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Conserved domains on  [gi|27383065|ref|NP_774594.1|]
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methyl accepting chemotaxis protein [Bradyrhizobium diazoefficiens USDA 110]

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List of domain hits

Name Accession Description Interval E-value
HAMP cd06225
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. ...
360-405 2.55e-04

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 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: 100122  Cd Length: 48  Bit Score: 39.54  E-value: 2.55e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 27383065 360 LMRPVRAILDAIARIGARDYSTPVPQSRyPDEFGTMAAALESLRES 405
Cdd:cd06225   1 ILRPLRRLAEAAQRIAAGDLDVRLPVTG-RDEIGELARAFNQMAER 45
MCP_signal super family cl21547
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
476-666 2.85e-37

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 cd11386:

Pssm-ID: 206779  Cd Length: 200  Bit Score: 138.14  E-value: 2.85e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 476 VASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTNATVEILDQTASRIGEVVKMINAIAGQTNL 555
Cdd:cd11386   3 LSASIEEVAASADQVAETSQQAAELAEKGREAAEDAINQMNQIDESVDEAVSAVEELEESSAEIGEIVEVIDDIAEQTNL 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 556 LALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATGQAVTAIR-------SIGGAISGIDEKMT 628
Cdd:cd11386  83 LALNAAIEAARAGEAGRGFAVVADEVRKLAEESAEAAKEIEELIEEIQEQTEEAVEAMEetseeveEGVELVEETGRAFE 162
                       170       180       190
                ....*....|....*....|....*....|....*...
gi 27383065 629 AIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVA 666
Cdd:cd11386 163 EIVASVEEVADGIQEISAATQEQSASTQEIAAAVEEIA 200
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
448-700 2.31e-43

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: 157.06  E-value: 2.31e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    448 VAASARELDATATDVRTLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTNA 527
Cdd:smart00283   2 VSEAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAVS 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    528 TVEILDQTASRIGEVVKMINAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATG 607
Cdd:smart00283  82 AVEELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETN 161
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    608 QAVTAIRSIG-------GAISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVLS 680
Cdd:smart00283 162 EAVAAMEESSseveegvELVEETGDALEEIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEIS 241
                          250       260
                   ....*....|....*....|
gi 27383065    681 ESVKKMSADADRLRVAVEGF 700
Cdd:smart00283 242 AAAEELSGLAEELDELVERF 261
 
Name Accession Description Interval E-value
HAMP cd06225
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. ...
360-405 2.55e-04

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 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: 100122  Cd Length: 48  Bit Score: 39.54  E-value: 2.55e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 27383065 360 LMRPVRAILDAIARIGARDYSTPVPQSRyPDEFGTMAAALESLRES 405
Cdd:cd06225   1 ILRPLRRLAEAAQRIAAGDLDVRLPVTG-RDEIGELARAFNQMAER 45
MCP_signal cd11386
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
476-666 2.85e-37

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  Cd Length: 200  Bit Score: 138.14  E-value: 2.85e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 476 VASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTNATVEILDQTASRIGEVVKMINAIAGQTNL 555
Cdd:cd11386   3 LSASIEEVAASADQVAETSQQAAELAEKGREAAEDAINQMNQIDESVDEAVSAVEELEESSAEIGEIVEVIDDIAEQTNL 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 556 LALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATGQAVTAIR-------SIGGAISGIDEKMT 628
Cdd:cd11386  83 LALNAAIEAARAGEAGRGFAVVADEVRKLAEESAEAAKEIEELIEEIQEQTEEAVEAMEetseeveEGVELVEETGRAFE 162
                       170       180       190
                ....*....|....*....|....*....|....*...
gi 27383065 629 AIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVA 666
Cdd:cd11386 163 EIVASVEEVADGIQEISAATQEQSASTQEIAAAVEEIA 200
HAMP pfam00672
HAMP domain;
340-405 5.04e-08

HAMP domain;


Pssm-ID: 250044  Cd Length: 70  Bit Score: 50.69  E-value: 5.04e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27383065   340 LAFLVALAVTLAGVYVVRTRLMRPVRAILDAIARIGARDYSTPVPQSRyPDEFGTMAAALESLRES 405
Cdd:pfam00672   3 LVLLIALLLLLLLAWLLARRLLRPLRRLAEAARRIASGDLDDRVPVSG-PDEIGELARAFNQMADR 67
HAMP smart00304
HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;
359-411 2.52e-04

HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;


Pssm-ID: 197640  Cd Length: 53  Bit Score: 39.54  E-value: 2.52e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 27383065    359 RLMRPVRAILDAIARIGARDYSTPVPQSRyPDEFGTMAAALESLRESAATAER 411
Cdd:smart00304   2 RLLRPLRRLAEAAQRIADGDLTVRLPVDG-RDEIGELARAFNEMADRLEETIA 53
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
448-700 2.31e-43

