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Conserved domains on  [gi|489203558|ref|WP_003112650|]
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MULTISPECIES: aerotaxis transducer Aer2 [Pseudomonas]

Protein Classification

methyl-accepting chemotaxis protein( domain architecture ID 15323726)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MCP_signal super family cl46910
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
 349-679 2.02e-109

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 PRK15041:

Pssm-ID: 481250 [Multi-domain]  Cd Length: 554  Bit Score: 341.93  E-value: 2.02e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 349 LAQGDLTQRIEADYQGTFGQLKDFSNDTAQSLSRMLGQIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEE 428
Cdd:PRK15041 232 IAGGDLVKPIEVDGSNEMGQLAESLRHMQGELMRTVGDVRNGANAIYSGASEIATGNNDLSSRTEQQAASLEETAASMEQ 311

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 429 LTSTVKLNAENARQANSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGE 508
Cdd:PRK15041 312 LTATVKQNAENARQASHLALSASETAQRGGKVVDNVVQTMRDISTSSQKIADIISVIDGIAFQTNILALNAAVEAARAGE 391

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 509 QGRGFAVVAGEVRTLAQRSAAAAKEIKTLISDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQSTGIE 588
Cdd:PRK15041 392 QGRGFAVVAGEVRNLAQRSAQAAREIKSLIEDSVGKVDVGSTLVESAGETMAEIVSAVTRVTDIMGEIASASDEQSRGID 471

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 589 EVNSAVSQMDDMTQQNAALVEEAAAAAEAMQEQAGLLNQSVAVFRLDTppsvvQLASARPSAPRPSAPAPLArsgMARAS 668
Cdd:PRK15041 472 QVGLAVAEMDRVTQQNAALVEESAAAAAALEEQASRLTEAVAVFRIQQ-----QQQQQRETSAVVKTVTPAT---PRKMA 543

                        330
                 ....*....|.
gi 489203558 669 KARKEDGWEEF 679
Cdd:PRK15041 544 VADSGENWETF 554
HAMP_N3 pfam18575
HAMP N-terminal domain 3; Aer2 soluble receptor from Pseudomonas aeruginosa contains three ...
 114-156 1.76e-15

HAMP N-terminal domain 3; Aer2 soluble receptor from Pseudomonas aeruginosa contains three successive HAMP domains in the N-terminal region. HAMP domains are widespread prokaryotic signaling modules. This entry is the third N-terminal HAMP domain (HAMP3). HAMP3 adopt a conformation resembling Af1503, with only minor differences in helical tilt and orientation. The basic construction of each HAMP domain consists of a monomeric unit of two parallel alpha helices (AS1 and AS2) joined by an elongated connector of 12-14 residues form a parallel four-helix bundle.


:

Pssm-ID: 465808  Cd Length: 43  Bit Score: 70.57  E-value: 1.76e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 489203558  114 VKMKVVSVVTAYGQGNFEPLMDRLPGKKAQITEAIDGVRERLR 156
Cdd:pfam18575   1 VKMKAMACVKAYGEGDFDAPLERLPGKKAFINETIEQVRGNLK 43
HAMP super family cl01054
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; ...
 66-111 1.79e-13

Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


The actual alignment was detected with superfamily member cd17527:

Pssm-ID: 470050  Cd Length: 46  Bit Score: 64.91  E-value: 1.79e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489203558  66 ESLEAGLAEMSRQHEAGWIDQTIPAERLEGRAARIAKGVNELVAAH 111
Cdd:cd17527    1 KSLIAEMQRMSAEHDAGDIDVRIDADKFQGSYREMAEGVNDMVAGH 46
HAMP_I cd17529
first HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain ...
 11-55 9.86e-10

first HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


:

Pssm-ID: 381746 [Multi-domain]  Cd Length: 44  Bit Score: 54.28  E-value: 9.86e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489203558  11 QQRADRIATLLQSFADGQLDTAVGEaPAPGYERLYDSLRALQRQL 55
Cdd:cd17529    1 GGEPADLAVLAKRFAAGDLDTKIGL-PAPDKTSLMASMRRLQRTL 44
NtrB super family cl34682
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
172-306 5.77e-09

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


The actual alignment was detected with superfamily member COG3852:

Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 58.32  E-value: 5.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 172 NARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGraeadirkqlpnFDAGRLMGANI-DVFHKNPAHQRHL---LANL 247
Cdd:COG3852    6 EELLRAILDSLPDAVIVLDADGRITYVNPAAERLLG------------LSAEELLGRPLaELFPEDSPLRELLeraLAEG 73

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489203558 248 TGVHKAELNL---GGRRFSLDV-VPVFNDANERLGSAVQWTDRTEEHRAEQEVSQLVQAAAAG 306
Cdd:COG3852   74 QPVTEREVTLrrkDGEERPVDVsVSPLRDAEGEGGVLLVLRDITERKRLERELRRAEKLAAVG 136
HAMP_2 super family cl40950
HAMP domain;
306-374 2.33e-06

HAMP domain;


The actual alignment was detected with superfamily member pfam18947:

Pssm-ID: 465927 [Multi-domain]  Cd Length: 67  Bit Score: 45.56  E-value: 2.33e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489203558  306 GDFSKRVEeagkeGFflrlakdlNSLVDTADRGLRDVSRMLGALAQGDLTQRIEADYQGTFGQLKDFSN 374
Cdd:pfam18947   4 GDFRKIVE-----GV--------NNTLDAIITPLNEAADYVDRISKGDIPEKITDEYKGDFNEIKNNLN 59
 
Name Accession Description Interval E-value
PRK15041 PRK15041
methyl-accepting chemotaxis protein;
349-679 2.02e-109

methyl-accepting chemotaxis protein;


Pssm-ID: 185001 [Multi-domain]  Cd Length: 554  Bit Score: 341.93  E-value: 2.02e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 349 LAQGDLTQRIEADYQGTFGQLKDFSNDTAQSLSRMLGQIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEE 428
Cdd:PRK15041 232 IAGGDLVKPIEVDGSNEMGQLAESLRHMQGELMRTVGDVRNGANAIYSGASEIATGNNDLSSRTEQQAASLEETAASMEQ 311

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 429 LTSTVKLNAENARQANSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGE 508
Cdd:PRK15041 312 LTATVKQNAENARQASHLALSASETAQRGGKVVDNVVQTMRDISTSSQKIADIISVIDGIAFQTNILALNAAVEAARAGE 391

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 509 QGRGFAVVAGEVRTLAQRSAAAAKEIKTLISDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQSTGIE 588
Cdd:PRK15041 392 QGRGFAVVAGEVRNLAQRSAQAAREIKSLIEDSVGKVDVGSTLVESAGETMAEIVSAVTRVTDIMGEIASASDEQSRGID 471

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 589 EVNSAVSQMDDMTQQNAALVEEAAAAAEAMQEQAGLLNQSVAVFRLDTppsvvQLASARPSAPRPSAPAPLArsgMARAS 668
Cdd:PRK15041 472 QVGLAVAEMDRVTQQNAALVEESAAAAAALEEQASRLTEAVAVFRIQQ-----QQQQQRETSAVVKTVTPAT---PRKMA 543

                        330
                 ....*....|.
gi 489203558 669 KARKEDGWEEF 679
Cdd:PRK15041 544 VADSGENWETF 554
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
133-634 2.45e-84

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


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 275.36  E-value: 2.45e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 133 LMDRLPGKKAQITEAIDGVRERLRGAAEATSAQLATAAYNARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEAD 212
Cdd:COG0840    7 LLALLLALLLLALSLLALLAAALLILLALLLAALTALALLLLLSLLALLLLLLLLALALLLVLLALLLLLALVVLLALLL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 213 IRKQLPNFDAGRLMGANIDVFHKNPAHQRHLLANLTGVHKAELNLGGRRFSLDVVPVFNDANERLGSAVQWTDRTEEHRA 292
Cdd:COG0840   87 ALLLLLLALLALALAALALLAALAALLALLELLLAALLAALAIALLALAALLALAALALALLALALLAAAAAAAAALAAL 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 293 EQEVSQLVQAAAAGDFSKRVEEAGKEGFFLRLAKDLNSLVDtadRGLRDVSRMLGALAQGDLTQRIEADYQGTFGQLKDF 372
Cdd:COG0840  167 LEAAALALAAAALALALLAAALLALVALAIILALLLSRSIT---RPLRELLEVLERIAEGDLTVRIDVDSKDEIGQLADA 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 373 SNDTAQSLSRMLGQIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEELTSTVKLNAENARQANSLAANASE 452
Cdd:COG0840  244 FNRMIENLRELVGQVRESAEQVASASEELAASAEELAAGAEEQAASLEETAAAMEELSATVQEVAENAQQAAELAEEASE 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 453 VATQGGTVVQKVVS--------------TMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAG 518
Cdd:COG0840  324 LAEEGGEVVEEAVEgieeiresveetaeTIEELGESSQEIGEIVDVIDDIAEQTNLLALNAAIEAARAGEAGRGFAVVAD 403

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 519 EVRTLAQRSAAAAKEIKTLISDSVDKVEN--------------GNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQS 584
Cdd:COG0840  404 EVRKLAERSAEATKEIEELIEEIQSETEEaveameegseeveeGVELVEEAGEALEEIVEAVEEVSDLIQEIAAASEEQS 483

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|
gi 489203558 585 TGIEEVNSAVSQMDDMTQQNAALVEEAAAAAEAMQEQAGLLNQSVAVFRL 634
Cdd:COG0840  484 AGTEEVNQAIEQIAAAAQENAASVEEVAAAAEELAELAEELQELVSRFKL 533
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
 386-633 6.47e-65

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: 215.23  E-value: 6.47e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558   386 QIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEELTSTVKLNAENARQANSLAANASEVATQGGTVVQKVV 465
Cdd:smart00283   1 DVSEAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558   466 STMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRTLAQRSAAAAKEIKTLISD----- 540
Cdd:smart00283  81 SAVEELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEiqeet 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558   541 ---------SVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQSTGIEEVNSAVSQMDDMTQQNAALVEEA 611
Cdd:smart00283 161 neavaameeSSSEVEEGVELVEETGDALEEIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEI 240

