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Conserved domains on  [gi|731187731]
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Chain A, Protein translation elongation factor 1A

Protein Classification

SelB and Translation_Factor_II_like domain-containing protein; selenocysteine-specific translation elongation factor( domain architecture ID 11461694)

SelB and Translation_Factor_II_like domain-containing protein; selenocysteine-specific translation elongation factor binds GTP and GDP and transfers selenocysteinyl-tRNA to the ribosome; selenocysteine-specific translation elongation factor binds GTP and GDP and transfers selenocysteyl-tRNA to the ribosome; selenocysteine-specific translation elongation factor is necessary for the incorporation of selenocysteine into proteins

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SelB super family cl34578
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 85-354 3.10e-34

Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure and biogenesis]; Selenocysteine-specific translation elongation factor SelB is part of the Pathway/BioSystem: Translation factors


The actual alignment was detected with superfamily member COG3276:

Pssm-ID: 442507 [Multi-domain]  Cd Length: 630  Bit Score: 133.12  E-value: 3.10e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  85 DIAVLCIP------PQgldahTGECIIALDLLGFKHGIIALTRSDSTH*HAIDELKAKLKVITSGTVLQDWECISLntnk 158
Cdd:COG3276   76 DLVLLVVAadegvmPQ-----TREHLAILDLLGIKRGIVVLTKADLVDEEWLELVEEEIRELLAGTFLEDAPIVPV---- 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 159 SAKNPfEGVDELKARINEVAEKIEAENAELnslPARIFIDHAFNVTGKGCVVLG-----VVKQGiskdkDKTKIFPLDRD 233
Cdd:COG3276  147 SAVTG-EGIDELRAALDALAAAVPARDADG---PFRLPIDRVFSIKGFGTVVTGtllsgTVRVG-----DELELLPSGKP 217

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 234 IEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFIISDKEIVTTDYTLECTVS---KFTKKIEPASVLHLFVGLQS 310
Cdd:COG3276  218 VRVRGIQVHGQPVEEAYAGQRVALNLAGVEKEEIERGDVLAAPGALRPTDRIDVRLRllpSAPRPLKHWQRVHLHHGTAE 297

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 731187731 311 EPVRVekILVDGNEVEeakPGSTCVLELSGNKKLAYSKQDRFLL 354
Cdd:COG3276  298 VLARV--VLLDREELA---PGEEALAQLRLEEPLVAARGDRFIL 336
 
Name Accession Description Interval E-value
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 85-354 3.10e-34

Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure and biogenesis]; Selenocysteine-specific translation elongation factor SelB is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 442507 [Multi-domain]  Cd Length: 630  Bit Score: 133.12  E-value: 3.10e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  85 DIAVLCIP------PQgldahTGECIIALDLLGFKHGIIALTRSDSTH*HAIDELKAKLKVITSGTVLQDWECISLntnk 158
Cdd:COG3276   76 DLVLLVVAadegvmPQ-----TREHLAILDLLGIKRGIVVLTKADLVDEEWLELVEEEIRELLAGTFLEDAPIVPV---- 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 159 SAKNPfEGVDELKARINEVAEKIEAENAELnslPARIFIDHAFNVTGKGCVVLG-----VVKQGiskdkDKTKIFPLDRD 233
Cdd:COG3276  147 SAVTG-EGIDELRAALDALAAAVPARDADG---PFRLPIDRVFSIKGFGTVVTGtllsgTVRVG-----DELELLPSGKP 217

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 234 IEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFIISDKEIVTTDYTLECTVS---KFTKKIEPASVLHLFVGLQS 310
Cdd:COG3276  218 VRVRGIQVHGQPVEEAYAGQRVALNLAGVEKEEIERGDVLAAPGALRPTDRIDVRLRllpSAPRPLKHWQRVHLHHGTAE 297

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 731187731 311 EPVRVekILVDGNEVEeakPGSTCVLELSGNKKLAYSKQDRFLL 354
Cdd:COG3276  298 VLARV--VLLDREELA---PGEEALAQLRLEEPLVAARGDRFIL 336
SelB_II cd03696
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ...
 194-275 5.02e-31

Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.


