NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1370484880|ref|XP_024309464|]
View 

selenocysteine-specific elongation factor isoform X10 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
eSelB_III cd04094
Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain ...
 62-201 1.71e-48

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: 159.02  E-value: 1.71e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370484880  62 TVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNfsqeylfqeqylskdltpavtd 141
Cdd:cd04094     1 TVTAAIALVCKISFFKGSIKSKSKFHITVGHQTVMARVTFFSDPGKDETEEDESAEFV---------------------- 58

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370484880 142 ndeaDKKAGQATEGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGIL 201
Cdd:cd04094    59 ----EDEDESLEEAKPGSEQYALLEFEKPVAAPPGDLFIGSRLDTDPHSNTCRLAFYGRV 114
Translation_Factor_II_like super family cl02787
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 13-57 7.92e-15

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.


The actual alignment was detected with superfamily member cd03696:

Pssm-ID: 445922 [Multi-domain]  Cd Length: 83  Bit Score: 68.71  E-value: 7.92e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370484880  13 QVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCAP 57
Cdd:cd03696    39 GKEVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFVLSE 83
POLO_box super family cl02916
Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The ...
 256-322 7.47e-03

Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases; The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides.


The actual alignment was detected with superfamily member cd13115:

Pssm-ID: 470700  Cd Length: 108  Bit Score: 35.74  E-value: 7.47e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370484880 256 GLKVHLSTGELGIIDSAfGQSGKFKIHIPGGLSPESKKILTPALKKRARAGRGEAT-RQEESAERSEP 322
Cdd:cd13115    32 GAKVHKTSGGIKIIDKS-GKSYTLKESDLSSLSPELRKLLDHFNECRQHCLRLESAlSSLESSSGSNS 98
 
Name Accession Description Interval E-value
eSelB_III cd04094
Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain ...
 62-201 1.71e-48

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: 159.02  E-value: 1.71e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370484880  62 TVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNfsqeylfqeqylskdltpavtd 141
Cdd:cd04094     1 TVTAAIALVCKISFFKGSIKSKSKFHITVGHQTVMARVTFFSDPGKDETEEDESAEFV---------------------- 58

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370484880 142 ndeaDKKAGQATEGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGIL 201
Cdd:cd04094    59 ----EDEDESLEEAKPGSEQYALLEFEKPVAAPPGDLFIGSRLDTDPHSNTCRLAFYGRV 114
SelB_II cd03696
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ...
 13-57 7.92e-15

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: 68.71  E-value: 7.92e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370484880  13 QVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCAP 57
Cdd:cd03696    39 GKEVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFVLSE 83
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 17-102 9.93e-04

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: 41.05  E-value: 9.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370484880  17 KVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERG-LVCAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVGHETV 95
Cdd:COG3276   219 RVRGIQVHGQPVEEAYAGQRVALNLAGVEKEEIERGdVLAAPGALRPTDRIDVRLRLLPSAPRPLKHWQRVHLHHGTAEV 298


                  ....*..
gi 1370484880  96 MGRLMFF 102
Cdd:COG3276   299 LARVVLL 305
POLO_box_Plk4_2 cd13115
Second (cryptic) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak); The polo-like Ser/Thr ...
 256-322 7.47e-03

Second (cryptic) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak); The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides.


Pssm-ID: 240558  Cd Length: 108  Bit Score: 35.74  E-value: 7.47e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370484880 256 GLKVHLSTGELGIIDSAfGQSGKFKIHIPGGLSPESKKILTPALKKRARAGRGEAT-RQEESAERSEP 322
Cdd:cd13115    32 GAKVHKTSGGIKIIDKS-GKSYTLKESDLSSLSPELRKLLDHFNECRQHCLRLESAlSSLESSSGSNS 98
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 14-57 7.76e-03

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: 37.99  E-value: 7.76e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370484880  14 VVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCAP 57
Cdd:COG5256   264 VVGEVKSIEMHHEELEQAEPGDNIGFNVRGVEKNDIKRGDVAGH 307
 
Name Accession Description Interval E-value
eSelB_III cd04094
Domain III of eukaryotic and archaeal elongation factor SelB; This model represents the domain ...
 62-201 1.71e-48

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: 159.02  E-value: 1.71e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370484880  62 TVHAALISVEKIPYFRGPLQTKAKFHITVGHETVMGRLMFFSPAPDNFDQEPILDSFNfsqeylfqeqylskdltpavtd 141
Cdd:cd04094     1 TVTAAIALVCKISFFKGSIKSKSKFHITVGHQTVMARVTFFSDPGKDETEEDESAEFV---------------------- 58

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370484880 142 ndeaDKKAGQATEGHCPRQQWALVEFEKPVTCPRLCLVIGSRLDADIHTNTCRLAFHGIL 201
Cdd:cd04094    59 ----EDEDESLEEAKPGSEQYALLEFEKPVAAPPGDLFIGSRLDTDPHSNTCRLAFYGRV 114
SelB_II cd03696
Domain II of elongation factor SelB; This subfamily represents the domain of elongation factor ...
 13-57 7.92e-15

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: 68.71  E-value: 7.92e-15
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1370484880  13 QVVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCAP 57
Cdd:cd03696    39 GKEVRVRSIQVHDKPVEEAKAGDRVALNLTGVDAKELERGFVLSE 83
SelB COG3276
Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure ...
 17-102 9.93e-04

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: 41.05  E-value: 9.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1370484880  17 KVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERG-LVCAPESLHTVHAALISVEKIPYFRGPLQTKAKFHITVGHETV 95
Cdd:COG3276   219 RVRGIQVHGQPVEEAYAGQRVALNLAGVEKEEIERGdVLAAPGALRPTDRIDVRLRLLPSAPRPLKHWQRVHLHHGTAEV 298


                  ....*..
gi 1370484880  96 MGRLMFF 102
Cdd:COG3276   299 LARVVLL 305
GTPBP_II cd03694
Domain II of the GTPBP family of GTP binding proteins; This group includes proteins similar to ...
 17-54 4.36e-03

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: 36.04  E-value: 4.36e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1370484880  17 KVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLV 54
Cdd:cd03694    47 TVKSIHRNRQPVDRARAGQSASFALKKIKRESLRKGMV 84
EF1_alpha_II cd03693
Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor ...
 14-55 7.46e-03

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: 35.24  E-value: 7.46e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1370484880  14 VVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVC 55
Cdd:cd03693    44 VTGEVKSVEMHHEPLEEAIPGDNVGFNVKGVSVKDIKRGDVA 85
POLO_box_Plk4_2 cd13115
Second (cryptic) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak); The polo-like Ser/Thr ...
 256-322 7.47e-03

Second (cryptic) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak); The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides.


Pssm-ID: 240558  Cd Length: 108  Bit Score: 35.74  E-value: 7.47e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1370484880 256 GLKVHLSTGELGIIDSAfGQSGKFKIHIPGGLSPESKKILTPALKKRARAGRGEAT-RQEESAERSEP 322
Cdd:cd13115    32 GAKVHKTSGGIKIIDKS-GKSYTLKESDLSSLSPELRKLLDHFNECRQHCLRLESAlSSLESSSGSNS 98
TEF1 COG5256
Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and ...
 14-57 7.76e-03

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: 37.99  E-value: 7.76e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1370484880  14 VVKKVKSMQMFHMPITSAMQGDRLGICVTQFDPKLLERGLVCAP 57
Cdd:COG5256   264 VVGEVKSIEMHHEELEQAEPGDNIGFNVRGVEKNDIKRGDVAGH 307
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH