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Conserved domains on  [gi|1540875149|gb|RTG90934|]
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translation initiation factor 5B [Schistosoma bovis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IF2_aeIF5B_IV cd16266
Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; ...
 109-203 1.67e-33

Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; This family represents the domain IV of prokaryotic Initiation Factor 2 (IF2) and its archaeal and eukaryotic homologs IF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.


:

Pssm-ID: 293911 [Multi-domain]  Cd Length: 87  Bit Score: 116.11  E-value: 1.67e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149 109 CKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPsrECVHLGRIFSIESNHKPVEEARTGMEVCIRIDptdgetPKL 188
Cdd:cd16266     1 AKIRILPGCVFRQSKPAIVGVEVLEGTLKPGVPLIVP--DGKDVGRVKSIQDNGENVKEAKKGQEVAVSIE------GPT 72

                          90
                  ....*....|....*
gi 1540875149 189 YGRHFDLNDLLVSKI 203
Cdd:cd16266    73 VGRHIEEGDILYVDI 87
PRK04004 super family cl44330
translation initiation factor IF-2; Validated
 1-236 1.17e-32

translation initiation factor IF-2; Validated


The actual alignment was detected with superfamily member PRK04004:

Pssm-ID: 457675 [Multi-domain]  Cd Length: 586  Bit Score: 124.52  E-value: 1.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149   1 MKASVMCEREPKWAVILAFDVRIDKDAQKLATQLNVKIFTSEIIYRLqtqMEKYISkcrpynlgvspsvgsiriqtsipl 80
Cdd:PRK04004  394 IEASTVAEKDPLYGVILAFNVKVLPDAEEEAEKSDVKIFTGDVIYQL---IEDYEK------------------------ 446

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149  81 iidvvivcYRDDLKTGNQRKHRDLAVFPCKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPSRECVhlGRIFSIES 160
Cdd:PRK04004  447 --------WVKEQKEAEKEKILEKIVRPAKIRILPGYVFRQSDPAIVGVEVLGGTIKPGVPLIKEDGKRV--GTIKQIQD 516

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1540875149 161 NHKPVEEARTGMEVCIRIdptDGETpklYGRHFDLNDLLVSKISRESIDVMKEYFRSDLKKEDwklMIELKESLDI 236
Cdd:PRK04004  517 QGENVKEAKAGMEVAISI---DGPT---VGRQIKEGDILYVDIPEEHAKILEQELKDELSDDE---KEALKEILEI 583
 
Name Accession Description Interval E-value
IF2_aeIF5B_IV cd16266
Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; ...
 109-203 1.67e-33

Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; This family represents the domain IV of prokaryotic Initiation Factor 2 (IF2) and its archaeal and eukaryotic homologs IF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.


Pssm-ID: 293911 [Multi-domain]  Cd Length: 87  Bit Score: 116.11  E-value: 1.67e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149 109 CKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPsrECVHLGRIFSIESNHKPVEEARTGMEVCIRIDptdgetPKL 188
Cdd:cd16266     1 AKIRILPGCVFRQSKPAIVGVEVLEGTLKPGVPLIVP--DGKDVGRVKSIQDNGENVKEAKKGQEVAVSIE------GPT 72

                          90
                  ....*....|....*
gi 1540875149 189 YGRHFDLNDLLVSKI 203
Cdd:cd16266    73 VGRHIEEGDILYVDI 87
PRK04004 PRK04004
translation initiation factor IF-2; Validated
 1-236 1.17e-32

translation initiation factor IF-2; Validated


Pssm-ID: 235195 [Multi-domain]  Cd Length: 586  Bit Score: 124.52  E-value: 1.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149   1 MKASVMCEREPKWAVILAFDVRIDKDAQKLATQLNVKIFTSEIIYRLqtqMEKYISkcrpynlgvspsvgsiriqtsipl 80
Cdd:PRK04004  394 IEASTVAEKDPLYGVILAFNVKVLPDAEEEAEKSDVKIFTGDVIYQL---IEDYEK------------------------ 446

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149  81 iidvvivcYRDDLKTGNQRKHRDLAVFPCKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPSRECVhlGRIFSIES 160
Cdd:PRK04004  447 --------WVKEQKEAEKEKILEKIVRPAKIRILPGYVFRQSDPAIVGVEVLGGTIKPGVPLIKEDGKRV--GTIKQIQD 516

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1540875149 161 NHKPVEEARTGMEVCIRIdptDGETpklYGRHFDLNDLLVSKISRESIDVMKEYFRSDLKKEDwklMIELKESLDI 236
Cdd:PRK04004  517 QGENVKEAKAGMEVAISI---DGPT---VGRQIKEGDILYVDIPEEHAKILEQELKDELSDDE---KEALKEILEI 583
GTP_EFTU_D4 pfam14578
Elongation factor Tu domain 4; Elongation factor Tu consists of several structural domains, ...
 108-199 1.18e-17

Elongation factor Tu domain 4; Elongation factor Tu consists of several structural domains, and this is usually the fourth.


