2YFA


Conserved Protein Domain Family
HBM

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pfam16591: HBM 
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Helical bimodular sensor domain
The HBM sensor domain has been identified primarily in bacterial chemoreceptors but is also present on histidine kinases. Characteristic features of this domain are its size of approximately 250 amino acids and its location in the bacterial periplasm. The McpS chemoreceptor of Pseudomonas putida KT2440 was found to possess an HBM sensor domain and its 3D structure in complex with physiologically relevant ligands has been reported. This domain is composed of 2 long and 4 short helices that form two modules each composed of a 4-helix bundle. The McpS chemoreceptor mediates chemotaxis towards a number of organic acids. Both modules of the McpS HBM domain contain a ligand binding site. Chemo-attractants binds to each of these sites and their binding was shown to trigger a chemotactic response. This domain is primarily found in different proteobacteria but also in archaea. Interestingly, amino acids in both ligand binding sites showed a high degree of conservation suggesting that members of this family sense similar ligands.
Statistics
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PSSM-Id: 318736
View PSSM: pfam16591
Aligned: 12 rows
Threshold Bit Score: 207.219
Threshold Setting Gi: 771497808
Created: 29-Jul-2016
Updated: 4-Aug-2016
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2YFA_A        14 LVPRGSHMGDIGQLNKDLTDLRIARLQYMIANGDDTAA-AnTLAKLDAFSKQQAYLATTFKSPENVKLLGELGDTISAYK 92
gi 81585895   43 AIVRSQQLSEIGLINDLTKDLRAERITYRVLNDDASKA-R-ISNILDQLNSMLTTLQQRSNVDESRQLLTEKMALLQRLR 120
gi 123658528  43 VIDRGDKLGNISVIYALTKDLRIARLNYEMSRGEHGPA-A-VNDFLKQLDDGLQDARAQLQQPESITMVDQQLDAVAEYQ 120
gi 123658204  39 LIDRSNWMSDITQLNSGLTKLRVTRLQYMLANGDETAA-QgVQNTLDDFSAQQKKLLASFQSPENIKLLQGLGATISAYQ 117
gi 81729192   43 MIDRSESLSDVSQLTSLTKDLRADRITDRVEKTPETTA-Q-VIKKLDEMKTHLTSLHRQSTEQATITLLNGQLQAVSELE 120
gi 503557757  39 VVERSERMTDVNELTHTLTDLRVARLQYLLSNGSATEAdK-VQQHIRTLSQLQQAIRPKFRSPENVRLINEQIELIDQYQ 117
gi 505288058  39 VIDRGDKLGEISELAAVAKDLRVSRLKFQSTRSPQDAK-L-VVDTLDQLDRSHGALYDKFSTAEDRRKMDQQRELATEYR 116
gi 503558185  39 LSYRMDRMGAVNKLMDDMGDMRLARGDYLQSQGNVDNAkA-LGAKIETTAQTLAGLKAFFTTPFNLKHLDDMTQSLQAYR 117
gi 500251238  40 LLERNQKQTRLSQVQEASYAVDTARTLFEQSGSDAHAQ-Q-VTGKIGEVRNHLQDIRTTLTAADDQRDIASALQYAERIE 117
gi 882840823  39 VIQRSGWMTEISQLNKTLTDLRIARLQFMLANGDAEST-ErLDKNLGIYLAQQTKLLDTFKNPINVAQLKEQAGYNAQYQ 117
gi 503557103  39 LVQRSDWTADIAHLNDTLTDLRITRLQYMLANGDETIA-EtVQKSLDGFKAQHGQVLAKFKSPENVRLLQAQGAQIDAYQ 117
gi 771497808  35 LISRSDRAQSAARLLDEANRIRYAQVSFETRGDPLHVE-A-VEQSVARIVELVQQQKGEFSDPQDLQRLQAIAADVQNYR 112
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2YFA_A        93 LSLNKMRQGYDATRAARVSMDSSAIRADQAMDALSQEVMARPEA---D-----SVRLAQYQLISKARQQLLQVRID--VR 162
gi 81585895  121 DNFSELQRSVASRVALREALQSQEHALSEAIDQLQTQALLKMPD---D-----SQQSGVLGLMDTLSRHVEGANQQslVP 192