                          250       260
                   ....*....|....*....|..
gi 489203558   612 AAAAEAMQEQAGLLNQSVAVFR 633
Cdd:smart00283 241 SAAAEELSGLAEELDELVERFK 262
MCP_signal cd11386
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
 413-604 1.82e-56

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: 190.53  E-value: 1.82e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 413 EQQASSLEETASSMEELTSTVKLNAENARQANSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQT 492
Cdd:cd11386    1 EELSASIEEVAASADQVAETSQQAAELAEKGREAAEDAINQMNQIDESVDEAVSAVEELEESSAEIGEIVEVIDDIAEQT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 493 NILALNAAVEAARAGEQGRGFAVVAGEVRTLAQRSAAAAKEIKTLISDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDI 572
Cdd:cd11386   81 NLLALNAAIEAARAGEAGRGFAVVADEVRKLAEESAEAAKEIEELIEEIQEQTEEAVEAMEETSEEVEEGVELVEETGRA 160

                        170       180       190
                 ....*....|....*....|....*....|..
gi 489203558 573 MSEIAAASAEQSTGIEEVNSAVSQMDDMTQQN 604
Cdd:cd11386  161 FEEIVASVEEVADGIQEISAATQEQSASTQEI 192
MCPsignal pfam00015
Methyl-accepting chemotaxis protein (MCP) signalling domain; This domain is thought to ...
 444-601 1.99e-53

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: 181.09  E-value: 1.99e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558  444 NSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRTL 523
Cdd:pfam00015   1 SDLAQLASEEAQDGGKEVANVVGQMEQIAQSSKKISDIISVIDEIAFQTNLLALNAAIEAARAGEQGRGFAVVADEVRKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558  524 AQRSAAAAKEIKTLI--------------SDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQSTGIEE 589
Cdd:pfam00015  81 AERSAQAAKEIEALIieiqkqtndstasiESTRQRVEVGSTIVESTGEALKEIVDAVAEIADIVQEIAAASDEQSAGIDQ 160

                         170
                  ....*....|..
gi 489203558  590 VNSAVSQMDDMT 601
Cdd:pfam00015 161 VNQAVARMDQVT 172
HAMP_N3 pfam18575
HAMP N-terminal domain 3; Aer2 soluble receptor from Pseudomonas aeruginosa contains three ...
 114-156 1.76e-15

HAMP N-terminal domain 3; Aer2 soluble receptor from Pseudomonas aeruginosa contains three successive HAMP domains in the N-terminal region. HAMP domains are widespread prokaryotic signaling modules. This entry is the third N-terminal HAMP domain (HAMP3). HAMP3 adopt a conformation resembling Af1503, with only minor differences in helical tilt and orientation. The basic construction of each HAMP domain consists of a monomeric unit of two parallel alpha helices (AS1 and AS2) joined by an elongated connector of 12-14 residues form a parallel four-helix bundle.


Pssm-ID: 465808  Cd Length: 43  Bit Score: 70.57  E-value: 1.76e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 489203558  114 VKMKVVSVVTAYGQGNFEPLMDRLPGKKAQITEAIDGVRERLR 156
Cdd:pfam18575   1 VKMKAMACVKAYGEGDFDAPLERLPGKKAFINETIEQVRGNLK 43
HAMP_III cd17528
third HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain ...
 112-155 1.86e-15

third HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


Pssm-ID: 381745  Cd Length: 44  Bit Score: 70.33  E-value: 1.86e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 489203558 112 IAVKMKVVSVVTAYGQGNFEPLMDRLPGKKAQITEAIDGVRERL 155
Cdd:cd17528    1 IAVKKKAMACVTAFGEGNFDAPLEKFPGKKAFINETIEQVRANL 44
HAMP_II cd17527
second HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling ...
 66-111 1.79e-13

second HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


Pssm-ID: 381744  Cd Length: 46  Bit Score: 64.91  E-value: 1.79e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489203558  66 ESLEAGLAEMSRQHEAGWIDQTIPAERLEGRAARIAKGVNELVAAH 111
Cdd:cd17527    1 KSLIAEMQRMSAEHDAGDIDVRIDADKFQGSYREMAEGVNDMVAGH 46
HAMP_I cd17529
first HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain ...
 11-55 9.86e-10

first HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


Pssm-ID: 381746 [Multi-domain]  Cd Length: 44  Bit Score: 54.28  E-value: 9.86e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489203558  11 QQRADRIATLLQSFADGQLDTAVGEaPAPGYERLYDSLRALQRQL 55
Cdd:cd17529    1 GGEPADLAVLAKRFAAGDLDTKIGL-PAPDKTSLMASMRRLQRTL 44
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
172-306 5.77e-09

