEIVDVIDDIAEQTNLLALNAAIEA 388

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 341 ARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRNAAGV 420
Cdd:COG0840   389 ARAGEAGRGFAVVADEVRKLAERSAEATKEIEELIEEIQSETEEAVEAMEEGSEEVEEGVELVEEAGEALEEIVEAVEEV 468

                         170
                  ....*....|.
gi 1278886390 421 ETAVKDVAISV 431
Cdd:COG0840   469 SDLIQEIAAAS 479
MCP_signal cd11386
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
 260-432 3.40e-21

Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW.


Pssm-ID: 206779 [Multi-domain]  Cd Length: 200  Bit Score: 90.76  E-value: 3.40e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 260 QEAAVHAWDMAV---QTRESAQNGANVIENSILMIDRIAQGMGAVSTDISRLNNQSESIDDMVETIRKFAMQTRLIALNA 336
Cdd:cd11386     8 EEVAASADQVAEtsqQAAELAEKGREAAEDAINQMNQIDESVDEAVSAVEELEESSAEIGEIVEVIDDIAEQTNLLALNA 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 337 AIEAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRN 416
Cdd:cd11386    88 AIEAARAGEAGRGFAVVADEVRKLAEESAEAAKEIEELIEEIQEQTEEAVEAMEETSEEVEEGVELVEETGRAFEEIVAS 167

                         170
                  ....*....|....*.
gi 1278886390 417 AAGVETAVKDVAISVK 432
Cdd:cd11386   168 VEEVADGIQEISAATQ 183
KinE COG5809
Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome ...
 1-261 5.57e-21

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: 95.04  E-value: 5.57e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390   1 MFSLKNmfSLNLQRSAISYDAICQNKP--VIEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSLVssPEYSQFW 78
Cdd:COG5809     1 MKSSKM--ELQLRKSEQRFRSLFENAPdaILILDLEGKILKVNPAAERIFGYTEDELLGTNILDFLHPDDE--KELREIL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  79 QRLARGESFSGKYLRLAKGN-RSVWLEASYIPVSDRRGRVIRVIKIAADISERVHS--ALEQ-----EAVVNAInrSMAI 150
Cdd:COG5809    77 KLLKEGESRDELEFELRHKNgKRLEFSSKLSPIFDQNGDIEGMLAISRDITERKRMeeALREseekfRLIFNHS--PDGI 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 151 ITFNPEGIVLEANENFVNATGYKRDEIIGKHHRLFCAEtLYKSDEYRHFWESLNQGEFFSGLFPRLNRQGDPLWFRATYN 230
Cdd:COG5809   155 IVTDLDGRIIYANPAACKLLGISIEELIGKSILELIHS-DDQENVAAFISQLLKDGGIAQGEVRFWTKDGRWRLLEASGA 233

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1278886390 231 PVfNSDGQLYKIVKFATDVTadvlrNQREQE 261
Cdd:COG5809   234 PI-KKNGEVDGIVIIFRDIT-----ERKKLE 258
MCPsignal pfam00015
Methyl-accepting chemotaxis protein (MCP) signalling domain; This domain is thought to ...
 268-431 9.64e-20

Methyl-accepting chemotaxis protein (MCP) signalling domain; This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs.


Pssm-ID: 333767 [Multi-domain]  Cd Length: 172  Bit Score: 85.95  E-value: 9.64e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 268 DMAVQTRESAQNGANVIENSILMIDRIAQgmgavstdisrlnnQSESIDDMVETIRKFAMQTRLIALNAAIEAARAGASG 347
Cdd:pfam00015   2 DLAQLASEEAQDGGKEVANVVGQMEQIAQ--------------SSKKISDIISVIDEIAFQTNLLALNAAIEAARAGEQG 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 348 RSFAVVAAEVRNLAASVSSATEEIEQVVASNSQLAKDVLCGIENSLMNTREGVTLMREAGEVMTSIQRNAAGVETAVKDV 427
Cdd:pfam00015  68 RGFAVVADEVRKLAERSAQAAKEIEALIIEIQKQTNDSTASIESTRQRVEVGSTIVESTGEALKEIVDAVAEIADIVQEI 147


                  ....
gi 1278886390 428 AISV 431
Cdd:pfam00015 148 AAAS 151
PAS COG2202
PAS domain [Signal transduction mechanisms];
129-293 1.91e-16