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: 157.06  E-value: 2.31e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    448 VAASARELDATATDVRTLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTNA 527
Cdd:smart00283   2 VSEAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAVS 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    528 TVEILDQTASRIGEVVKMINAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATG 607
Cdd:smart00283  82 AVEELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETN 161
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    608 QAVTAIRSIG-------GAISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVLS 680
Cdd:smart00283 162 EAVAAMEESSseveegvELVEETGDALEEIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEIS 241
                          250       260
                   ....*....|....*....|
gi 27383065    681 ESVKKMSADADRLRVAVEGF 700
Cdd:smart00283 242 AAAEELSGLAEELDELVERF 261
Tar COG0840
Methyl-accepting chemotaxis protein [Cell motility, Signal transduction mechanisms];
310-700 1.29e-38

Methyl-accepting chemotaxis protein [Cell motility, Signal transduction mechanisms];


Pssm-ID: 223910 [Multi-domain]  Cd Length: 408  Bit Score: 147.44  E-value: 1.29e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 310 VAVANKALDQSIARAEAVQAKALTNlvVQSLAFLVALAVTLAGVYVVRTRLMRPVRAILDAIARIGARDYSTPVPQSRyP 389
Cdd:COG0840  36 LLLSLNLILDDAASAEAAALKAVLK--FLLISLLVAIIVVLVLAILLLRAILEPISDLLEVVERIAAGDLTKRIDESS-N 112
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 390 DEFGTMAAALESLRESaataerlgqeresqqalqlarsgtvdaaCRSFDDTVQAVIHGVAASARELDATATDVRTLVSES 469
Cdd:COG0840 113 DEFGQLAKSFNEMILN----------------------------LRQIIDAVQDNAEALSGASEEIAASATELSARADQQ 164
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 470 SSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQ----AERTNATVEILDQTASRIGEVVKM 545
Cdd:COG0840 165 AESLEEVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQAVEQmqeiAEELAEVVKKLSESSQEIEEITSV 244
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 546 INAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATGQAVTAIR-------SIGG 618
Cdd:COG0840 245 INSIAEQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADSAKEIGLLIEEIQNEAADAVEHMEesasevsEGVK 324
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 619 AISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVLSESVKKMSADADRLRVAVE 698
Cdd:COG0840 325 LVEETGSSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASIEELDDVTQENAAAVEELAAASEELKELAEKLLELVA 404

                ..
gi 27383065 699 GF 700
Cdd:COG0840 405 KF 406
PRK09793 PRK09793
methyl-accepting protein IV; Provisional
441-683 2.52e-28

methyl-accepting protein IV; Provisional


Pssm-ID: 182079 [Multi-domain]  Cd Length: 533  Bit Score: 118.64  E-value: 2.52e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  441 VQAVIHGVAASARELDATATDVR-------TLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGE-------ISA 506
Cdd:PRK09793 245 ITAIFASLKTMQQALRGTVSDVRkgsqemhIGIAEIVAGNNDLSSRTEQQAASLAQTAASMEQLTATVGQnadnarqASE 324
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  507 QVQSSAREAREAVSQAERTNATVEILDQTASRIGEVVKMINAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAA 586
Cdd:PRK09793 325 LAKNAATTAQAGGVQVSTMTHTMQEIATSSQKIGDIISVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRNLAS 404
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  587 QTATATEEISRQVEE----IQGATGQAVTAIRS---IGGAISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVT 659
Cdd:PRK09793 405 RSAQAAKEIKGLIEEsvnrVQQGSKLVNNAAATmtdIVSSVTRVNDIMGEIASASEEQRRGIEQVAQAVSQMDQVTQQNA 484
                        250       260
                 ....*....|....*....|....
gi 27383065  660 DTIGSVAKLNQETGNAGTVLSESV 683
Cdd:PRK09793 485 SLVEEAAVATEQLANQADHLSSRV 508
MCPsignal pfam00015
Methyl-accepting chemotaxis protein (MCP) signalling domain; This domain is thought to ...
491-700 1.23e-26

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: 249510 [Multi-domain]  Cd Length: 213  Bit Score: 108.69  E-value: 1.23e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   491 AAATEELSASVGEISAQVQSSAREAREAVSqaertnaTVEILDQTASRIGEVVKMINAIAGQTNLLALNATIEAARAGEA 570
Cdd:pfam00015   1 AQASDLAQLASEEALDEMSQIGQVVDDAVE-------TMEELETSSKKISDIISVIDEIAFQTNLLALNAAIEAARAGEQ 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   571 GRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATGQA--------------VTAIRSIGGAISGIDEKMTAIAAAVEQ 636
Cdd:pfam00015  74 GRGFAVVADEVRKLAERSAQAAKEIEALIEEIVKQTNDStasiqqtrtevevgSTIVESTGEALKEIVDAVAEIADIVQE 153
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 27383065   637 QRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVLSESvkkmsadADRLRVAVEGF 700
Cdd:pfam00015 154 IAAASDEQSAGIDQVNQAVARIDQVTQQNAALVEESAAAAETLEEQ-------AEELTASVAQF 210
NarQ COG3850
Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms] ...
337-399 3.87e-06

Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms];


Pssm-ID: 226368 [Multi-domain]  Cd Length: 574  Bit Score: 48.50  E-value: 3.87e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 27383065 337 VQSLAFLVALAVTLAGVYVVRTRLMRPVRAILDAIARIGARDYSTPVPQSrYPDEFGTMAAAL 399
Cdd:COG3850 152 VQLAGMLLILLLVVFTIYWLRRRVVRPLNQLTSAAQRIGRRQFDQRPTDT-GRNELGLLGRAF 213
PRK10600 PRK10600
nitrate/nitrite sensor protein NarX; Provisional
335-416 3.57e-04

nitrate/nitrite sensor protein NarX; Provisional


Pssm-ID: 182581 [Multi-domain]  Cd Length: 569  Bit Score: 42.35  E-value: 3.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  335 LVVQSLAFLVALaVTLAGVYVVRTRLMRPVRAILdAIAR-IGARDYSTPVPQSRYpDEFGTMAAAL----ESLRESAATA 409
Cdd:PRK10600 125 LVHRVFAVFMAL-LLVFTIIWLRRRLLQPWRQLL-SMANaVSHRDFTQRANISGR-DEMAMLGTALnnmsAELAESYAVL 201

                 ....*..
gi 27383065  410 ERLGQER 416
Cdd:PRK10600 202 EQRVQEK 208
PHA03247 PHA03247
large tegument protein UL36; Provisional
322-554 5.42e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 38.77  E-value: 5.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   322 ARAEAVQAKALTNLVVQS------LAFLVALAVTLAGvYVVRTRLMRPVRAildAIARIGArdystpvpqsrypdeFGTM 395
Cdd:PHA03247 1156 VRAHGVLADAVAALSPAVrdpacpLAFLVALADSAAG-YVKATRLALDARR---AIARLGA---------------LGAA 1216
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   396 AAALeslresaATAERlgqeRESQQAlQLARSGTVDAACRSfddtVQAVIHGVAASARELDAtatdvrTLVSESssqTAA 475
Cdd:PHA03247 1217 AADL-------AVAVR----RENPQA-EGDRAALLEAAARA----VTAAREGLAACEGEFGG------LLHAEG---SAG 1271
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   476 VASSAEQATNNLETIAAAT----EELSASVGEISAQVqsSAREAReavSQAERTNATVE-ILDQTASRIG-EVVKM--IN 547
Cdd:PHA03247 1272 DPSPSGRALQELGKVVGATrrraDELEAAAADLAEKM--AARRAR---ASRERWAADVEaALDRVENRAEfDAVELrrLQ 1346

                  ....*..
gi 27383065   548 AIAGQTN 554
Cdd:PHA03247 1347 ALAATHG 1353
 
Name Accession Description Interval E-value
HAMP cd06225
Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. ...
360-405 2.55e-04

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 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: 100122  Cd Length: 48  Bit Score: 39.54  E-value: 2.55e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 27383065 360 LMRPVRAILDAIARIGARDYSTPVPQSRyPDEFGTMAAALESLRES 405
Cdd:cd06225   1 ILRPLRRLAEAAQRIAAGDLDVRLPVTG-RDEIGELARAFNQMAER 45
MCP_signal cd11386
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
476-666 2.85e-37

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  Cd Length: 200  Bit Score: 138.14  E-value: 2.85e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 476 VASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTNATVEILDQTASRIGEVVKMINAIAGQTNL 555
Cdd:cd11386   3 LSASIEEVAASADQVAETSQQAAELAEKGREAAEDAINQMNQIDESVDEAVSAVEELEESSAEIGEIVEVIDDIAEQTNL 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 556 LALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATGQAVTAIR-------SIGGAISGIDEKMT 628
Cdd:cd11386  83 LALNAAIEAARAGEAGRGFAVVADEVRKLAEESAEAAKEIEELIEEIQEQTEEAVEAMEetseeveEGVELVEETGRAFE 162
                       170       180       190
                ....*....|....*....|....*....|....*...
gi 27383065 629 AIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVA 666
Cdd:cd11386 163 EIVASVEEVADGIQEISAATQEQSASTQEIAAAVEEIA 200
HAMP pfam00672
HAMP domain;
340-405 5.04e-08