Pssm-ID: 293897 [Multi-domain]  Cd Length: 83  Bit Score: 113.01  E-value: 5.02e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 194 RIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFII 273
Cdd:cd03696    2 RLPIDHVFSIKGAGTVVTGTVLSGKVKVGDELEIPPLGKEVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFVL 81


                 ..
gi 731187731 274 SD 275
Cdd:cd03696   82 SE 83
PRK12317 PRK12317
elongation factor 1-alpha; Reviewed
 191-300 1.89e-09

elongation factor 1-alpha; Reviewed


Pssm-ID: 237055 [Multi-domain]  Cd Length: 425  Bit Score: 58.78  E-value: 1.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 191 LPARIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERG 270
Cdd:PRK12317 224 KPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELPQAEPGDNIGFNVRGVGKKDIKRG 303

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 731187731 271 --------------------FIISDKEIVTTDYT---------LECTVSKFTKKIEPAS 300
Cdd:PRK12317 304 dvcghpdnpptvaeeftaqiVVLQHPSAITVGYTpvfhahtaqVACTFEELVKKLDPRT 362
 
Name Accession Description Interval E-value
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 85-354 3.10e-34

Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure and biogenesis]; Selenocysteine-specific translation elongation factor SelB is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 442507 [Multi-domain]  Cd Length: 630  Bit Score: 133.12  E-value: 3.10e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  85 DIAVLCIP------PQgldahTGECIIALDLLGFKHGIIALTRSDSTH*HAIDELKAKLKVITSGTVLQDWECISLntnk 158
Cdd:COG3276   76 DLVLLVVAadegvmPQ-----TREHLAILDLLGIKRGIVVLTKADLVDEEWLELVEEEIRELLAGTFLEDAPIVPV---- 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 159 SAKNPfEGVDELKARINEVAEKIEAENAELnslPARIFIDHAFNVTGKGCVVLG-----VVKQGiskdkDKTKIFPLDRD 233
Cdd:COG3276  147 SAVTG-EGIDELRAALDALAAAVPARDADG---PFRLPIDRVFSIKGFGTVVTGtllsgTVRVG-----DELELLPSGKP 217

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 234 IEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFIISDKEIVTTDYTLECTVS---KFTKKIEPASVLHLFVGLQS 310
Cdd:COG3276  218 VRVRGIQVHGQPVEEAYAGQRVALNLAGVEKEEIERGDVLAAPGALRPTDRIDVRLRllpSAPRPLKHWQRVHLHHGTAE 297

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....
gi 731187731 311 EPVRVekILVDGNEVEeakPGSTCVLELSGNKKLAYSKQDRFLL 354
Cdd:COG3276  298 VLARV--VLLDREELA---PGEEALAQLRLEEPLVAARGDRFIL 336
SelB_II cd03696
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ...
 194-275 5.02e-31

Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.


Pssm-ID: 293897 [Multi-domain]  Cd Length: 83  Bit Score: 113.01  E-value: 5.02e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 194 RIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFII 273
Cdd:cd03696    2 RLPIDHVFSIKGAGTVVTGTVLSGKVKVGDELEIPPLGKEVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFVL 81


                 ..
gi 731187731 274 SD 275
Cdd:cd03696   82 SE 83
eSelB_III cd04094
Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain ...
 278-368 9.28e-19

Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain III of archaeal and eukaryotic selenocysteine (Sec)-specific eukaryotic elongation factor (eEFSec or eSelB), which is homologous to domain III of EF-Tu. SelB is a specialized translation elongation factor responsible for the co-translational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop, called Sec insertion sequence (SECIS) element.


Pssm-ID: 294009  Cd Length: 114  Bit Score: 80.82  E-value: 9.28e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 278 IVTTDYTLECTVSKFTKKIEPASVLHLFVGLQSEPVRVEKILVDGNE-----------------VEEAKPGSTCVLELSG 340
Cdd:cd04094    1 TVTAAIALVCKISFFKGSIKSKSKFHITVGHQTVMARVTFFSDPGKDeteedesaefvededesLEEAKPGSEQYALLEF 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 731187731 341 NKKLAYSKQDRFLLANLDL-----TQRFAAYGF 368
Cdd:cd04094   81 EKPVAAPPGDLFIGSRLDTdphsnTCRLAFYGR 113
Translation_Factor_II_like cd01342
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 193-274 6.15e-17

Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of three structural domains. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E. coli IF-2 to 30S subunits.