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 78.91  E-value: 1.91e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 129 ERVHSALEQEAVVNAInrSMAIITFNPEGIVLEANENFVNATGYKRDEIIGKHHRLFCAEtLYKSDEYRHFWESLNQGEF 208
Cdd:COG2202     5 ALEESERRLRALVESS--PDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPP-EDDDEFLELLRAALAGGGV 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 209 FSGLFPRLNRQGDPLWFRATYNPVFNSDGQLYKIVKFATDVTAdvlrnQREQEAAVhawdmavqtRESAQNGANVIENS- 287
Cdd:COG2202    82 WRGELRNRRKDGSLFWVELSISPVRDEDGEITGFVGIARDITE-----RKRAEEAL---------RESEERLRLLVENAp 147


                  ....*...
gi 1278886390 288 --ILMIDR 293
Cdd:COG2202   148 dgIFVLDL 155
PRK15041 PRK15041
methyl-accepting chemotaxis protein;
249-413 4.31e-14

methyl-accepting chemotaxis protein;


Pssm-ID: 185001 [Multi-domain]  Cd Length: 554  Bit Score: 74.22  E-value: 4.31e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 249 VTADVLRNQreqEAAVHAWDMAVQTRESAQNGANVIENsilmidrIAQGMGAVSTdisrlnnQSESIDDMVETIRKFAMQ 328
Cdd:PRK15041  312 LTATVKQNA---ENARQASHLALSASETAQRGGKVVDN-------VVQTMRDIST-------SSQKIADIISVIDGIAFQ 374

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 329 TRLIALNAAIEAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVvasnsqlakdvlcgIENSLMNTREGVTLMREAGE 408
Cdd:PRK15041  375 TNILALNAAVEAARAGEQGRGFAVVAGEVRNLAQRSAQAAREIKSL--------------IEDSVGKVDVGSTLVESAGE 440


                  ....*
gi 1278886390 409 VMTSI 413
Cdd:PRK15041  441 TMAEI 445
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 159-246 6.89e-13

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: 63.90  E-value: 6.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 159 VLEANENFVNATGYKRDEIIGK---HHRLFCAETLYKsdEYRHFWESLNQGEFFSGLFPRLNRQGDPLWFRATYNPVFNS 235
Cdd:pfam08447   1 IIYWSPRFEEILGYTPEELLGKgesWLDLVHPDDRER--VREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDE 78

                          90
                  ....*....|.
gi 1278886390 236 DGQLYKIVKFA 246
Cdd:pfam08447  79 NGKPVRVIGVA 89
PRK15048 PRK15048
methyl-accepting chemotaxis protein II; Provisional
 249-413 7.67e-13

methyl-accepting chemotaxis protein II; Provisional


Pssm-ID: 185008 [Multi-domain]  Cd Length: 553  Bit Score: 70.04  E-value: 7.67e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 249 VTADVLRNQreqEAAVHAWDMAVQTRESAQNGANVIENSILMIDRIAqgmgavstdisrlnNQSESIDDMVETIRKFAMQ 328
Cdd:PRK15048  310 LTATVKQNA---DNARQASQLAQSASDTAQHGGKVVDGVVKTMHEIA--------------DSSKKIADIISVIDGIAFQ 372

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 329 TRLIALNAAIEAARAGASGRSFAVVAAEVRNLAASVSSATEEIEQVvasnsqlakdvlcgIENSLMNTREGVTLMREAGE 408
Cdd:PRK15048  373 TNILALNAAVEAARAGEQGRGFAVVAGEVRNLASRSAQAAKEIKAL--------------IEDSVSRVDTGSVLVESAGE 438


                  ....*
gi 1278886390 409 VMTSI 413
Cdd:PRK15048  439 TMNNI 443
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 27-131 1.50e-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: 60.89  E-value: 1.50e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  27 PVIEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSLVssPEYSQFWQRLARGESFSGKYLRLAKGNRSVWLEAS 106
Cdd:pfam08448   7 ALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDA--ARLERALRRALEGEEPIDFLEELLLNGEERHYELR 84

                          90       100
                  ....*....|....*....|....*
gi 1278886390 107 YIPVSDRRGRVIRVIKIAADISERV 131
Cdd:pfam08448  85 LTPLRDPDGEVIGVLVISRDITERR 109
PAS_3 pfam08447
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 40-124 2.04e-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.