HAMP domain;


Pssm-ID: 250044  Cd Length: 70  Bit Score: 50.69  E-value: 5.04e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 27383065   340 LAFLVALAVTLAGVYVVRTRLMRPVRAILDAIARIGARDYSTPVPQSRyPDEFGTMAAALESLRES 405
Cdd:pfam00672   3 LVLLIALLLLLLLAWLLARRLLRPLRRLAEAARRIASGDLDDRVPVSG-PDEIGELARAFNQMADR 67
HAMP smart00304
HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;
359-411 2.52e-04

HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain;


Pssm-ID: 197640  Cd Length: 53  Bit Score: 39.54  E-value: 2.52e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 27383065    359 RLMRPVRAILDAIARIGARDYSTPVPQSRyPDEFGTMAAALESLRESAATAER 411
Cdd:smart00304   2 RLLRPLRRLAEAAQRIADGDLTVRLPVDG-RDEIGELARAFNEMADRLEETIA 53
MCP_signal cd11386
Methyl-accepting chemotaxis protein (MCP), signaling domain; Methyl-accepting chemotaxis ...
452-550 8.85e-04

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  Cd Length: 200  Bit Score: 39.91  E-value: 8.85e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 452 ARELDATATDVRTLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTNATVEi 531
Cdd:cd11386 112 AEESAEAAKEIEELIEEIQEQTEEAVEAMEETSEEVEEGVELVEETGRAFEEIVASVEEVADGIQEISAATQEQSASTQ- 190
                        90
                ....*....|....*....
gi 27383065 532 ldqtasrigEVVKMINAIA 550
Cdd:cd11386 191 ---------EIAAAVEEIA 200
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
448-700 2.31e-43

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: 157.06  E-value: 2.31e-43
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    448 VAASARELDATATDVRTLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTNA 527
Cdd:smart00283   2 VSEAVEEIAAGAEEQAEELEELAERMEELSASIEEVAANADEIAATAQSAAEAAEEGREAVEDAITAMDQIREVVEEAVS 81
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    528 TVEILDQTASRIGEVVKMINAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATG 607
Cdd:smart00283  82 AVEELEESSDEIGEIVSVIDDIADQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSAESAKEIESLIKEIQEETN 161
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    608 QAVTAIRSIG-------GAISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVLS 680
Cdd:smart00283 162 EAVAAMEESSseveegvELVEETGDALEEIVDSVEEIADLVQEIAAATDEQAAGSEEVNAAIDEIAQVTQETAAMSEEIS 241
                          250       260
                   ....*....|....*....|
gi 27383065    681 ESVKKMSADADRLRVAVEGF 700
Cdd:smart00283 242 AAAEELSGLAEELDELVERF 261
Tar COG0840
Methyl-accepting chemotaxis protein [Cell motility, Signal transduction mechanisms];
310-700 1.29e-38

Methyl-accepting chemotaxis protein [Cell motility, Signal transduction mechanisms];


Pssm-ID: 223910 [Multi-domain]  Cd Length: 408  Bit Score: 147.44  E-value: 1.29e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 310 VAVANKALDQSIARAEAVQAKALTNlvVQSLAFLVALAVTLAGVYVVRTRLMRPVRAILDAIARIGARDYSTPVPQSRyP 389
Cdd:COG0840  36 LLLSLNLILDDAASAEAAALKAVLK--FLLISLLVAIIVVLVLAILLLRAILEPISDLLEVVERIAAGDLTKRIDESS-N 112
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 390 DEFGTMAAALESLRESaataerlgqeresqqalqlarsgtvdaaCRSFDDTVQAVIHGVAASARELDATATDVRTLVSES 469
Cdd:COG0840 113 DEFGQLAKSFNEMILN----------------------------LRQIIDAVQDNAEALSGASEEIAASATELSARADQQ 164
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 470 SSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQ----AERTNATVEILDQTASRIGEVVKM 545
Cdd:COG0840 165 AESLEEVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQAVEQmqeiAEELAEVVKKLSESSQEIEEITSV 244
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 546 INAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATGQAVTAIR-------SIGG 618
Cdd:COG0840 245 INSIAEQTNLLALNAAIEAARAGEAGRGFAVVADEVRKLAERSADSAKEIGLLIEEIQNEAADAVEHMEesasevsEGVK 324
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 619 AISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVLSESVKKMSADADRLRVAVE 698
Cdd:COG0840 325 LVEETGSSLGEIAAAIEEVSQLISEIAAATEEQTAVLEEINASIEELDDVTQENAAAVEELAAASEELKELAEKLLELVA 404