Pssm-ID: 293888 [Multi-domain]  Cd Length: 80  Bit Score: 74.61  E-value: 6.15e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 193 ARIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVqaKDIERGFI 272
Cdd:cd01342    1 LVMQVFKVFYIPGRGRVAGGRVESGTLKVGDEIRILPKGITGRVTSIERFHEEVDEAKAGDIVGIGILGV--KDILTGDT 78


                 ..
gi 731187731 273 IS 274
Cdd:cd01342   79 LT 80
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 65-270 3.06e-11

Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]; Translation elongation factor EF-1alpha (GTPase) is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 444074 [Multi-domain]  Cd Length: 423  Bit Score: 64.18  E-value: 3.06e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  65 VDAHSYPKTLKSLITALNISDIAVLCIP-PQGLDAHTGECIIALDLLGFKHGIIALTRSDST------H*HAIDELKAKL 137
Cdd:COG5256   90 IDAPGHRDFVKNMITGASQADAAILVVSaKDGVMGQTREHAFLARTLGINQLIVAVNKMDAVnysekrYEEVKEEVSKLL 169

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 138 KVI-----------TSGtvlqdWECISLnTNKSAKNP-------FEGVDELKarineVAEKieaenaeLNSLPARIFIDH 199
Cdd:COG5256  170 KMVgykvdkipfipVSA-----WKGDNV-VKKSDNMPwyngptlLEALDNLK-----EPEK-------PVDKPLRIPIQD 231

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 731187731 200 AFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERG 270
Cdd:COG5256  232 VYSISGIGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELEQAEPGDNIGFNVRGVEKNDIKRG 302
EF1_alpha_II cd03693
Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor ...
 192-277 2.11e-10

Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor 1-alpha (EF-1A) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF-1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF-1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.


Pssm-ID: 293894 [Multi-domain]  Cd Length: 91  Bit Score: 56.81  E-value: 2.11e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 192 PARIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGF 271
Cdd:cd03693    4 PLRLPIQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPAGVTGEVKSVEMHHEPLEEAIPGDNVGFNVKGVSVKDIKRGD 83


                 ....*.
gi 731187731 272 IISDKE 277
Cdd:cd03693   84 VAGDSK 89
PRK12317 PRK12317
elongation factor 1-alpha; Reviewed
 191-300 1.89e-09

elongation factor 1-alpha; Reviewed


Pssm-ID: 237055 [Multi-domain]  Cd Length: 425  Bit Score: 58.78  E-value: 1.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 191 LPARIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERG 270
Cdd:PRK12317 224 KPLRIPIQDVYSISGVGTVPVGRVETGVLKVGDKVVFMPAGVVGEVKSIEMHHEELPQAEPGDNIGFNVRGVGKKDIKRG 303

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 731187731 271 --------------------FIISDKEIVTTDYT---------LECTVSKFTKKIEPAS 300
Cdd:PRK12317 304 dvcghpdnpptvaeeftaqiVVLQHPSAITVGYTpvfhahtaqVACTFEELVKKLDPRT 362
GTPBP_II cd03694
Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to ...
 197-275 6.84e-09

Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to GTPBP1 and GTPBP2. GTPBP1 is structurally related to elongation factor 1 alpha, a key component of the protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.


Pssm-ID: 293895 [Multi-domain]  Cd Length: 87  Bit Score: 52.22  E-value: 6.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 197 IDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLD----RDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFI 272
Cdd:cd03694    5 IDDIYSVPGVGTVVSGTVSKGVIREGDTLLLGPDAdgkfRPVTVKSIHRNRQPVDRARAGQSASFALKKIKRESLRKGMV 84


                 ...
gi 731187731 273 ISD 275
Cdd:cd03694   85 LVS 87
PTZ00141 PTZ00141
elongation factor 1- alpha; Provisional
 44-296 1.00e-08

elongation factor 1- alpha; Provisional


Pssm-ID: 185474 [Multi-domain]  Cd Length: 446  Bit Score: 56.68  E-value: 1.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  44 KGTSSDIT*YNNDKEGRN*VFVDAHSYPKTLKSLITALNISDIAVLCIP-PQG-------LDAHTGECIIALDLLGFKHG 115
Cdd:PTZ00141  69 RGITIDIALWKFETPKYYFTIIDAPGHRDFIKNMITGTSQADVAILVVAsTAGefeagisKDGQTREHALLAFTLGVKQM 148