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 58.32  E-value: 5.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 172 NARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGraeadirkqlpnFDAGRLMGANI-DVFHKNPAHQRHL---LANL 247
Cdd:COG3852    6 EELLRAILDSLPDAVIVLDADGRITYVNPAAERLLG------------LSAEELLGRPLaELFPEDSPLRELLeraLAEG 73

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489203558 248 TGVHKAELNL---GGRRFSLDV-VPVFNDANERLGSAVQWTDRTEEHRAEQEVSQLVQAAAAG 306
Cdd:COG3852   74 QPVTEREVTLrrkDGEERPVDVsVSPLRDAEGEGGVLLVLRDITERKRLERELRRAEKLAAVG 136
HAMP_2 pfam18947
HAMP domain;
306-374 2.33e-06

HAMP domain;


Pssm-ID: 465927 [Multi-domain]  Cd Length: 67  Bit Score: 45.56  E-value: 2.33e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489203558  306 GDFSKRVEeagkeGFflrlakdlNSLVDTADRGLRDVSRMLGALAQGDLTQRIEADYQGTFGQLKDFSN 374
Cdd:pfam18947   4 GDFRKIVE-----GV--------NNTLDAIITPLNEAADYVDRISKGDIPEKITDEYKGDFNEIKNNLN 59
PAS_8 pfam13188
PAS domain; PAS domains are involved in many signalling proteins where they are used as a ...
 173-224 9.63e-05

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: 41.00  E-value: 9.63e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 489203558  173 ARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGR--AEADIRKQLPNFDAGR 224
Cdd:pfam13188   1 ERLRALFESSPDGILVLDEGGRIIYVNPAALELLGYelLGELLGELLDLLDPLL 54
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 173-216 5.11e-04

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 38.92  E-value: 5.11e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 489203558   173 ARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIRKQ 216
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGK 44
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
137-308 2.52e-03

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 41.11  E-value: 2.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 137 LPGKKAQITEAIDGVRERLRgaaeatsaqlATAAYNARIksaLDNVSANVMIADNDLNIIYMNRTVSEMLGraeadirkq 216
Cdd:PRK11360 239 LPGELGEISQAINNLAQALR----------ETRSLNELI---LESIADGVIAIDRQGKITTMNPAAEVITG--------- 296

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 217 lpnFDAGRLMGANIDVFHKNPAHQRHLLANLTGVHKAELNL--------GGRRFSLDVVPVFNDANERLGSAVQWTDRTE 288
Cdd:PRK11360 297 ---LQRHELVGKPYSELFPPNTPFASPLLDTLEHGTEHVDLeisfpgrdRTIELSVSTSLLHNTHGEMIGALVIFSDLTE 373

                        170       180
                 ....*....|....*....|
gi 489203558 289 EHRAEQEVSQLVQAAAAGDF 308
Cdd:PRK11360 374 RKRLQRRVARQERLAALGEL 393
 
Name Accession Description Interval E-value
PRK15041 PRK15041
methyl-accepting chemotaxis protein;
349-679 2.02e-109

methyl-accepting chemotaxis protein;


Pssm-ID: 185001 [Multi-domain]  Cd Length: 554  Bit Score: 341.93  E-value: 2.02e-109
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 349 LAQGDLTQRIEADYQGTFGQLKDFSNDTAQSLSRMLGQIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEE 428
Cdd:PRK15041 232 IAGGDLVKPIEVDGSNEMGQLAESLRHMQGELMRTVGDVRNGANAIYSGASEIATGNNDLSSRTEQQAASLEETAASMEQ 311

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 429 LTSTVKLNAENARQANSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGE 508
Cdd:PRK15041 312 LTATVKQNAENARQASHLALSASETAQRGGKVVDNVVQTMRDISTSSQKIADIISVIDGIAFQTNILALNAAVEAARAGE 391

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 509 QGRGFAVVAGEVRTLAQRSAAAAKEIKTLISDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQSTGIE 588
Cdd:PRK15041 392 QGRGFAVVAGEVRNLAQRSAQAAREIKSLIEDSVGKVDVGSTLVESAGETMAEIVSAVTRVTDIMGEIASASDEQSRGID 471

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 589 EVNSAVSQMDDMTQQNAALVEEAAAAAEAMQEQAGLLNQSVAVFRLDTppsvvQLASARPSAPRPSAPAPLArsgMARAS 668
Cdd:PRK15041 472 QVGLAVAEMDRVTQQNAALVEESAAAAAALEEQASRLTEAVAVFRIQQ-----QQQQQRETSAVVKTVTPAT---PRKMA 543

                        330
                 ....*....|.
gi 489203558 669 KARKEDGWEEF 679
Cdd:PRK15041 544 VADSGENWETF 554
PRK15048 PRK15048
methyl-accepting chemotaxis protein II; Provisional
 349-679 6.03e-107

methyl-accepting chemotaxis protein II; Provisional


Pssm-ID: 185008 [Multi-domain]  Cd Length: 553  Bit Score: 335.44  E-value: 6.03e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 349 LAQGDLTQRIEADYQGTFGQLKDFSNDTAQSLSRMLGQIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEE 428
Cdd:PRK15048 230 IAGGNLANTLTIDGRSEMGDLAQSVSHMQRSLTDTVTHVREGSDAIYAGTREIAAGNTDLSSRTEQQASALEETAASMEQ 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 429 LTSTVKLNAENARQANSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGE 508
Cdd:PRK15048 310 LTATVKQNADNARQASQLAQSASDTAQHGGKVVDGVVKTMHEIADSSKKIADIISVIDGIAFQTNILALNAAVEAARAGE 389