                ..
gi 27383065 699 GF 700
Cdd:COG0840 405 KF 406
PRK09793 PRK09793
methyl-accepting protein IV; Provisional
441-683 2.52e-28

methyl-accepting protein IV; Provisional


Pssm-ID: 182079 [Multi-domain]  Cd Length: 533  Bit Score: 118.64  E-value: 2.52e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  441 VQAVIHGVAASARELDATATDVR-------TLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGE-------ISA 506
Cdd:PRK09793 245 ITAIFASLKTMQQALRGTVSDVRkgsqemhIGIAEIVAGNNDLSSRTEQQAASLAQTAASMEQLTATVGQnadnarqASE 324
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  507 QVQSSAREAREAVSQAERTNATVEILDQTASRIGEVVKMINAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAA 586
Cdd:PRK09793 325 LAKNAATTAQAGGVQVSTMTHTMQEIATSSQKIGDIISVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRNLAS 404
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  587 QTATATEEISRQVEE----IQGATGQAVTAIRS---IGGAISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVT 659
Cdd:PRK09793 405 RSAQAAKEIKGLIEEsvnrVQQGSKLVNNAAATmtdIVSSVTRVNDIMGEIASASEEQRRGIEQVAQAVSQMDQVTQQNA 484
                        250       260
                 ....*....|....*....|....
gi 27383065  660 DTIGSVAKLNQETGNAGTVLSESV 683
Cdd:PRK09793 485 SLVEEAAVATEQLANQADHLSSRV 508
PRK15048 PRK15048
methyl-accepting chemotaxis protein II; Provisional
453-700 2.60e-27

methyl-accepting chemotaxis protein II; Provisional


Pssm-ID: 185008 [Multi-domain]  Cd Length: 553  Bit Score: 115.87  E-value: 2.60e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  453 RELDATATDVRTLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTNATV--- 529
Cdd:PRK15048 259 RSLTDTVTHVREGSDAIYAGTREIAAGNTDLSSRTEQQASALEETAASMEQLTATVKQNADNARQASQLAQSASDTAqhg 338
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  530 ------------EILDqTASRIGEVVKMINAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISR 597
Cdd:PRK15048 339 gkvvdgvvktmhEIAD-SSKKIADIISVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRNLASRSAQAAKEIKA 417
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  598 QVEEIQGATGQAVTAIRSIGGAISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGT 677
Cdd:PRK15048 418 LIEDSVSRVDTGSVLVESAGETMNNIVNAVTRVTDIMGEIASASDEQSRGIDQVALAVSEMDRVTQQNASLVQESAAAAA 497
                        250       260
                 ....*....|....*....|...
gi 27383065  678 VLSESvkkmsadADRLRVAVEGF 700
Cdd:PRK15048 498 ALEEQ-------ASRLTQAVSAF 513
MCPsignal pfam00015
Methyl-accepting chemotaxis protein (MCP) signalling domain; This domain is thought to ...
491-700 1.23e-26

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: 249510 [Multi-domain]  Cd Length: 213  Bit Score: 108.69  E-value: 1.23e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   491 AAATEELSASVGEISAQVQSSAREAREAVSqaertnaTVEILDQTASRIGEVVKMINAIAGQTNLLALNATIEAARAGEA 570
Cdd:pfam00015   1 AQASDLAQLASEEALDEMSQIGQVVDDAVE-------TMEELETSSKKISDIISVIDEIAFQTNLLALNAAIEAARAGEQ 73
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   571 GRGFAVVAGEVKSLAAQTATATEEISRQVEEIQGATGQA--------------VTAIRSIGGAISGIDEKMTAIAAAVEQ 636
Cdd:pfam00015  74 GRGFAVVADEVRKLAERSAQAAKEIEALIEEIVKQTNDStasiqqtrtevevgSTIVESTGEALKEIVDAVAEIADIVQE 153
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 27383065   637 QRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVLSESvkkmsadADRLRVAVEGF 700
Cdd:pfam00015 154 IAAASDEQSAGIDQVNQAVARIDQVTQQNAALVEESAAAAETLEEQ-------AEELTASVAQF 210
PRK15041 PRK15041
methyl-accepting chemotaxis protein I; Provisional
454-698 5.27e-25

methyl-accepting chemotaxis protein I; Provisional


Pssm-ID: 185001 [Multi-domain]  Cd Length: 554  Bit Score: 108.50  E-value: 5.27e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  454 ELDATATDVR-------TLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAERTN 526
Cdd:PRK15041 262 ELMRTVGDVRnganaiySGASEIATGNNDLSSRTEQQAASLEETAASMEQLTATVKQNAENARQASHLALSASETAQRGG 341
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  527 ATVEILDQT-------ASRIGEVVKMINAIAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATATEEISRQV 599
Cdd:PRK15041 342 KVVDNVVQTmrdistsSQKIADIISVIDGIAFQTNILALNAAVEAARAGEQGRGFAVVAGEVRNLAQRSAQAAREIKSLI 421
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  600 EEIQGATGQAVTAIRSIGGAISGIDEKMTAIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVL 679
Cdd:PRK15041 422 EDSVGKVDVGSTLVESAGETMAEIVSAVTRVTDIMGEIASASDEQSRGIDQVGLAVAEMDRVTQQNAALVEESAAAAAAL 501
                        250
                 ....*....|....*....
gi 27383065  680 SESVKKMSADADRLRVAVE 698
Cdd:PRK15041 502 EEQASRLTEAVAVFRIQQQ 520
NarQ COG3850
Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms] ...
337-399 3.87e-06

Signal transduction histidine kinase, nitrate/nitrite-specific [Signal transduction mechanisms];


Pssm-ID: 226368 [Multi-domain]  Cd Length: 574  Bit Score: 48.50  E-value: 3.87e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 27383065 337 VQSLAFLVALAVTLAGVYVVRTRLMRPVRAILDAIARIGARDYSTPVPQSrYPDEFGTMAAAL 399
Cdd:COG3850 152 VQLAGMLLILLLVVFTIYWLRRRVVRPLNQLTSAAQRIGRRQFDQRPTDT-GRNELGLLGRAF 213
MA smart00283
Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Thought to undergo ...
439-557 2.55e-04

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: 41.89  E-value: 2.55e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    439 DTVQAVIHGVAASARELDATATDVRTLVSESSSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREA 518
Cdd:smart00283 133 DEVRKLAERSAESAKEIESLIKEIQEETNEAVAAMEESSSEVEEGVELVEETGDALEEIVDSVEEIADLVQEIAAATDEQ 212
                           90       100       110       120
                   ....*....|....*....|....*....|....*....|...
gi 27383065    519 VSQAERTNATVE----ILDQTASRIGEVVKMINAIAGQTNLLA 557
Cdd:smart00283 213 AAGSEEVNAAIDeiaqVTQETAAMSEEISAAAEELSGLAEELD 255
PRK10600 PRK10600
nitrate/nitrite sensor protein NarX; Provisional
335-416 3.57e-04

nitrate/nitrite sensor protein NarX; Provisional


Pssm-ID: 182581 [Multi-domain]  Cd Length: 569  Bit Score: 42.35  E-value: 3.57e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  335 LVVQSLAFLVALaVTLAGVYVVRTRLMRPVRAILdAIAR-IGARDYSTPVPQSRYpDEFGTMAAAL----ESLRESAATA 409
Cdd:PRK10600 125 LVHRVFAVFMAL-LLVFTIIWLRRRLLQPWRQLL-SMANaVSHRDFTQRANISGR-DEMAMLGTALnnmsAELAESYAVL 201

                 ....*..
gi 27383065  410 ERLGQER 416
Cdd:PRK10600 202 EQRVQEK 208
DUF812 pfam05667
Protein of unknown function (DUF812); This family consists of several eukaryotic proteins of ...
411-667 6.32e-04

Protein of unknown function (DUF812); This family consists of several eukaryotic proteins of unknown function.


Pssm-ID: 253309 [Multi-domain]  Cd Length: 536  Bit Score: 41.67  E-value: 6.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   411 RLGQERESQQALQLARSGTVDAACRSFDDTVqavihgvaaSARELDATATDVRTLVSESSSQTAAVASSAEQATNNLETI 490
Cdd:pfam05667 193 RLDQKAAEYLRQAAQAGTTGSSSADDLADLL---------SKFRLDSWDKGSRFTRTEKVEQAATAAAEVPPAEMDTEED 263
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   491 AAAT-----EELSASVGEISAQVQSSAREAREAVSQAERTNATVEILDQTASRIGEVVKM-----INAIAGQTNLLALNA 560
Cdd:pfam05667 264 RTKEreaelEALQEQIDELESSIEEVLSEIKALASKIKQVNEELTTVRQENEELEEEYKIkkrtvELLPDAENNVAKLQA 343
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   561 TIEAARAG--------EAGRgfAVVAGEVKSLAAQTATATEEISRQVEEIQGATgqavtaiRSIGGAISGIDEKMTAIAA 632
Cdd:pfam05667 344 LVVASSERllelaqqwEAHR--TPLIDEYRSLKEKNRNKEDETQRQLDEIKKLR-------NKIEELESELQTKEQLYKQ 414
                         250       260       270
                  ....*....|....*....|....*....|....*
gi 27383065   633 AVEQQRAATTEISRnfqqaAQGTREVTDTIGSVAK 667
Cdd:pfam05667 415 LLDEYENAPKSVSR-----SAYTRRILEIIKNIKK 444
PRK15347 PRK15347
two component system sensor kinase SsrA; Provisional
326-426 1.02e-03