gi 123658528 121 KAFADMTRATANREAARSQLGATADNAVARVAEVENSLLQ-------------GDSVAQFNSVIDLSKLIQQARFQ--VR 185
gi 123658204 118 DSLNKMRNAYRSGDAARLAMNQNAERANDLINGINSWVKQLPLS---D------ERFTQFQAITQAKEAFQLARYE--VR 186
gi 81729192  121 KSFAEIRSNRQSRNQIRQRLDQRSEQALQAVAQVEAEVLKSVSQ---Eqd--sSERMEEFTNISQLRQQIQVARYQ--VQ 193
gi 503557757 118 KAYDKTNAVYASANKTRAEMIEVAERALELVDKVREEVLRGAAA---D-----AAGLTRYQAVARTKDDLQTLRYR--ML 187
gi 505288058 117 RLFGELLKSFDARDAAKQNLIRNAALITGGLEKAEQTLVAGGA----------TESLRPLQQLADLGRQVMLARFQ--VL 184
gi 503558185 118 VGVDGLKAAYQQIDASRLVRRTTGDKALQLLDGLDKYVTESADV---E-----T-QYKVYRAVKDVQMQFLFARFE--TR 186
gi 500251238 118 RSFQELKQARESREQSRGVMVSSAGEALKALGELEEQIYQTLEQsadD-----PLVVQQARALAELTRRVLESRYL--VR 190
gi 882840823 118 NSLNDMRKAYNQANGSRQVIDGAATRLSELTASVSNHVIQLPEY---D-----EDRFAQLLAISLIKEDVQRAQYL--LR 187
gi 503557103 118 LSLNKMRGGFRASNDARQEMTRNAVSAGEAIDEINAAVMNLPPY---D-----DSRAAQFQAITKAKEDWQLVRYQ--VR 187
gi 771497808 113 QRFLDLAALWERKVKTRSSWVEAGNTSDALIAALEARWAGTPDA---PvlhedTRSAAIGLQAGEVSKHNRMVRFM--VR 187
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2YFA_A       163 GYIAENSSANEQAALRQLDAALADTDNLKRQLP--S-EDARLQQFENAVLAYRDAVRQFRDAVANITTSRAEMTVQGADI 239
gi 81585895  193 AYTFVPVEDFAKVGDNALNAADSSLAQLLEGLAplGlPRAISEQPGVELSKYRTSLDQYRRAAVRVEQLQNNMEIMGNEL 272
gi 123658528 186 GYTYSAKPEAKQPALDAIDNALNNLTSLPSRLP--EqHVANLQQASDSLKAYRMAVSAYSDAEEASAAALKRMAAQGDRL 263
gi 123658204 187 GYVTTNNPDTEQKAVTQLNAAIAEMDQLKSHFS--StQRDALQQLETALSGYRSSLQAFKVAFTNAVEARKEMTDQGADI 264
gi 81729192  194 AYTFTTKDADETAAITAIDEALKEVEQIAQTQA--DdPLQGLVPATEALKGYRDSLSEFKQIQTKAEADQESMESLGEKL 271
gi 503557757 188 SYTADTNEQTERALSQQIENTDQGLESLTSAFN--GdYRDLIQQLESAVGSYRALVDTYRTAVAERVQLRDAMTEQVLEI 265
gi 505288058 185 AYTSNDNPALETPAVDALQQAIQAVQTGMRGAP--VeLAADYQNALDALSAYRAALDSYRHEVNASQAARDRMRDGGVQI 262
gi 503558185 187 AYTYSNNPKSFDAAAGAVDKTLASLGVLRQALD--SaDGAALAELGQVVQGYRDSLQTHQAALQQINASSAEVQKQGDNM 264
gi 500251238 191 GYIFQHTEESAQLAYAGLDRSREQADLLRGLLP--VdQHSHLDRMTSALQRYRAAIETFKVGMDATIQARTALASEIGGL 268
gi 882840823 188 VYMAAPGNDAAKAIYTQLDAAQATLGRHAGALD--DdSGAAVQQIRSVLGEYRGAIESLETATQAIAKARQEMTDQQKEI 265
gi 503557103 188 GYTGSPNADAERVAVAQIDTTIKDMDAFRQAFA--AeHPQRVNQVTAALDKYRDAVMAFKAAIDTIAVARKELTDEGYEI 265
gi 771497808 188 GYLMTETEQSLQQLQQQFSTLQAAVDRLDAQLA--GtPGVDLQPLRDSVATYIRQFGQLPPIVAAQVQARQEMQEIFDSI 265
                        250
                 ....*....|....*....
2YFA_A       240 VKRSDALYQIQLERRDIES 258
gi 81585895  273 RTVSLDLGKRKVEQRDREA 291
gi 123658528 264 MDLSKQLTVAQTTKRDSDA 282
gi 123658204 265 VSRSDALYQIQLDRRDIES 283
gi 81729192  272 LESVAALTLLQTAQRDSEA 290
gi 503557757 266 VKGSDALLAMQVKLRDSDS 284
gi 505288058 263 EKISNELTLSETAKRDAGV 281
gi 503558185 265 LHISQELYANQMQLRAEDT 283
gi 500251238 269 LEINGNLYRNQQTKMLGET 287
gi 882840823 266 VRISDSLYQFQLDQLDVES 284
gi 503557103 266 VRISKELTAIQMERRNSET 284
gi 771497808 266 YRNTNEIVQSQTERRSAEA 284
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