Pssm-ID: 430001 [Multi-domain]  Cd Length: 89  Bit Score: 60.05  E-value: 2.04e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  40 ASPLFLSTMGYRADEIIG--HHHRIFCPPSLVSsPEYSQFWQRLARGESFSGKYLRLAKGNRSVWLEASYIPVSDRRGRV 117
Cdd:pfam08447   4 WSPRFEEILGYTPEELLGkgESWLDLVHPDDRE-RVREALWEALKGGEPYSGEYRIRRKDGEYRWVEARARPIRDENGKP 82


                  ....*..
gi 1278886390 118 IRVIKIA 124
Cdd:pfam08447  83 VRVIGVA 89
PRK09793 PRK09793
methyl-accepting chemotaxis protein IV;
268-428 2.35e-11

methyl-accepting chemotaxis protein IV;


Pssm-ID: 182079 [Multi-domain]  Cd Length: 533  Bit Score: 65.48  E-value: 2.35e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 268 DMAVQTRESAQNGANVIENSILMIDRIAQGMGAVSTdisrlnnQSESIDDMVETIRKFAMQTRLIALNAAIEAARAGASG 347
Cdd:PRK09793  317 DNARQASELAKNAATTAQAGGVQVSTMTHTMQEIAT-------SSQKIGDIISVIDGIAFQTNILALNAAVEAARAGEQG 389

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 348 RSFAVVAAEVRNLAASVSSATEEIEQVvasnsqlakdvlcgIENSLMNTREGVTLMREAGEVMTSIQRNAAGVETAVKDV 427
Cdd:PRK09793  390 RGFAVVAGEVRNLASRSAQAAKEIKGL--------------IEESVNRVQQGSKLVNNAAATMTDIVSSVTRVNDIMGEI 455


                  .
gi 1278886390 428 A 428
Cdd:PRK09793  456 A 456
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 156-251 8.54e-11

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: 58.24  E-value: 8.54e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 156 EGIVLEANENFVNATGYKRDEIIGKHHRLFCAETlYKSDEYRHFWESLNQGEFFSGLFPRLNrqGDPLWFRATYNPVFNS 235
Cdd:pfam13426   1 DGRIIYVNDAALRLLGYTREELLGKSITDLFAEP-EDSERLREALREGKAVREFEVVLYRKD--GEPFPVLVSLAPIRDD 77

                          90
                  ....*....|....*.
gi 1278886390 236 DGQLYKIVKFATDVTA 251
Cdd:pfam13426  78 GGELVGIIAILRDITE 93
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 147-249 8.77e-09

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: 53.02  E-value: 8.77e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 147 SMAIITFNPEGIVLEANENFVNATGYKRDEIIGKHHRLFCAEtlykSDEYRH---FWESLNQGEFFSGLFPRLNRQGDPL 223
Cdd:cd00130     2 PDGVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHP----EDREELrerLENLLSGGEPVTLEVRLRRKDGSVI 77

                          90       100
                  ....*....|....*....|....*.
gi 1278886390 224 WFRATYNPVFNSDGQLYKIVKFATDV 249
Cdd:cd00130    78 WVLVSLTPIRDEGGEVIGLLGVVRDI 103
PAS cd00130
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 27-127 5.36e-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. 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: 50.71  E-value: 5.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  27 PVIEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSlvSSPEYSQFWQRLARGESFSGKYLRL-AKGNRSVWLEA 105
Cdd:cd00130     4 GVIVLDLDGRILYANPAAEQLLGYSPEELIGKSLLDLIHPE--DREELRERLENLLSGGEPVTLEVRLrRKDGSVIWVLV 81

                          90       100
                  ....*....|....*....|..
gi 1278886390 106 SYIPVSDRRGRVIRVIKIAADI 127
Cdd:cd00130    82 SLTPIRDEGGEVIGLLGVVRDI 103
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 145-251 6.35e-08

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: 50.49  E-value: 6.35e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 145 NRSMAIITFNPEGIVLEANENFVNATGYKRDEIIGKHHRLFCAETLYksDEYRHFWESLNQGEFFSGLFPRLNRQGDPLW 224
Cdd:pfam08448   3 SLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKTLAELLPPEDA--ARLERALRRALEGEEPIDFLEELLLNGEERH 80

