Conserved Protein Domain Family
PBP1_rhizopine_binding_like

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cd06301: PBP1_rhizopine_binding_like 
Periplasmic binding proteins specific to rhizopines
Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Statistics
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PSSM-Id: 107296
View PSSM: cd06301
Aligned: 31 rows
Threshold Bit Score: 246.371
Threshold Setting Gi: 26986263
Created: 8-Jan-2008
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
putative ligand
Feature 1:putative ligand binding site [chemical binding site]
Evidence:
  • Comment:based on sequence similarity to the periplasmic transport protein receptor for D-glucose and D-galactose

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                               #                                                                   
YP_470140                22 TIGVSMqsfdnnFQTLLREGLQARAsk-lnGVSLQIEDaqtdvSKQRSQVDNFIAsGVDAIIMTladtsaatgiseaark 100 Rhiz...
ZP_02083826              68 EVSVIIetfdntFASFVMNAMKKYEeehkdKIHITYLDskqdaNTQISQVENQILnGTQAIICLavdakqsepivracke 147 Clos...
YP_887903                36 RIGVTVydm-ssFITAGKEGMDAYAkd--nNIELIWNSanldvSTQASQVDSMINqGVDAIIVVpvqadslapqvasaka 112 Myco...
REF_retlidb:RHE_CH01210  30 VVGYANmadtdvFVMARKNAFIEASks-dpAVEVNFSDanndvSKQLDQIDNFIAqKVNAIVVVpvdyqgivpgvekanq 108 Rhiz...
AAY37608                 30 KIGAAVyglkgqFMQNWVRELKEHPavkdgTVKITVFDgnydaLTQNNQIETMITqHYDAIIFVpidtkagvgtvarame 109 Pseu...
ABA53508                 38 RIGAAVygmkgqFMQNWVREIKAHPavksgAVQLTVFDgnydaLTQNNQIETMLTqQYSGILFVpidtkagigvaaraga 117 Burk...
YP_996812                54 KVGAAVyglkaeFAQLWVNALKKHPlvkdgTVKLTVFDgkydaLTQNNQFETMITqKYDGILFVpidlqagadavskaae 133 Verm...
AAL51574                 23 KIGAAPyglnaeFMQVWSEALKKHPavkngEVELTIFDgrydaLVQQEQFNTMITqKFDAIIFVpidieagatavqaasd 102 Bruc...
YP_425339                29 RIAVLMygnkaeFVQLMERYGKEHPavkagIAEVTFYDgrydaAVQNDQAQMAINtKQDAIVVNpmdyeanidiatnakm 108 Rhod...
AAS63709                 35 KIAILMygmkaeFVQLMEKSAKEHPavtqgLTTLTLFDgrydpLVQNNQAETAIRtRYDAIIIVpidfeanvdvvtmank 114 Yers...
Feature 1                           #                                                            #          
YP_470140               101 aGIPLVYLNLepenidklpekqaYVGSKETDSGRLGAEAACdllkkegkaNDAQAYILMGdlahqASRDRTSSVKATlsa 180 Rhiz...
ZP_02083826             148 aGVPLIAFNRifen------cdsFVGADGAVAGSLLARFTGek-----tgGKGNVAIVNGimgqeNQFIRRDAIVETlge 216 Clos...
YP_887903               113 kGIPLVPVNAaldsk----diagNVQPDDVAAGAQEMQMMAdr-----lgGKGNIVILQGplgqsGELDRSKGIEQVlak 183 Myco...
REF_retlidb:RHE_CH01210 109 aGIPVIALGIqsag-----gkytFVGSKNIDAGRLQGEYMKeh-----lpKGAKILYLEGtpglsHTQERKKGFEDAlgr 178 Rhiz...
AAY37608                110 nDIPVIASNTrvag-----nkvpYVGNDDVEGGRLQAQAMVdk-----lkGKGNVVIIQGpigqsAQIDREKGELEVlsk 179 Pseu...
ABA53508                118 sDTPLVASNTmlat-----pkvpYIGNDDVEGGRLQAEALArr-----igGKGNVVIIQGpigqsAQIDREKGEMEVlak 187 Burk...
YP_996812               134 aNIPVVGSNGrvnsd----kllsYVGSNDVIAGAMQAQAVVda-----mgGKGNVVILEGpigqsGQVERRQGNLSVlak 204 Verm...