two component system sensor kinase SsrA; Provisional


Pssm-ID: 237951 [Multi-domain]  Cd Length: 921  Bit Score: 41.17  E-value: 1.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  326 AVQAKALTNLVVQ---SLAFLVALAVTLagVYVVRTRLMRPVRAILDAIARIGARDYSTPVPQSRYpDEFGTMAAA---- 398
Cdd:PRK15347 286 NLANEALKPALQQlpfALLILVLLTSVL--FLLLRRYLAKPLWRFVDIINKTGPAALEPRLPENRL-DELGSIAKAynql 362
                         90       100
                 ....*....|....*....|....*...
gi 27383065  399 LESLRESAATAERLGQEResQQALQLAR 426
Cdd:PRK15347 363 LDTLNEQYDTLENKVAER--TQALAEAK 388
DUF390 pfam04094
Protein of unknown function (DUF390); This is a family of long proteins currently only found ...
365-603 1.75e-03

Protein of unknown function (DUF390); This is a family of long proteins currently only found in the rice genome. They have no known function. However they may be some kind of transposable element.


Pssm-ID: 112890 [Multi-domain]  Cd Length: 843  Bit Score: 40.19  E-value: 1.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   365 RAILDAIARIGARDYSTPVPQSRYPDEFGTMAAALEslrESAATAERLGQERESQQALQLARSGTVDAACRSFDDTVQAV 444
Cdd:pfam04094 502 QGVLDAAAAREQRAAENEAASRQREEALEARAMALE---ERACAKERDLADREAAVAIREATLAAHEAACAEEEFALRLR 578
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   445 IHGVAASARELDATATDVRTLVSESSSQTAAvasSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAREAVSQAER 524
Cdd:pfam04094 579 EDALTERERALEEAEAAAQQLADSLFLREAA---QEEQARRNLEGARAERAALDQRAAELEARAKELDARAHSGGAAAGD 655
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   525 TNATVEiLDQTASRIGEVVKMINAIAGQTNLLALNATI-------EAARAGEAGRGFAVVAGEVKSLAAQTATATEEISR 597
Cdd:pfam04094 656 GDLAAR-LAAAEHSIADLQCALDSSAGEVEALRLAGEVgpgmlrdAVSRLDCAGRQAGLWGGRCAKYAANQGGLAQRLSE 734

                  ....*.
gi 27383065   598 QVEEIQ 603
Cdd:pfam04094 735 MAGALQ 740
AAA_27 pfam13514
AAA domain; This domain is found in a number of double-strand DNA break proteins. This domain ...
366-698 4.83e-03

AAA domain; This domain is found in a number of double-strand DNA break proteins. This domain contains a P-loop motif.


Pssm-ID: 257834 [Multi-domain]  Cd Length: 1112  Bit Score: 39.02  E-value: 4.83e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    366 AILDAIARIGARDYSTPVPQSRYPDEFGTMAAALESLRESAATAERLGQERESQQALQLARSGTVDAACRSFDDtVQAVI 445
Cdd:pfam13514  581 AALDEAWRAQAAAAGTPTSPAAMEDWLAERDTAREQVRDAFKARAELDELLDRRARLRAALRAALAAVADLGEE-LEELL 659
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    446 HGVAASARELDATATDvRTLVSESSSQTAAVASSAEQATNNLE-TIAAATEELSASVGEISAQVQSSAREAREAVSQAER 524
Cdd:pfam13514  660 TLARQLLEEAEKQSAR-RASLDERLSQAEHALETAEERHDEAQsALEEWQEQWYDLLLEAGLGGRASPVGALDALELLQN 738
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    525 TNATVEILDQTASRIGEVVKMINAIAGQTNLLAlnatieAARAGE-AGRGFAVVAGEVKSLAAQTATATEEISRQVEEIQ 603
Cdd:pfam13514  739 IKEKLQAADDLRQRIAQMERDLARFAEEVEALA------KALAPEmLATPADELARALKARLKRARDTAAEADRLAEEIE 812
                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065    604 GATGQAVTAirsiGGAISGIDEKMTAIAAAVeqqRAATTEISRNFQQAAQGTREVTDTIgSVAKLNQETGNAGTVLSESV 683
Cdd:pfam13514  813 EAEKQVSTA----AAALDELEARLTALLRAA---RVTTIEELLAAVERSDTYRELRRRL-AALERTLERICGGLSLEALA 884
                          330
                   ....*....|....*.
gi 27383065    684 KKMSA-DADRLRVAVE 698
Cdd:pfam13514  885 AEKAAlDPAELPARLE 900
Tar COG0840
Methyl-accepting chemotaxis protein [Cell motility, Signal transduction mechanisms];
469-707 5.13e-03