                          90       100
                  ....*....|....*....|....*..
gi 1278886390 225 FRATYNPVFNSDGQLYKIVKFATDVTA 251
Cdd:pfam08448  81 YELRLTPLRDPDGEVIGVLVISRDITE 107
PRK13558 PRK13558
bacterio-opsin activator; Provisional
 105-261 1.05e-07

bacterio-opsin activator; Provisional


Pssm-ID: 237426 [Multi-domain]  Cd Length: 665  Bit Score: 54.07  E-value: 1.05e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 105 ASYIPVSDRrgrvirvikiaaDISERVHSALEQEAVVNAINRSMAIITFN-----------------PEGIVLE------ 161
Cdd:PRK13558  103 AAYVPAVSD------------DATAAIAERIESAVPEHSRDTEARMPISDltvesdrrlkeraldeaPVGITIAdatlpd 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 162 -----ANENFVNATGYKRDEIIGKHHRLFCAEtlyKSDEYR--HFWESLNQGEFFSGLFPRLNRQGDPLWFRATYNPVFN 234
Cdd:PRK13558  171 epliyINDAFERITGYSPDEVLGRNCRFLQGE---DTNEERvaELREAIDEERPTSVELRNYRKDGSTFWNQVDIAPIRD 247

                         170       180       190
                  ....*....|....*....|....*....|
gi 1278886390 235 SDGQLYKIVKFATDVTADV---LRNQREQE 261
Cdd:PRK13558  248 EDGTVTHYVGFQTDVTERKeaeLALQRERR 277
PRK11359 PRK11359
cyclic-di-GMP phosphodiesterase; Provisional
 49-266 2.81e-07

cyclic-di-GMP phosphodiesterase; Provisional


Pssm-ID: 183097 [Multi-domain]  Cd Length: 799  Bit Score: 52.85  E-value: 2.81e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  49 GYRADEIIGHHHRIFCPPSLVSS-PEYSQFWQR--LARGESFSGKYLRLAKGNRSVWLEASYIPVsDRRGRVIRvIKIAA 125
Cdd:PRK11359   46 GYKREEVIGNNIDMLIPRDLRPAhPEYIRHNREggKARVEGMSRELQLEKKDGSKIWTRFALSKV-SAEGKVYY-LALVR 123

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 126 DISERVHSALEQEAVVNAINRS-MAIITFNPEGIVLEANENFVNATGYKRDEIIGKHHRLFCAETLYKSDEYRHFWESLN 204
Cdd:PRK11359  124 DASVEMAQKEQTRQLIIAVDHLdRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLW 203

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1278886390 205 QGEFFSGLFPRLNRQGDPLWFRATYNPVFNSDGQLYKIVKFATDVTADvlRNQREQEAAVHA 266
Cdd:PRK11359  204 KTARDQDEFLLLTRTGEKIWIKASISPVYDVLAHLQNLVMTFSDITEE--RQIRQLEGNILA 263
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 19-131 1.06e-06

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: 47.29  E-value: 1.06e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  19 YDAICQNKPV--IEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSLvSSPEYSQFWQRLARGESFSGKYLRLA- 95
Cdd:TIGR00229   5 YRAIFESSPDaiIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEED-REEVRERIERRLEGEPEPVSEERRVRr 83

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1278886390  96 KGNRSVWLEASYIPVSdRRGRVIRVIKIAADISERV 131
Cdd:TIGR00229  84 KDGSEIWVEVSVSPIR-TNGGELGVVGIVRDITERK 118
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
132-261 1.66e-06

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 49.84  E-value: 1.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 132 HSALEQEAVVNAInrSMAIITFNPEGIVLEANENFVNATGYKRDEIIGKHhrlfCAETLYKSDEYR-HFWESLNQGE-FF 209
Cdd:COG3852     4 ESEELLRAILDSL--PDAVIVLDADGRITYVNPAAERLLGLSAEELLGRP----LAELFPEDSPLReLLERALAEGQpVT 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1278886390 210 SGLFPRLNRQGDPLWFRATYNPVFNSDGQLYkIVKFATDVTAdvlRNQREQE 261
Cdd:COG3852    78 EREVTLRRKDGEERPVDVSVSPLRDAEGEGG-VLLVLRDITE---RKRLERE 125
sensory_box TIGR00229
PAS domain S-box; The PAS domain was previously described. This sensory box, or S-box domain ...
 149-261 3.88e-06