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 509 QGRGFAVVAGEVRTLAQRSAAAAKEIKTLISDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQSTGIE 588
Cdd:PRK15048 390 QGRGFAVVAGEVRNLASRSAQAAKEIKALIEDSVSRVDTGSVLVESAGETMNNIVNAVTRVTDIMGEIASASDEQSRGID 469

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 589 EVNSAVSQMDDMTQQNAALVEEAAAAAEAMQEQAGLLNQSVAVFRLDTPPSVVQlasarpsAPRPSAPAPLARSGMARAS 668
Cdd:PRK15048 470 QVALAVSEMDRVTQQNASLVQESAAAAAALEEQASRLTQAVSAFRLAASPLTNK-------PQTPSRPASEQPPAQPRLR 542

                        330
                 ....*....|.
gi 489203558 669 KARKEDGWEEF 679
Cdd:PRK15048 543 IAEQDPNWETF 553
PRK09793 PRK09793
methyl-accepting chemotaxis protein IV;
342-651 4.00e-85

methyl-accepting chemotaxis protein IV;


Pssm-ID: 182079 [Multi-domain]  Cd Length: 533  Bit Score: 277.72  E-value: 4.00e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 342 VSRMLGALAQGDLTQRIEA----DYQGTFGQLKDFSndtaQSLSRMLGQIREAADTINTAASEIASGNAELSARTEQQAS 417
Cdd:PRK09793 221 IGSHFDSIAAGNLARPIAVygrnEITAIFASLKTMQ----QALRGTVSDVRKGSQEMHIGIAEIVAGNNDLSSRTEQQAA 296

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 418 SLEETASSMEELTSTVKLNAENARQANSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQTNILAL 497
Cdd:PRK09793 297 SLAQTAASMEQLTATVGQNADNARQASELAKNAATTAQAGGVQVSTMTHTMQEIATSSQKIGDIISVIDGIAFQTNILAL 376

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 498 NAAVEAARAGEQGRGFAVVAGEVRTLAQRSAAAAKEIKTLISDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIA 577
Cdd:PRK09793 377 NAAVEAARAGEQGRGFAVVAGEVRNLASRSAQAAKEIKGLIEESVNRVQQGSKLVNNAAATMTDIVSSVTRVNDIMGEIA 456

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489203558 578 AASAEQSTGIEEVNSAVSQMDDMTQQNAALVEEAAAAAEAMQEQAGLLNQSVAVFRLDTPPSVVQLASARPSAP 651
Cdd:PRK09793 457 SASEEQRRGIEQVAQAVSQMDQVTQQNASLVEEAAVATEQLANQADHLSSRVAVFTLEEHEVARHESAQLQIAP 530
Tar COG0840
Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms];
133-634 2.45e-84

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


Pssm-ID: 440602 [Multi-domain]  Cd Length: 533  Bit Score: 275.36  E-value: 2.45e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 133 LMDRLPGKKAQITEAIDGVRERLRGAAEATSAQLATAAYNARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEAD 212
Cdd:COG0840    7 LLALLLALLLLALSLLALLAAALLILLALLLAALTALALLLLLSLLALLLLLLLLALALLLVLLALLLLLALVVLLALLL 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 213 IRKQLPNFDAGRLMGANIDVFHKNPAHQRHLLANLTGVHKAELNLGGRRFSLDVVPVFNDANERLGSAVQWTDRTEEHRA 292
Cdd:COG0840   87 ALLLLLLALLALALAALALLAALAALLALLELLLAALLAALAIALLALAALLALAALALALLALALLAAAAAAAAALAAL 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 293 EQEVSQLVQAAAAGDFSKRVEEAGKEGFFLRLAKDLNSLVDtadRGLRDVSRMLGALAQGDLTQRIEADYQGTFGQLKDF 372
Cdd:COG0840  167 LEAAALALAAAALALALLAAALLALVALAIILALLLSRSIT---RPLRELLEVLERIAEGDLTVRIDVDSKDEIGQLADA 243

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 373 SNDTAQSLSRMLGQIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEELTSTVKLNAENARQANSLAANASE 452
Cdd:COG0840  244 FNRMIENLRELVGQVRESAEQVASASEELAASAEELAAGAEEQAASLEETAAAMEELSATVQEVAENAQQAAELAEEASE 323

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 453 VATQGGTVVQKVVS--------------TMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAG 518
Cdd:COG0840  324 LAEEGGEVVEEAVEgieeiresveetaeTIEELGESSQEIGEIVDVIDDIAEQTNLLALNAAIEAARAGEAGRGFAVVAD 403

