Conserved Protein Domain Family
PBP1_ycjW_transcription_regulator_like

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cd06294: PBP1_ycjW_transcription_regulator_like 
Ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors
This group includes the ligand-binding domain of uncharacterized transcription regulator ycjW which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Statistics
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PSSM-Id: 107289
View PSSM: cd06294
Aligned: 38 rows
Threshold Bit Score: 270.602
Threshold Setting Gi: 116618000
Created: 25-Jan-2008
Updated: 17-Jan-2013
Structure
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Aligned Rows:
 
putative ligandputative
Feature 1:putative ligand binding site [chemical binding site]
Evidence:
  • Comment:based on sequence similarity to other members of the LacI family.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                          ##  #                                            #            
gi 3025088    62 AIMVIStrstkt-tagnpFFSEVLHAITAKAeeegFDVILQTshnpaedlQKCESKIKQKMIKGIIMLsspadesffaql 140
gi 24413090   61 NIGVIFpplvlpdrlsepFFMEILSTLTNEAkehgFTVSIATsmsseellEQVKLMHLQKRVDGFIVLysdqkdpireyl 140
gi 24379951   61 CVGVVFppltspdrlsepFFMEILAAINNEAsrnkFTVSIATsntltdlkDQVQLMYRQGRVDGFIVLyserrdpvrqyl 140
gi 28377112   61 TIGVVLpvdhhe-ifsnpFFLEMIRGINEVCskngAMTTLATgissdelvHNIDVMIAQGHIKTFILLysekndpvverl 139
gi 28811033   75 NIGLVFppittsdrlsepFFMEILSTITNEAkeshFTVSIATgislddliEQVKLMHLQKRVDGFIILysdqddpvkkyl 154
gi 4104694    62 TIGVVFppvad--kasqpFFMKILTSINETArdydVSIAIATghsvgelkKQVELQFSEKRVDGFIVLyagksdevrdyl 139
gi 149752508  62 TIGIILpasake-vyensFYLEAIQGISHYCngrqYMTTIVTgqdeaeilDAVRSMSRSGKVDGFIILyskkddpvidyl 140
gi 55738951   62 SLGFVLppltdrenisqpFYMEIITAINEEAssnsQVVSIATdalleelvKQVELMYRQKRADGFIILysetndpvkdyl 141
gi 160937932 185 TVGIILppsewe-ayqnpFYLEMIRGISQYCnqkqYINTVITgqnedeilQAIKTMARTGLAEGFIVLysreqdpvldyl 263
gi 163790437  62 TIGVILpvsqgq-gfqntFFLSMIRGISKACnekkYMVSLASgtteaellESIQTMAEGGRVDGFIVLyskkddpiieyl 140
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                  #             #                                   #                   
gi 3025088   141 dkyDIPVVVIGkvegqyahvySVDTDNFGDSIALTDALIesghQNIACLHApldvhvSVDRVNGYKQSlaahni-avrde 219
gi 24413090  141 lkyKLPFVVVGaangyeneitYIDNDNQLMGKSAIDYLYkkghKSIQFVTDdlnsevSEERYLGYFKGarkl-----gln 215
gi 24379951  141 iknKIPFVIVGapvdykdettYVDNDNQLMAETAVTYLNqkghKQILFVTNdqesdvYIERFIGYQKGmqal-----glq 215
gi 28377112  140 kqfDVQYVVIGkpyqdvnktsYVDNDNIQAGTDAAQYLIdhghRRIGFLYSdlsrmvQSDRMLGYQRVmmqn----qlpn 215
