Conserved Protein Domain Family
SelB

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cd04171: SelB 
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome
SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains bacterial SelBs, as well as, one from archaea.
Statistics
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PSSM-Id: 206734
View PSSM: cd04171
Aligned: 24 rows
Threshold Bit Score: 210.925
Threshold Setting Gi: 41406462
Created: 14-Mar-2006
Updated: 17-Jan-2013
Structure
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Aligned Rows:
  next features
Feature 1:GTP/Mg2+ binding site [chemical binding site]
Evidence:
  • Comment:Based on sequence similarity with elongation factor EF-Tu.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1           ######                                                                      
gi 2822107    2 IIATAGHVDHGKTTLLQAITGVNADRLPEEKKRGMTIDLGYAYWPqpd-grVPGFIDVPGHEKFLSNMLAGVGGIDHALL 80
gi 24371706   2 IMVTAGHVDHGKSTLIRALTGMNTDRLPEEKRRGMTIDLGYAFMPlrd-gtRLAFIDVPGHEKFINNMLVGVSHVRHALL 80
gi 26987234   2 IVGTAGHIDHGKTALLLALTGQAGDQRQEERARGMTIDLGYRYAAlsegapLTGFIDVPGHERFIHNMLAGAHGIDLVLL 81
gi 16262460   2 IVGTAGHIDHGKTTLVKALTGVDTDRLKEEKARGITIDLGFAYARfak-daVTGFVDVPGHERFIHTMLAGAGGIDYAML 80
gi 15600001   2 IVGTAGHIDHGKTSLLRALTGIEGDRRPAERQRGITIDLGYLYADlgd-gsPTGFIDVPGHERFVHNMLAGASGIDCVLL 80
gi 32262290   9 IVGLAGHIDHGKTTLIKALNGFDGDSLEEEKQRGITLDLSFSHLHlp--srNVAFIDVPGHNKLVKNMIAGAFGIDVLLL 86
gi 53722683   2 IVGTAGHIDHGKTTLVRALTGVDTDRLKEEKARGISIELGYAYTPlpn-gdVLGFIDVPGHEKLVHTMAAGACGIDFALV 80
gi 34482951   5 IVGTAGHIDHGKTALIRALNGFEGDTTPEEKKRGITVDLSFSNLFlr--ekNIAFIDVPGHEKLVKNMIAGAFGFDAMLL 82
gi 57238422   5 IIGTAGHIDHGKTSLIKALNGFEGDSLKEEQERQITINLSFSNLKlk--dkNISFIDVPGHKDLVKTMVSGAFGFSICLF 82
gi 57168291   5 LIGTAGHIDHGKTSLIKAINGFEGDSLKEEKERQITINLSFSNLNyk--qkHLSFIDVPGHKDLVKTMISGAFGFSACLF 82
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                      ## #                                           ##
gi 2822107   81 VVACDDGVMaQTREHLAILQLTGnpMLTVALTKADRVDea--rVDEVERQVKEVLre----------ygFAEAKLFITAA 148
gi 24371706  81 VLACDDGVMpQTREHLQILALLPlnSLTLVLTKRDLVDdq--tAAKLASEGITLLae----------ygIEASGVFEVCA 148
gi 26987234  82 VVAADDGVMpQTREHLAIIELLGipQALVAISKCDRVEps--rLAEVQMQVSELLap----------gpYAGARQFPLSS 149
gi 16262460  81 VVAADDGIKpQTLEHLAILDLLGvsRGLVAITKADLADpa--rLENLTDEIGAVLss----------tsLRDAEILPVSV 148
gi 15600001  81 VVAADDGLMpQTREHLAIVELLGirRALVALTKIDRVEpq--rVQQVRTQVEHLLas----------gpLARSPIFPLSS 148
gi 32262290  87 VIAANEGIMpQSIEHLLIADMLGisSCICVITKIDKLEnpsleLPRLESDIVALFktcdmklydtialsLHSSTMPLTNA 166
gi 53722683  81 VIAADDGVMpQTREHLSILQLLGvaHGALALTKCDRVDaa--rVARVRDEIRAWLaa----------spLADAPVFETRA 148
gi 34482951  83 VVSAVEGIKpQTLEHLHIAHLLEipTLIVALTKSDLVDqe--tLLKRESEILNTLktl---------psLHLHRLLSVSI 151
gi 57238422  83 VVDINEGLKeQSLEHLEILKILDikNIILVLSKCDLCEn----IEQKSVEILEELkn----------ldYPILKVFHTSI 148
gi 57168291  83 VVDINEGLKeQSIEHLEVLELLGvkDIILVLSKCDLCEn----PKEQEQKILNSLe-------------FIPMKVFHTSI 145
                       170       180
                ....*....|....*....|....*
Feature 1       #                        
gi 2822107  149 TEgrg--mdALREHLLQLPEREHAS 171
gi 24371706 149 SDagdagveTLKQHILDIAEQQSTQ 173
gi 26987234 150 ISgeg--vdALRQALLEAEAGTRQR 172
gi 16262460 149 AAgqg--ieLLKERLAAAECATAAS 171
gi 15600001 149 STgeg--veALREALGGLAGEVRER 171
gi 32262290 167 YDsls-qlkRLKTSLDSIPKPQKID 190
gi 53722683 149 SEpddagvaALNAHLRDTALAWRAR 173
gi 34482951 152 YDpds--leRLKESLYELSKPATRD 174
gi 57238422 149 KNnqg--ieELKNYLYTIENKENDE 171
gi 57168291 146 KDqes--ieRLKNYLLNLECKNANA 168

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