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 519 EVRTLAQRSAAAAKEIKTLISDSVDKVEN--------------GNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQS 584
Cdd:COG0840  404 EVRKLAERSAEATKEIEELIEEIQSETEEaveameegseeveeGVELVEEAGEALEEIVEAVEEVSDLIQEIAAASEEQS 483

                        490       500       510       520       530
                 ....*....|....*....|....*....|....*....|....*....|
gi 489203558 585 TGIEEVNSAVSQMDDMTQQNAALVEEAAAAAEAMQEQAGLLNQSVAVFRL 634
Cdd:COG0840  484 AGTEEVNQAIEQIAAAAQENAASVEEVAAAAEELAELAEELQELVSRFKL 533
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
 386-633 6.47e-65

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: 215.23  E-value: 6.47e-65
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558   386 QIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEELTSTVKLNAENARQANSLAANASEVATQGGTVVQKVV 465
Cdd:smart00283   1 DVSEAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAV 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558   466 STMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRTLAQRSAAAAKEIKTLISD----- 540
Cdd:smart00283  81 SAVEELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEiqeet 160

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558   541 ---------SVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQSTGIEEVNSAVSQMDDMTQQNAALVEEA 611
Cdd:smart00283 161 neavaameeSSSEVEEGVELVEETGDALEEIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEI 240

                          250       260
                   ....*....|....*....|..
gi 489203558   612 AAAAEAMQEQAGLLNQSVAVFR 633
Cdd:smart00283 241 SAAAEELSGLAEELDELVERFK 262
MCP_signal cd11386
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
 413-604 1.82e-56

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: 190.53  E-value: 1.82e-56
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 413 EQQASSLEETASSMEELTSTVKLNAENARQANSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQT 492
Cdd:cd11386    1 EELSASIEEVAASADQVAETSQQAAELAEKGREAAEDAINQMNQIDESVDEAVSAVEELEESSAEIGEIVEVIDDIAEQT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 493 NILALNAAVEAARAGEQGRGFAVVAGEVRTLAQRSAAAAKEIKTLISDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDI 572
Cdd:cd11386   81 NLLALNAAIEAARAGEAGRGFAVVADEVRKLAEESAEAAKEIEELIEEIQEQTEEAVEAMEETSEEVEEGVELVEETGRA 160

                        170       180       190
                 ....*....|....*....|....*....|..
gi 489203558 573 MSEIAAASAEQSTGIEEVNSAVSQMDDMTQQN 604
Cdd:cd11386  161 FEEIVASVEEVADGIQEISAATQEQSASTQEI 192
MCPsignal pfam00015
Methyl-accepting chemotaxis protein (MCP) signalling domain; This domain is thought to ...
 444-601 1.99e-53

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: 181.09  E-value: 1.99e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558  444 NSLAANASEVATQGGTVVQKVVSTMSSINESARKIADIIGVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRTL 523
Cdd:pfam00015   1 SDLAQLASEEAQDGGKEVANVVGQMEQIAQSSKKISDIISVIDEIAFQTNLLALNAAIEAARAGEQGRGFAVVADEVRKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558  524 AQRSAAAAKEIKTLI--------------SDSVDKVENGNTLVAQAGQTMSDIVVAIRRVTDIMSEIAAASAEQSTGIEE 589
Cdd:pfam00015  81 AERSAQAAKEIEALIieiqkqtndstasiESTRQRVEVGSTIVESTGEALKEIVDAVAEIADIVQEIAAASDEQSAGIDQ 160

                         170
                  ....*....|..
gi 489203558  590 VNSAVSQMDDMT 601
Cdd:pfam00015 161 VNQAVARMDQVT 172
HAMP_N3 pfam18575
HAMP N-terminal domain 3; Aer2 soluble receptor from Pseudomonas aeruginosa contains three ...
 114-156 1.76e-15

HAMP N-terminal domain 3; Aer2 soluble receptor from Pseudomonas aeruginosa contains three successive HAMP domains in the N-terminal region. HAMP domains are widespread prokaryotic signaling modules. This entry is the third N-terminal HAMP domain (HAMP3). HAMP3 adopt a conformation resembling Af1503, with only minor differences in helical tilt and orientation. The basic construction of each HAMP domain consists of a monomeric unit of two parallel alpha helices (AS1 and AS2) joined by an elongated connector of 12-14 residues form a parallel four-helix bundle.


Pssm-ID: 465808  Cd Length: 43  Bit Score: 70.57  E-value: 1.76e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 489203558  114 VKMKVVSVVTAYGQGNFEPLMDRLPGKKAQITEAIDGVRERLR 156
Cdd:pfam18575   1 VKMKAMACVKAYGEGDFDAPLERLPGKKAFINETIEQVRGNLK 43
HAMP_III cd17528
third HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain ...
 112-155 1.86e-15

third HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


Pssm-ID: 381745  Cd Length: 44  Bit Score: 70.33  E-value: 1.86e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 489203558 112 IAVKMKVVSVVTAYGQGNFEPLMDRLPGKKAQITEAIDGVRERL 155
Cdd:cd17528    1 IAVKKKAMACVTAFGEGNFDAPLEKFPGKKAFINETIEQVRANL 44
HAMP_II cd17527
second HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling ...
 66-111 1.79e-13

second HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


Pssm-ID: 381744  Cd Length: 46  Bit Score: 64.91  E-value: 1.79e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 489203558  66 ESLEAGLAEMSRQHEAGWIDQTIPAERLEGRAARIAKGVNELVAAH 111
Cdd:cd17527    1 KSLIAEMQRMSAEHDAGDIDVRIDADKFQGSYREMAEGVNDMVAGH 46
HAMP_I cd17529
first HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain ...
 11-55 9.86e-10

first HAMP domain of aerotaxis transducer Aer2 and similar domains; HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established.