gi 28811033  155 mtnNLPFVIVGapqgdtnkttYIDNDNQLMAKTAVEHLYqkghHNILFITDdllsevTSERYLGYLKGcfkr-----slk 229
gi 4104694   140 lenKVPFVLVGtptegkneitHVDNDNMLLGREAVRLLAqlnhQNISFVTDtketevFEERYQGFKDEae---------r 210
gi 149752508 141 fneGLLYILIGkatqytnqtiYIDNDNLLAGREAAEYLYqlghRQIAYLGSdsslmfSADRKAGYQLAlashqlpvrpey 220
gi 55738951  142 lkeKVPFVVVGaavdnndkvtYIDNDNKELGQEAVNFLRakghQKIGFVTDdlfgqvGQEHYQGYIEAtnef-----nle 216
gi 160937932 264 yeeGLLYVLIGkacrnvnqtiYVDNDNVLAGREAAEYLLnlghVRIACLSGdhsllyNHDRKMGYMLAlaergi-pfdgq 342
gi 163790437 141 hqeKTPYVMIGkpykyenemlYVDNDNIIAGKDATNYLLqlghKKIVFVGEntkqmvIQARLKGYTRAledagv-lvdpn 219
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               #                                                       #                
gi 3025088   220 WIVDGGYTh-ETALKAARQLLSqsp--lpeAVFAtDSLKLMSIYRAAAEKniaipqqLAVVGYSNEtlsfiltPAPGGID 296
gi 24413090  216 QKPALLFD--RGNPQVLEEFINrvkeeettALIViGDTVSVRVMQFLSFYklkvpddISIMTFNNSlfshlihPYLSTFD 293
gi 24379951  216 SYDSALFD--SKQASTLEAFIKtvqkkkitALLIiGDVVSLRIIQFLSYYgiavpedMSIVSFNNSsyatilhPYLTTFD 293
gi 28377112  216 IMLEERFEthAAGVKTLHKFFEqyp--dvtGFVAvDDMLALKLQQVLHNDpnwkvkqFSLIGFNNSifsdlahPMLTSIA 293
gi 28811033  230 TKPMLLFD--RKDPVSVEILMEtissfkatALVVvGDVLAIRMVQLLSFYdikvpddMSIITFNNSnyaklihPYLTTFD 307
gi 4104694   211 LGLSHDLL--FMDSNFSLRNET--------ALVVmDDVLSLKVVERLRSQglnvpedVSLITYNNSifgamihPYLTTFD 280
gi 149752508 221 CVEVKNVS--ENNEEAIRGLLMqkd--rptAILVsDDILAVSLERVCLENhlaipedLSIISFNNSlfarltsPQLTSID 296
gi 55738951  217 TYPELVFS--SRVIDSLIESLQsyq---ltALIVkDDLIALRFIHWLNNQgiripedYAIISFNNSifaeimhPFLTTYD 291
gi 160937932 343 LCVEVPSVp-EEQDQALAALFAred--rptAVLVsDDILAVALEKACIGLglsipgdVSILSFNNSllarltfPPLTSVD 419
gi 163790437 220 LILDVTLPk-AAYRKKTQQLFEtdd--fptGIVAsDDLIALNMSYLLSEFglkipndVSIIGFNNSifaekfrPELTSID 296
                        250       260       270
                 ....*....|....*....|....*....|....*.
Feature 1        #                                   
gi 3025088   297 VPtQELGQQSCELLFrlisg--kpspQNITVATHMT 330
gi 24413090  294 INvNNLGRTSVRRLIdiikspdkvfsETIIVPFTLE 329
gi 24379951  294 INvNRLGRASLNCLLekvqk-rqskdQKVIVPFTLK 328
gi 28377112  294 VFpQRLGEEAAKIAMadhpa--delsTAVIVPHQIV 327
gi 28811033  308 INvENLGKMSFKQLLdiinsneqnlsQTIFVPFSLK 343
gi 4104694   281 IHiEQLGASAIKKILdlrdn-kenlpEKTIIPFELI 315
gi 149752508 297 IGaGQLGSEAASQIInhien-pnllaTKIIVPHHLI 331
gi 55738951  292 INiKELGKESVQRLLdllkn-pqtkaQKITIPFRLI 326
gi 160937932 420 VNaCQLGIEAAAQMIshven-pelvaTKIIVPHHMV 454
gi 163790437 297 LHtDSLTSQAVYQLIqlilg-kqtlaVKIILPHQII 331

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