AAL51574                103 aGIPVVGSNTrvnsd----llaaYVGSDDTVSGYMEAKDVLdk-----igCKGNVVILEGpigqsAQISRLEGNKKAlae 173 Bruc...
YP_425339               109 aGIPVVVTNArlntd----emtaEVVSDDVLGGYLEAKDVLtk-----lgCKGNVVIIEGpkggsGEIQRGQGNEKAlae 179 Rhod...
AAS63709                115 aNIPVIVANArlntd----katsGIFSDDVQGGYLEAKAVLdk-----mqCQGNVVVIEGpigqsAQIQRGQGNDKAiae 185 Yers...
Feature 1                                                                                         #         
YP_470140               181 gdckgvtiADEQTAAWTSTNAMDLTTNWLTag--rpIDVIFANNDEMALGAIQALKASGVsmddVIVIGIDATQDALaam 258 Rhiz...
ZP_02083826             217 my-pdmqvVIEGAGDWKRDKALQLVETWLQsg--tdIDAILCLNDDMAMGTQLAVEQAGKsd-dIIVCGVNGDPDGInav 292 Clos...
YP_887903               184 yp--dikvLAKDTANWKRDEAVNKMKNWISgfg-pqIDGVVAQNDDMGLGALQALKESGRt--gVPIVGIDGIEDGLnav 258 Myco...
REF_retlidb:RHE_CH01210 179 s---dvttLASLSANYDRAEGMKVTEDWIQsf--pkFDAIVAANDQMALGALEALQGADRlk-gVMISGVDGTADALnai 252 Rhiz...
AAY37608                180 hp--dikiIEKKTANWSRAEAQTLTEDWLNahqnggISGIISQNDDMALGALQAVKSRNLkpadVPITSIDGMPDAIqaa 257 Pseu...
ABA53508                188 yp--gikvIEKKTANWSRAEAMNLMEDWLNahp-kqINGVIAQNDDMALGALQAIKNRGLtpkdIPITSIDGMPDAIqaa 264 Burk...
YP_996812               205 yp--nvkvLEMKTANWSRAEALSLTENWLTaha-gkINGIIGQNDEMALGAIEAVKAKGLdpktIPTAGIDGVSDAVrav 281 Verm...
AAL51574                174 cp--dvkvLEDQTANWSRAEAQTLMENWLTahp-gqINGVIGQNDEMALGAIEAIKAANLkpgdFAIAGIDGITDALhav 250 Bruc...
YP_425339               180 cpagavkvLERKTANWSRAEALDLMQNWLSkhp-gkINGVIGQNDEMALGAIEAIKAADLnvkdFAIAGIDGVTDALhav 258 Rhod...
AAS63709                186 cgpgkinvLERKTANWSRAEAMPLMENWLQkhr-gkINGVIGQNDEMALGAIEAIKSAGLnvqdFAIAGIDGVSDAIrav 264 Yers...
Feature 1                             #                                                       
YP_470140               259 aagDLDVTVFQNAKQQAASAVDAAValahg---------------------navdKEVWVPFELVT 303 Rhizobium etli CFN 42
ZP_02083826             293 rdgKIAATVFQNPDRQAEEALEAALqyihg---------------------ekpeSKIMIPFELVT 337 Clostridium boltea...
YP_887903               259 ksgDFIGTSLQNGTVELAAGLAVANrlakg---------------------epvnKEPVYIMPAIT 303 Mycobacterium smeg...
REF_retlidb:RHE_CH01210 253 kagTMSQTIFQDAAGQAKAAFEVVEglkkg---------------------edapAEKLVPFASIT 297 Rhizobium etli CFN 42
AAY37608                258 -kkNEITTFLQDAQAQSQGALDVALrtlagkdykpqsviw-eryakdvkwgdgtdKNYILPWVPVT 321 Pseudomonas syring...
ABA53508                265 -krGEITTFLQDAQAQSQGALDLVLrqlvgagykpqsviw-qryakdlkwdggtaKRYILPWVPVT 328 Burkholderia pseud...
YP_996812               282 -kaGIMASVLQDASAQSQGALDVLLrkligasykprsamwaqygaaglqwddgaaRAYNIPWTPIT 346 Verminephrobacter ...
AAL51574                251 -keGTMTSILQDANAQAQGALDLAIfhakkgdykpqsdi--waqypdmpfndgkdKNYNVPWTPVT 313 Brucella melitensi...
YP_425339               259 -kaGEMTSILQDARGQIQGSIDVALravkgpdykpmspiw-eqykadlawadgqsKRYDIPWTVVT 322 Rhodospirillum rub...
AAS63709                265 -kqGEMMSILQDGQAQIQGAIDIAMrsvqgeryqpmstiw-qqyqgkmdwqqgtaKMYEVPWTEVT 328 Yersinia pestis bi...

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