Pssm-ID: 381746 [Multi-domain]  Cd Length: 44  Bit Score: 54.28  E-value: 9.86e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489203558  11 QQRADRIATLLQSFADGQLDTAVGEaPAPGYERLYDSLRALQRQL 55
Cdd:cd17529    1 GGEPADLAVLAKRFAAGDLDTKIGL-PAPDKTSLMASMRRLQRTL 44
NtrB COG3852
Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms];
172-306 5.77e-09

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


Pssm-ID: 443061 [Multi-domain]  Cd Length: 361  Bit Score: 58.32  E-value: 5.77e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 172 NARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGraeadirkqlpnFDAGRLMGANI-DVFHKNPAHQRHL---LANL 247
Cdd:COG3852    6 EELLRAILDSLPDAVIVLDADGRITYVNPAAERLLG------------LSAEELLGRPLaELFPEDSPLRELLeraLAEG 73

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489203558 248 TGVHKAELNL---GGRRFSLDV-VPVFNDANERLGSAVQWTDRTEEHRAEQEVSQLVQAAAAG 306
Cdd:COG3852   74 QPVTEREVTLrrkDGEERPVDVsVSPLRDAEGEGGVLLVLRDITERKRLERELRRAEKLAAVG 136
HAMP_2 pfam18947
HAMP domain;
306-374 2.33e-06

HAMP domain;


Pssm-ID: 465927 [Multi-domain]  Cd Length: 67  Bit Score: 45.56  E-value: 2.33e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489203558  306 GDFSKRVEeagkeGFflrlakdlNSLVDTADRGLRDVSRMLGALAQGDLTQRIEADYQGTFGQLKDFSN 374
Cdd:pfam18947   4 GDFRKIVE-----GV--------NNTLDAIITPLNEAADYVDRISKGDIPEKITDEYKGDFNEIKNNLN 59
PAS_8 pfam13188
PAS domain; PAS domains are involved in many signalling proteins where they are used as a ...
 173-224 9.63e-05

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: 41.00  E-value: 9.63e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 489203558  173 ARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGR--AEADIRKQLPNFDAGR 224
Cdd:pfam13188   1 ERLRALFESSPDGILVLDEGGRIIYVNPAALELLGYelLGELLGELLDLLDPLL 54
PAS_4 pfam08448
PAS fold; The PAS fold corresponds to the structural domain that has previously been defined ...
 179-291 1.18e-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 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: 42.02  E-value: 1.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558  179 LDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIRKQ-----LPNFDAGRLMganidvfhknpAHQRHLLANLTGVHKA 253
Cdd:pfam08448   1 LDSLPDALAVLDPDGRVRYANAAAAELFGLPPEELLGKtlaelLPPEDAARLE-----------RALRRALEGEEPIDFL 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 489203558  254 E---LNLGGRRFSLDVVPVFNDANERLGSAVQWTDRTEEHR 291
Cdd:pfam08448  70 EellLNGEERHYELRLTPLRDPDGEVIGVLVISRDITERRR 110
VgrG COG3501
Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly ...
 314-580 1.25e-04

Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly [Intracellular trafficking, secretion, and vesicular transport, Mobilome: prophages, transposons, General function prediction only];


Pssm-ID: 442724 [Multi-domain]  Cd Length: 743  Bit Score: 45.14  E-value: 1.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 314 EAGKEGFFLRLAKDLNSLVDTADRGLRDVSRmlgalaqgdlTQRIEADYQGTFGQLKDFSNDTAQSLSRMLGQIREAADT 393
Cdd:COG3501  489 KAGQEEIFLHAEKDMNTLVDNDETITVGNDR----------TEEVGTDETGTVAGNQGLTVSGDQTVVVGGNQTLVVGGA 558

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 394 INTAASEIASGNAELSARTEQQASSLEETASSMEELTSTVKLNAENARQANSLAANASEVATQGGTVVQKVVSTMSSINE 473
Cdd:COG3501  559 RTLVVGGNLAAVVGGAAATAGGAQATLVAGALLLLAAGGALTTVGGGGTTTGGGAAATAGGGGAGAAAGGAATAAAGAAA 638

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 474 SARKIADIIGVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGevRTLAQRSAAAAKEIKTLISDSVDKVENGNTLVA 553
Cdd:COG3501  639 TSAAGGASSAAAAAGGAAGAGGGGLAAAGGGGAAAAGGAGAGGAG--GGAGALAAGAAAVAAAAAGGAGGGAAAGGIIGA 716