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: 45.74  E-value: 3.88e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 149 AIITFNPEGIVLEANENFVNATGYKRDEIIGKHHRLFCAETLYKSDEYRHFWESLNQGEFFSGLFPRLNRQGDPLWFRAT 228
Cdd:TIGR00229  15 AIIVIDLEGNILYVNPAFEEIFGYSAEELIGRNVLELIPEEDREEVRERIERRLEGEPEPVSEERRVRRKDGSEIWVEVS 94

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1278886390 229 YNPVFNSDGQLYkIVKFATDVTAdvlRNQREQE 261
Cdd:TIGR00229  95 VSPIRTNGGELG-VVGIVRDITE---RKEAEEA 123
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 37-129 1.16e-05

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: 43.60  E-value: 1.16e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  37 INKAsplFLSTMGYRADEIIGHHHRIFCPPSLVSSPeYSQFWQRLARGESFSGKYLRlaKGNRSVWLEASYIPVSDRRGR 116
Cdd:pfam13426   7 VNDA---ALRLLGYTREELLGKSITDLFAEPEDSER-LREALREGKAVREFEVVLYR--KDGEPFPVLVSLAPIRDDGGE 80

                          90
                  ....*....|...
gi 1278886390 117 VIRVIKIAADISE 129
Cdd:pfam13426  81 LVGIIAILRDITE 93
KinA COG5805
Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle ...
 107-239 1.29e-05

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: 47.42  E-value: 1.29e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 107 YIPVSDRRGRVI----RVIKIAADISERVHSALEqeavvnaiNRSMAIITFNPEGIVLEANENFVNATGYKRDEIIGKHH 182
Cdd:COG5805     8 FIHEVKKDGTPIwinnEVLRMAIEITEELETILE--------NLPDAIIAVNREGKVIYINPAMEKLLGYTSEEIIGKTI 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1278886390 183 RLFCAETLYKSDEYRHfwESLNQGEFFSGLFPRLNRQGDPLWFRATYNPVFNSDGQL 239
Cdd:COG5805    80 FDFLEKEYHYRVKTRI--ERLQKGYDVVMIEQIYCKDGELIYVEVKLFPIYNQNGQA 134
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
27-138 1.52e-05

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 46.76  E-value: 1.52e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  27 PVIEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPslvSSPEYSQFWQRLARGESFSGKYLRL-AKGNRSVWLEA 105
Cdd:COG3852    19 AVIVLDADGRITYVNPAAERLLGLSAEELLGRPLAELFPE---DSPLRELLERALAEGQPVTEREVTLrRKDGEERPVDV 95

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1278886390 106 SYIPVSDRRGRVIRVIkIAADISERVHsaLEQE 138
Cdd:COG3852    96 SVSPLRDAEGEGGVLL-VLRDITERKR--LERE 125
PRK11359 PRK11359
cyclic-di-GMP phosphodiesterase; Provisional
 25-129 4.42e-05

cyclic-di-GMP phosphodiesterase; Provisional


Pssm-ID: 183097 [Multi-domain]  Cd Length: 799  Bit Score: 45.92  E-value: 4.42e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  25 NKPVIEFSPEGVINKASPLFLSTMGYRADEIIGHHhrifcPPSLVSSPEYSQ-----FWQRLARGESFSGKYLRLAKGNR 99
Cdd:PRK11359  146 DRPVIVLDPERRIVQCNRAFTEMFGYCISEASGMQ-----PDTLLNIPEFPAdnrirLQQLLWKTARDQDEFLLLTRTGE 220

                          90       100       110
                  ....*....|....*....|....*....|
gi 1278886390 100 SVWLEASYIPVSDRRGRVIRVIKIAADISE 129
Cdd:PRK11359  221 KIWIKASISPVYDVLAHLQNLVMTFSDITE 250
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 138-250 7.90e-05

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: 44.76  E-value: 7.90e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 138 EAVVNAInrSMAIITFNPEGIVLEANENFVNATGYKRDEIIGKH-HRLFCAETLYksdeyrhfwESLNQGEFFSGLFPRL 216
Cdd:COG3829    14 EAILDSL--DDGIIVVDADGRITYVNRAAERILGLPREEVIGKNvTELIPNSPLL---------EVLKTGKPVTGVIQKT 82

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1278886390 217 NRQGDPlwFRATYNPVFNsDGQLYKIVKFATDVT 250
Cdd:COG3829    83 GGKGKT--VIVTAIPIFE-DGEVIGAVETFRDIT 113
NtrY COG5000
Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism ...
 93-326 1.54e-04