Pssm-ID: 405293 [Multi-domain]  Cd Length: 86  Bit Score: 74.98  E-value: 1.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149 108 PCKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPS-REcvhLGRIFSIESNHKPVEEARTGMEVCIRIdptdgETP 186
Cdd:pfam14578   1 PGKIRILPGYVFRRSDPAIVGVEVLGGIIKPGYPLIREDgRE---VGEIMQIQDNGKSLDEAKAGQEVAISI-----EGK 72

                          90
                  ....*....|...
gi 1540875149 187 KLYGRHFDLNDLL 199
Cdd:pfam14578  73 IMVGRQIKEGDIL 85
IF-2 pfam11987
Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main ...
 14-47 8.33e-09

Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes, Bacteria and Archaea). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyzes the hydrolysis of GTP following initiation-complex formation.


Pssm-ID: 463421 [Multi-domain]  Cd Length: 116  Bit Score: 52.06  E-value: 8.33e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1540875149  14 AVILAFDVRIDKDAQKLATQLNVKIFTSEIIYRL 47
Cdd:pfam11987  78 AIIIGFNVRPDAKARKLAEKEGVDIRYYNIIYDL 111
InfB COG0532
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 14-47 4.14e-04

Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440298 [Multi-domain]  Cd Length: 502  Bit Score: 40.77  E-value: 4.14e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1540875149  14 AVILAFDVRIDKDAQKLATQLNVKIFTSEIIYRL 47
Cdd:COG0532   354 AIIIGFNVRPDAKARKLAEREGVDIRYYSIIYDL 387
 
Name Accession Description Interval E-value
IF2_aeIF5B_IV cd16266
Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; ...
 109-203 1.67e-33

Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5; This family represents the domain IV of prokaryotic Initiation Factor 2 (IF2) and its archaeal and eukaryotic homologs IF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.


Pssm-ID: 293911 [Multi-domain]  Cd Length: 87  Bit Score: 116.11  E-value: 1.67e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149 109 CKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPsrECVHLGRIFSIESNHKPVEEARTGMEVCIRIDptdgetPKL 188
Cdd:cd16266     1 AKIRILPGCVFRQSKPAIVGVEVLEGTLKPGVPLIVP--DGKDVGRVKSIQDNGENVKEAKKGQEVAVSIE------GPT 72

                          90
                  ....*....|....*
gi 1540875149 189 YGRHFDLNDLLVSKI 203
Cdd:cd16266    73 VGRHIEEGDILYVDI 87
PRK04004 PRK04004
translation initiation factor IF-2; Validated
 1-236 1.17e-32

translation initiation factor IF-2; Validated


Pssm-ID: 235195 [Multi-domain]  Cd Length: 586  Bit Score: 124.52  E-value: 1.17e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149   1 MKASVMCEREPKWAVILAFDVRIDKDAQKLATQLNVKIFTSEIIYRLqtqMEKYISkcrpynlgvspsvgsiriqtsipl 80
Cdd:PRK04004  394 IEASTVAEKDPLYGVILAFNVKVLPDAEEEAEKSDVKIFTGDVIYQL---IEDYEK------------------------ 446

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149  81 iidvvivcYRDDLKTGNQRKHRDLAVFPCKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPSRECVhlGRIFSIES 160
Cdd:PRK04004  447 --------WVKEQKEAEKEKILEKIVRPAKIRILPGYVFRQSDPAIVGVEVLGGTIKPGVPLIKEDGKRV--GTIKQIQD 516

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1540875149 161 NHKPVEEARTGMEVCIRIdptDGETpklYGRHFDLNDLLVSKISRESIDVMKEYFRSDLKKEDwklMIELKESLDI 236
Cdd:PRK04004  517 QGENVKEAKAGMEVAISI---DGPT---VGRQIKEGDILYVDIPEEHAKILEQELKDELSDDE---KEALKEILEI 583
PRK14845 PRK14845
translation initiation factor IF-2; Provisional
 1-236 3.95e-22

translation initiation factor IF-2; Provisional


Pssm-ID: 237833 [Multi-domain]  Cd Length: 1049  Bit Score: 94.57  E-value: 3.95e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149    1 MKASVMCEREPKWAVILAFDVRIDKDAQKLATQLNVKIFTSEIIYRLQTQMEKYISKcrpynlgvspsvgsiriqtsipl 80
Cdd:PRK14845   850 IEALSYKQENPLYGVILGFNVKVLPEAQEEAEKYGVKIFVDNIIYKLVEDYTEWVKE----------------------- 906