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 116 IIALTRSDST--------H*HAIDELKAKLKVITSGTVLQDWECIS--LNTN---KSAKNP-------FEGVDELKARIN 175
Cdd:PTZ00141 149 IVCINKMDDKtvnysqerYDEIKKEVSAYLKKVGYNPEKVPFIPISgwQGDNmieKSDNMPwykgptlLEALDTLEPPKR 228

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 176 EVaEKieaenaelnslPARIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRV 255
Cdd:PTZ00141 229 PV-DK-----------PLRLPLQDVYKIGGIGTVPVGRVETGILKPGMVVTFAPSGVTTEVKSVEMHHEQLAEAVPGDNV 296

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 731187731 256 G*RLKNVQAKDIERGFIISDkeiVTTDYTLECtvSKFTKKI 296
Cdd:PTZ00141 297 GFNVKNVSVKDIKRGYVASD---SKNDPAKEC--ADFTAQV 332
SelB cd04171
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 43-184 1.04e-08

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.


Pssm-ID: 206734 [Multi-domain]  Cd Length: 170  Bit Score: 54.15  E-value: 1.04e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  43 KKGTSSDIT-*YNNDKEGRN*VFVDAHSYPKTLKSLITALNISDIAVLCIPP-QGLDAHTGECIIALDLLGFKHGIIALT 120
Cdd:cd04171   32 KRGITIDLGfAYLDLPDGKRLGFIDVPGHEKFVKNMLAGAGGIDAVLLVVAAdEGIMPQTREHLEILELLGIKKGLVVLT 111

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 731187731 121 RSDSTH*HAIDELKAKLKVITSGTVLQDWECISLntnkSAKNPfEGVDELKARINEVAEKIEAE 184
Cdd:cd04171  112 KADLVDEDRLELVEEEILELLAGTFLADAPIFPV----SSVTG-EGIEELKNYLDELAEPQSKD 170
tufA CHL00071
elongation factor Tu
 140-295 3.09e-08

elongation factor Tu


Pssm-ID: 177010 [Multi-domain]  Cd Length: 409  Bit Score: 54.96  E-value: 3.09e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 140 ITSGTVLQDWECISLNTN-KSAKNPFegVDELKARINEVAEKIEAENAELNSlPARIFIDHAFNVTGKGCVVLGVVKQGI 218
Cdd:CHL00071 170 IVSGSALLALEALTENPKiKRGENKW--VDKIYNLMDAVDSYIPTPERDTDK-PFLMAIEDVFSITGRGTVATGRIERGT 246

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 731187731 219 SKDKDKTKIFPLD--RDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFIISDKEIVTTDYTLECTVSKFTKK 295
Cdd:CHL00071 247 VKVGDTVEIVGLRetKTTTVTGLEMFQKTLDEGLAGDNVGILLRGIQKEDIERGMVLAKPGTITPHTKFEAQVYILTKE 325
PLN00043 PLN00043
elongation factor 1-alpha; Provisional
 43-277 3.25e-08

elongation factor 1-alpha; Provisional


Pssm-ID: 165621 [Multi-domain]  Cd Length: 447  Bit Score: 55.10  E-value: 3.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  43 KKGTSSDIT*YNNDKEGRN*VFVDAHSYPKTLKSLITALNISDIAVLCIppqglDAHTG--ECIIALDLLGFKHGIIALT 120
Cdd:PLN00043  68 ERGITIDIALWKFETTKYYCTVIDAPGHRDFIKNMITGTSQADCAVLII-----DSTTGgfEAGISKDGQTREHALLAFT 142

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 121 RSDSTH*HAIDELKAKLKVITSGTVLQDWECISLNTNKSAKNP----------FEGVDELKARIN----------EVAEK 180
Cdd:PLN00043 143 LGVKQMICCCNKMDATTPKYSKARYDEIVKEVSSYLKKVGYNPdkipfvpisgFEGDNMIERSTNldwykgptllEALDQ 222