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: 43.80  E-value: 1.54e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  93 RLAKGNRSVWLEasyIPVSDRRGRVIRVI-KIAADIsERVHSALEQ-----EAVVNAInrSMAIITFNPEGIVLEANENF 166
Cdd:COG5000    46 AVAAGDLSVRLP---VTGDDEIGELARAFnRMTDQL-KEQREELEErrrylETILENL--PAGVIVLDADGRITLANPAA 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 167 VNATGYKRDEIIGKHhrlfCAETLYKSDEYRHFWESLNQGEffSGLFPRLNRQGDPLWFRATynpVFNSDGQLYKIvkfa 246
Cdd:COG5000   120 ERLLGIPLEELIGKP----LEELLPELDLAELLREALERGW--QEEIELTRDGRRTLLVRAS---PLRDDGYVIVF---- 186

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 247 TDVTaDVLRNQREQeaavhAW-DMAVQ-TREsaqnganvIENSI----LMIDRIAQGMGAVSTD--------ISRLNNQS 312
Cdd:COG5000   187 DDIT-ELLRAERLA-----AWgELARRiAHE--------IKNPLtpiqLSAERLRRKLADKLEEdredleraLDTIIRQV 252

                         250
                  ....*....|....
gi 1278886390 313 ESIDDMVETIRKFA 326
Cdd:COG5000   253 DRLKRIVDEFLDFA 266
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 149-249 1.58e-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. 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: 40.86  E-value: 1.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390 149 AIITFNPEGIVLEANENFVNATGYKRDEIIGKH-HRLFcaETLYKSDEYRHFWESLNQGEFFSGLFPRLNR-QGDPLWFR 226
Cdd:pfam00989  13 GIFVVDEDGRILYVNAAAEELLGLSREEVIGKSlLDLI--PEEDDAEVAELLRQALLQGEESRGFEVSFRVpDGRPRHVE 90

                          90       100
                  ....*....|....*....|...
gi 1278886390 227 ATYNPVFNSDGQLYKIVKFATDV 249
Cdd:pfam00989  91 VRASPVRDAGGEILGFLGVLRDI 113
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 9-159 1.33e-03

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: 40.91  E-value: 1.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390   9 SLNLQRSAISYDAIcqnkpvIEFSPEGV--------INKASPLFLSTMGYRADEIIGHHHRIFCPPSLVsspeysqfWQR 80
Cdd:COG3829     3 ELELKELEEELEAI------LDSLDDGIivvdadgrITYVNRAAERILGLPREEVIGKNVTELIPNSPL--------LEV 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  81 LARGESFSGKYLRLAKGNRSVwlEASYIPVSDrRGRVIRVIKIAADISERVHsaLEQEAVVNAINRSM-AIITFnpEGIV 159
Cdd:COG3829    69 LKTGKPVTGVIQKTGGKGKTV--IVTAIPIFE-DGEVIGAVETFRDITELKR--LERKLREEELERGLsAKYTF--DDII 141
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 138-181 1.40e-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: 36.99  E-value: 1.40e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 1278886390  138 EAVVNAINrsMAIITFNPEGIVLEANENFVNATGYKRDEIIGKH 181
Cdd:smart00091   4 RAILESLP--DGIFVLDLDGRILYANPAAEELLGYSPEELIGKS 45
PAS pfam00989
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 27-127 2.78e-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. 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: 37.40  E-value: 2.78e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278886390  27 PVIEFSPEGVINKASPLFLSTMGYRADEIIGHHHRIFCPPSlVSSPEYSQFWQRL-ARGESFSGKYLRLAKGNRSVWLEA 105
Cdd:pfam00989  13 GIFVVDEDGRILYVNAAAEELLGLSREEVIGKSLLDLIPEE-DDAEVAELLRQALlQGEESRGFEVSFRVPDGRPRHVEV 91

                          90       100
                  ....*....|....*....|..
gi 1278886390 106 SYIPVSDRRGRVIRVIKIAADI 127
Cdd:pfam00989  92 RASPVRDAGGEILGFLGVLRDI 113
PAC smart00086
Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain); PAC motif ...
 94-130 8.60e-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: 34.08  E-value: 8.60e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1278886390   94 LAKGNRSVWLEASYIPVSDRRGRVIRVIKIAADISER 130
Cdd:smart00086   7 RRKDGSYIWVLVSASPIRDEDGEVEGILGVVRDITER 43
 
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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