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149   81 iidvvivcyrddlkTGNQRKHRDLA--VFPCKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPSREcvHLGRIFSI 158
Cdd:PRK14845   907 --------------EEEKKKRELFEklIKPGIIRLLPDCIFRRSNPAIVGVEVLEGTLRVGVTLIKEDGM--KVGTVRSI 970

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149  159 ESNHKPVEEARTGMEVCIRIDPTdgetpkLYGRHFDLNDLLVSKISRESIDVMKEYFRSDLK---KEDWKLMIELKESLD 235
Cdd:PRK14845   971 KDRGENVKEAKAGKAVAIAIEGA------ILGRHVDEGETLYVDVPESHVRELYHKYMDRLRddeKEALKMYMELKQKNN 1044


                   .
gi 1540875149  236 I 236
Cdd:PRK14845  1045 P 1045
GTP_EFTU_D4 pfam14578
Elongation factor Tu domain 4; Elongation factor Tu consists of several structural domains, ...
 108-199 1.18e-17

Elongation factor Tu domain 4; Elongation factor Tu consists of several structural domains, and this is usually the fourth.


Pssm-ID: 405293 [Multi-domain]  Cd Length: 86  Bit Score: 74.98  E-value: 1.18e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1540875149 108 PCKLRILPEMIFNKRAPIVVGVRVEAGIVRVGTPICVPS-REcvhLGRIFSIESNHKPVEEARTGMEVCIRIdptdgETP 186
Cdd:pfam14578   1 PGKIRILPGYVFRRSDPAIVGVEVLGGIIKPGYPLIREDgRE---VGEIMQIQDNGKSLDEAKAGQEVAISI-----EGK 72

                          90
                  ....*....|...
gi 1540875149 187 KLYGRHFDLNDLL 199
Cdd:pfam14578  73 IMVGRQIKEGDIL 85
Translation_Factor_II_like cd01342
Domain II of Elongation factor Tu (EF-Tu)-like proteins; Elongation factor Tu consists of ...
 124-178 3.40e-09

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: 52.27  E-value: 3.40e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1540875149 124 PIVVGVRVEAGIVRVGTPICVPSRecVHLGRIFSIESNHKPVEEARTGMEVCIRI 178
Cdd:cd01342    15 GRVAGGRVESGTLKVGDEIRILPK--GITGRVTSIERFHEEVDEAKAGDIVGIGI 67
IF-2 pfam11987
Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main ...
 14-47 8.33e-09

Translation-initiation factor 2; IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes, Bacteria and Archaea). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyzes the hydrolysis of GTP following initiation-complex formation.


Pssm-ID: 463421 [Multi-domain]  Cd Length: 116  Bit Score: 52.06  E-value: 8.33e-09
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1540875149  14 AVILAFDVRIDKDAQKLATQLNVKIFTSEIIYRL 47
Cdd:pfam11987  78 AIIIGFNVRPDAKARKLAEKEGVDIRYYNIIYDL 111
InfB COG0532
Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; ...
 14-47 4.14e-04

Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440298 [Multi-domain]  Cd Length: 502  Bit Score: 40.77  E-value: 4.14e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1540875149  14 AVILAFDVRIDKDAQKLATQLNVKIFTSEIIYRL 47
Cdd:COG0532   354 AIIIGFNVRPDAKARKLAEREGVDIRYYSIIYDL 387
EF1_alpha_II cd03693
Domain II of elongation factor 1-alpha; This family represents domain II of elongation factor ...
 125-171 1.17e-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: 37.17  E-value: 1.17e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1540875149 125 IVVGvRVEAGIVRVGTPICVPSRECVhlGRIFSIESNHKPVEEARTG 171
Cdd:cd03693    21 VPVG-RVETGILKPGMVVTFAPAGVT--GEVKSVEMHHEPLEEAIPG 64
GTP_EFTU_D2 pfam03144
Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this ...
 126-174 2.08e-03

Elongation factor Tu domain 2; Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain.


Pssm-ID: 427163 [Multi-domain]  Cd Length: 73  Bit Score: 35.70  E-value: 2.08e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1540875149 126 VVGVRVEAGIVRVGTPI---CVPSRECVHLGRIFSIESNHKPVEEARTGMEV 174
Cdd:pfam03144   3 VATGRVESGTLKKGDKVrilPNGTGKKKIVTRVTSLLMFHAPLREAVAGDNA 54
 
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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