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 181 IeAENAELNSLPARIFIDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLK 260
Cdd:PLN00043 223 I-NEPKRPSDKPLRLPLQDVYKIGGIGTVPVGRVETGVIKPGMVVTFGPTGLTTEVKSVEMHHESLQEALPGDNVGFNVK 301

                        250
                 ....*....|....*..
gi 731187731 261 NVQAKDIERGFIISDKE 277
Cdd:PLN00043 302 NVAVKDLKRGYVASNSK 318
eRF3_II cd04089
Domain II of the eukaryotic class II release factor; In eukaryotes, translation termination is ...
 207-275 1.17e-06

Domain II of the eukaryotic class II release factor; In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribosome. eRF3 is a GTPase, which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF-1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils.


Pssm-ID: 293906 [Multi-domain]  Cd Length: 82  Bit Score: 45.94  E-value: 1.17e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 731187731 207 GCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFIISD 275
Cdd:cd04089   14 GTVVMGKVESGTIRKGQKLVLMPNKTKVEVTGIYIDEEEVDSAKPGENVKLKLKGVEEEDISPGFVLCS 82
SelB_euk cd01889
SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome; ...
 23-179 4.43e-05

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 eukaryotic SelBs and some from archaea.


Pssm-ID: 206676 [Multi-domain]  Cd Length: 192  Bit Score: 43.89  E-value: 4.43e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  23 NVAIIGTEKSGRTSLAA------------------------NLGKKGTSSDIT*YNNDKEGRN*-----VFVDAHSYPKT 73
Cdd:cd01889    2 NVGLLGHVDSGKTSLAKalseiastaafdknpqsqergitlDLGFSSFEVDKPKHLEDNENPQIenyqiTLVDCPGHASL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731  74 LKSLITALNISDIAVLCIPPQ-GLDAHTGECIIALDLLGfKHGIIALTRSD----STH*HAIDELKAKLKVITSGTVLQD 148
Cdd:cd01889   82 IRTIIGGAQIIDLMLLVVDAKkGIQTQTAECLVIGELLC-KPLIVVLNKIDlipeEERKRKIEKMKKRLQKTLEKTRLKD 160

                        170       180       190
                 ....*....|....*....|....*....|.
gi 731187731 149 WECISLntnkSAKnPFEGVDELKARINEVAE 179
Cdd:cd01889  161 SPIIPV----SAK-PGEGEAELGGELKNLIV 186
PLN03127 PLN03127
Elongation factor Tu; Provisional
 197-294 2.37e-04

Elongation factor Tu; Provisional


Pssm-ID: 178673 [Multi-domain]  Cd Length: 447  Bit Score: 42.89  E-value: 2.37e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 731187731 197 IDHAFNVTGKGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRS----IQSHDVDIDSAPAGTRVG*RLKNVQAKDIERGFI 272
Cdd:PLN03127 266 IEDVFSIQGRGTVATGRVEQGTIKVGEEVEIVGLRPGGPLKTtvtgVEMFKKILDQGQAGDNVGLLLRGLKREDVQRGQV 345

                         90       100
                 ....*....|....*....|..
gi 731187731 273 ISDKEIVTTDYTLECTVSKFTK 294
Cdd:PLN03127 346 ICKPGSIKTYKKFEAEIYVLTK 367
eRF3_II_like cd03698
Domain II of the eukaryotic class II release factor-like proteins; This model represents the ...
 206-275 7.75e-04

Domain II of the eukaryotic class II release factor-like proteins; This model represents the domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribosome. eRF3 is a GTPase, which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF-1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils. This group also contains proteins similar to S. cerevisiae Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation and to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression.


Pssm-ID: 293899 [Multi-domain]  Cd Length: 84  Bit Score: 37.87  E-value: 7.75e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 731187731 206 KGCVVLGVVKQGISKDKDKTKIFPLDRDIEIRSIQSH-DVDIDSAPAGTRVG*RLKNVQAKDIERGFIISD 275
Cdd:cd03698   14 RGTTVTGKLEAGSIQKNQVLYDMPSQQDAEVKNIIRNsDEETDWAIAGDTVTLRLRGIEVEDIQPGDILSS 84
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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