                        250       260
                 ....*....|....*....|....*..
gi 489203558 554 QAGQTMSDIVVAIRRVTDIMSEIAAAS 580
Cdd:COG3501  717 GGTGIGGGGATAGGGAGASGGGAAAGA 743
PAS_9 pfam13426
PAS domain; This domain is found in many signalling proteins in which it functions as a sensor ...
 192-288 2.57e-04

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: 40.52  E-value: 2.57e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558  192 DLNIIYMNRTVSEMLGRAEADIrkqlpnfdagrlMGANIDVFHKNPAHQRHL---LANLTGVHKAELNL---GGRRF--S 263
Cdd:pfam13426   1 DGRIIYVNDAALRLLGYTREEL------------LGKSITDLFAEPEDSERLreaLREGKAVREFEVVLyrkDGEPFpvL 68

                          90       100
                  ....*....|....*....|....*
gi 489203558  264 LDVVPVFNDANERLGSAVQWTDRTE 288
Cdd:pfam13426  69 VSLAPIRDDGGELVGIIAILRDITE 93
PAS COG2202
PAS domain [Signal transduction mechanisms];
164-295 4.60e-04

PAS domain [Signal transduction mechanisms];


Pssm-ID: 441804 [Multi-domain]  Cd Length: 258  Bit Score: 42.70  E-value: 4.60e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 164 AQLATAAYNARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIRKQLPNFDAGRlmganiDVFHKNPAHQRHL 243
Cdd:COG2202    2 AEEALEESERRLRALVESSPDAIIITDLDGRILYVNPAFERLTGYSAEELLGKTLRDLLPP------EDDDEFLELLRAA 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489203558 244 LANLTGVHKAELNL--GGRRF--SLDVVPVFNDANERLGSAVQWTDRTEEHRAEQE 295
Cdd:COG2202   76 LAGGGVWRGELRNRrkDGSLFwvELSISPVRDEDGEITGFVGIARDITERKRAEEA 131
PAS smart00091
PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising ...
 173-216 5.11e-04

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


Pssm-ID: 214512  Cd Length: 67  Bit Score: 38.92  E-value: 5.11e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 489203558   173 ARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIRKQ 216
Cdd:smart00091   1 ERLRAILESLPDGIFVLDLDGRILYANPAAEELLGYSPEELIGK 44
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 163-298 9.75e-04

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: 42.07  E-value: 9.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 163 SAQLATAAYNARIKSALDNVSANVMIADNDLNIIYMNRTVSEMLGRAEADIrkqlpnfdagrlMGANI-DVFHKNPAHQr 241
Cdd:COG3829    1 AEELELKELEEELEAILDSLDDGIIVVDADGRITYVNRAAERILGLPREEV------------IGKNVtELIPNSPLLE- 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489203558 242 hLLANLTGVHKAELNLGGRRFSLDV--VPVFNDaNERLGSAVQWTDRTEEHRAEQEVSQ 298
Cdd:COG3829   68 -VLKTGKPVTGVIQKTGGKGKTVIVtaIPIFED-GEVIGAVETFRDITELKRLERKLRE 124
PRK11360 PRK11360
two-component system sensor histidine kinase AtoS;
137-308 2.52e-03

two-component system sensor histidine kinase AtoS;


Pssm-ID: 236901 [Multi-domain]  Cd Length: 607  Bit Score: 41.11  E-value: 2.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 137 LPGKKAQITEAIDGVRERLRgaaeatsaqlATAAYNARIksaLDNVSANVMIADNDLNIIYMNRTVSEMLGraeadirkq 216
Cdd:PRK11360 239 LPGELGEISQAINNLAQALR----------ETRSLNELI---LESIADGVIAIDRQGKITTMNPAAEVITG--------- 296

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558 217 lpnFDAGRLMGANIDVFHKNPAHQRHLLANLTGVHKAELNL--------GGRRFSLDVVPVFNDANERLGSAVQWTDRTE 288
Cdd:PRK11360 297 ---LQRHELVGKPYSELFPPNTPFASPLLDTLEHGTEHVDLeisfpgrdRTIELSVSTSLLHNTHGEMIGALVIFSDLTE 373

                        170       180
                 ....*....|....*....|
gi 489203558 289 EHRAEQEVSQLVQAAAAGDF 308
Cdd:PRK11360 374 RKRLQRRVARQERLAALGEL 393
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
 373-464 5.13e-03

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: 39.19  E-value: 5.13e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203558   373 SNDTAQSLSRMLGQIREAADTINTAASEIASGNAELSARTEQQASSLEETASSMEELTSTVKlnaENARQANSLAANASE 452
Cdd:smart00283 170 SSSEVEEGVELVEETGDALEEIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQ---ETAAMSEEISAAAEE 246

                           90
                   ....*....|..
gi 489203558   453 VATQGGTVVQKV 464
Cdd:smart00283 247 LSGLAEELDELV 258
 
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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