Methyl-accepting chemotaxis protein [Cell motility, Signal transduction mechanisms];


Pssm-ID: 223910 [Multi-domain]  Cd Length: 408  Bit Score: 38.43  E-value: 5.13e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 469 SSSQTAAVASSAEQATNNLETIAAATEELSASVGEISAQVQSSAREAreAVSQAERTNATVEILDQTASRIGEVVKMINA 548
Cdd:COG0840   1 SNLEAPLNLELIELAAGEADAGLLKLKKLIDELGKLLLSLNLILDDA--ASAEAAALKAVLKFLLISLLVAIIVVLVLAI 78
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065 549 IAGQTNLLALNATIEAARAGEAGRGFAVVAGEVKSLAAQTATAteeISRQVEEIQGATGQAVTAIRSIGGAISGIDEKMT 628
Cdd:COG0840  79 LLLRAILEPISDLLEVVERIAAGDLTKRIDESSNDEFGQLAKS---FNEMILNLRQIIDAVQDNAEALSGASEEIAASAT 155
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 27383065 629 AIAAAVEQQRAATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGNAGTVLSESVKKMSADADRLRVAVEGFLGAVKTA 707
Cdd:COG0840 156 ELSARADQQAESLEEVASAIEELSETVKEVAFNAKEAAALASEASQVAEEGGEEVRQAVEQMQEIAEELAEVVKKLSES 234
PHA03247 PHA03247
large tegument protein UL36; Provisional
322-554 5.42e-03

large tegument protein UL36; Provisional


Pssm-ID: 223021 [Multi-domain]  Cd Length: 3151  Bit Score: 38.77  E-value: 5.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   322 ARAEAVQAKALTNLVVQS------LAFLVALAVTLAGvYVVRTRLMRPVRAildAIARIGArdystpvpqsrypdeFGTM 395
Cdd:PHA03247 1156 VRAHGVLADAVAALSPAVrdpacpLAFLVALADSAAG-YVKATRLALDARR---AIARLGA---------------LGAA 1216
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   396 AAALeslresaATAERlgqeRESQQAlQLARSGTVDAACRSfddtVQAVIHGVAASARELDAtatdvrTLVSESssqTAA 475
Cdd:PHA03247 1217 AADL-------AVAVR----RENPQA-EGDRAALLEAAARA----VTAAREGLAACEGEFGG------LLHAEG---SAG 1271
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065   476 VASSAEQATNNLETIAAAT----EELSASVGEISAQVqsSAREAReavSQAERTNATVE-ILDQTASRIG-EVVKM--IN 547
Cdd:PHA03247 1272 DPSPSGRALQELGKVVGATrrraDELEAAAADLAEKM--AARRAR---ASRERWAADVEaALDRVENRAEfDAVELrrLQ 1346

                  ....*..
gi 27383065   548 AIAGQTN 554
Cdd:PHA03247 1347 ALAATHG 1353
Smc COG1196
Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning];
361-694 8.19e-03

Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 224117 [Multi-domain]  Cd Length: 1163  Bit Score: 38.16  E-value: 8.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  361 MRPV--RAILDAIAriGARDYstpvpQSRYPDEFGTMAAALESLRESAATAERLGQERES--QQALQLARSGTVDAACRS 436
Cdd:COG1196  152 AKPEerRKLIEEAA--GVSKY-----KERKEEAERKLERTEENLERLEDLLEELEKQLEKleRQAEKAERYQELKAELRE 224
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  437 FDDTVQAvihgvaasaRELDATATDVRTLVSESSSQTAAVASSAEQatnnLETIAAATEELSASVGEISAQVQSSAREAR 516
Cdd:COG1196  225 LELALLL---------AKLKELRKELEELEEELSRLEEELEELQEE----LEEAEKEIEELKSELEELREELEELQEELL 291
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  517 EAVSQAERTNATVEILDQTASRIGEVVKMI--NAIAGQTNLLALNATIEAARAGEAGrgfavVAGEVKSLAAQTATATEE 594
Cdd:COG1196  292 ELKEEIEELEGEISLLRERLEELENELEELeeRLEELKEKIEALKEELEERETLLEE-----LEQLLAELEEAKEELEEK 366
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27383065  595 ISRQVEEIQGATGQAVTAIRSIGGAISGIDEKMTAIAAAVEQqraATTEISRNFQQAAQGTREVTDTIGSVAKLNQETGN 674
Cdd:COG1196  367 LSALLEELEELFEALREELAELEAELAEIRNELEELKREIES---LEERLERLSERLEDLKEELKELEAELEELQTELEE 443
                        330       340
                 ....*....|....*....|
gi 27383065  675 AGTVLSESVKKMSADADRLR 694
Cdd:COG1196  444 LNEELEELEEQLEELRDRLK 463
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.14
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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