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Conserved domains on  [gi|1391189030|gb|AWM13088|]
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translation initiation factor IF-1 [Flavobacterium sediminis]

Protein Classification

translation initiation factor IF-1( domain architecture ID 10011353)

initiation factor 1 together with initiation factor 2 and 3 play an important role in the correct assembly of the functional initiation complex for protein biosynthesis in prokaryotes

Gene Ontology:  GO:0043022|GO:0019843|GO:0003743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
infA PRK00276
translation initiation factor IF-1; Validated
 1-71 7.77e-47

translation initiation factor IF-1; Validated


:

Pssm-ID: 178954  Cd Length: 72  Bit Score: 142.99  E-value: 7.77e-47
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1391189030  1 MAKQSAIEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:PRK00276   1 MAKEDVIEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRH 71
 
Name Accession Description Interval E-value
infA PRK00276
translation initiation factor IF-1; Validated
 1-71 7.77e-47

translation initiation factor IF-1; Validated


Pssm-ID: 178954  Cd Length: 72  Bit Score: 142.99  E-value: 7.77e-47
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1391189030  1 MAKQSAIEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:PRK00276   1 MAKEDVIEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRH 71
InfA COG0361
Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; ...
 1-71 6.79e-41

Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-1 is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440130  Cd Length: 73  Bit Score: 127.91  E-value: 6.79e-41
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1391189030  1 MA-KQSAIEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:COG0361    1 MAkKEDLIEVEGVVEEVLPNARFRVRLENGHERLARISGKMRKNRIRILPGDRVLVEPSPYDLTKGRIVYRY 72
S1_IF1 cd04451
S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like ...
 7-70 4.44e-39

S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of the mRNA.


Pssm-ID: 239898  Cd Length: 64  Bit Score: 123.01  E-value: 4.44e-39
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1391189030  7 IEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYR 70
Cdd:cd04451    1 IEMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64
infA TIGR00008
translation initiation factor IF-1; This family consists of translation initiation factor IF-1 ...
 3-71 1.29e-38

translation initiation factor IF-1; This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575). [Protein synthesis, Translation factors]


Pssm-ID: 188015  Cd Length: 69  Bit Score: 122.06  E-value: 1.29e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1391189030  3 KQSAIEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:TIGR00008  1 KEDKIEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDRVKVELSPYDLTRGRITYRL 69
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 8-70 1.13e-30

Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.


Pssm-ID: 460099  Cd Length: 62  Bit Score: 101.69  E-value: 1.13e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1391189030  8 EQDGTIVEALSNAMFRVELENGHVVIAHISGKMRmHYIKLLPGDKVKLEMSPYDLTKARITYR 70
Cdd:pfam01176  1 EVIGKVVEALGNNLFEVELDNGHTRLAHIPGKMR-NRIWIKRGDYVLVEPSPYDLTKGRIVYR 62
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
10-71 6.65e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 41.82  E-value: 6.65e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1391189030  10 DGTIVEaLSNAMFRVELENGHVVIAHISGKMRMH----YIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:smart00316  7 EGTVTE-ITPGGAFVDLGNGVEGLIPISELSDKRvkdpEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
 
Name Accession Description Interval E-value
infA PRK00276
translation initiation factor IF-1; Validated
 1-71 7.77e-47

translation initiation factor IF-1; Validated


Pssm-ID: 178954  Cd Length: 72  Bit Score: 142.99  E-value: 7.77e-47
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1391189030  1 MAKQSAIEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:PRK00276   1 MAKEDVIEMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRH 71
InfA COG0361
Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; ...
 1-71 6.79e-41

Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; Translation initiation factor IF-1 is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440130  Cd Length: 73  Bit Score: 127.91  E-value: 6.79e-41
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1391189030  1 MA-KQSAIEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:COG0361    1 MAkKEDLIEVEGVVEEVLPNARFRVRLENGHERLARISGKMRKNRIRILPGDRVLVEPSPYDLTKGRIVYRY 72
S1_IF1 cd04451
S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like ...
 7-70 4.44e-39

S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of the mRNA.


Pssm-ID: 239898  Cd Length: 64  Bit Score: 123.01  E-value: 4.44e-39
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1391189030  7 IEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYR 70
Cdd:cd04451    1 IEMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64
infA TIGR00008
translation initiation factor IF-1; This family consists of translation initiation factor IF-1 ...
 3-71 1.29e-38

translation initiation factor IF-1; This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575). [Protein synthesis, Translation factors]


Pssm-ID: 188015  Cd Length: 69  Bit Score: 122.06  E-value: 1.29e-38
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1391189030  3 KQSAIEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:TIGR00008  1 KEDKIEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDRVKVELSPYDLTRGRITYRL 69
infA CHL00010
translation initiation factor 1
 1-71 2.11e-35

translation initiation factor 1


Pssm-ID: 214332  Cd Length: 78  Bit Score: 114.32  E-value: 2.11e-35
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1391189030  1 MAKQSAIEQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:CHL00010   1 MKKENKIEMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRL 71
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 8-70 1.13e-30

Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.


Pssm-ID: 460099  Cd Length: 62  Bit Score: 101.69  E-value: 1.13e-30
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1391189030  8 EQDGTIVEALSNAMFRVELENGHVVIAHISGKMRmHYIKLLPGDKVKLEMSPYDLTKARITYR 70
Cdd:pfam01176  1 EVIGKVVEALGNNLFEVELDNGHTRLAHIPGKMR-NRIWIKRGDYVLVEPSPYDLTKGRIVYR 62
S1 smart00316
Ribosomal protein S1-like RNA-binding domain;
10-71 6.65e-07

Ribosomal protein S1-like RNA-binding domain;


Pssm-ID: 197648 [Multi-domain]  Cd Length: 72  Bit Score: 41.82  E-value: 6.65e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1391189030  10 DGTIVEaLSNAMFRVELENGHVVIAHISGKMRMH----YIKLLPGDKVKLEMSPYDLTKARITYRY 71
Cdd:smart00316  7 EGTVTE-ITPGGAFVDLGNGVEGLIPISELSDKRvkdpEEVLKVGDEVKVKVLSVDEEKGRIILSL 71
S1_IF1A cd05793
S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A ...
 11-71 5.54e-05

S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.


Pssm-ID: 240219  Cd Length: 77  Bit Score: 37.12  E-value: 5.54e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1391189030 11 GTIVEALSNAMFRVELENGHVVIAHISGKMRMH-YIKllPGDKVKLEMSPYDLTKARITYRY 71
Cdd:cd05793    4 GQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRvWIN--EGDIVLVAPWDFQDDKADIIYKY 63
S1_YloQ_GTPase cd04466
S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. ...
 9-57 6.68e-04

S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.


Pssm-ID: 239912 [Multi-domain]  Cd Length: 68  Bit Score: 34.08  E-value: 6.68e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 1391189030  9 QDGTIVEALSNaMFRVELENGHVVIAHISGKMRMHYIKLLPGDKVKLEM 57
Cdd:cd04466    1 MEGLIIKAIGG-FYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEP 48
eIF1a smart00652
eukaryotic translation initiation factor 1A;
8-71 8.30e-04

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 34.15  E-value: 8.30e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1391189030   8 EQDGTIVEALSNAMFRVELENGHVVIAHISGKMRMH-YIKllPGDKVKLEMSPYDLTKARITYRY 71
Cdd:smart00652  6 QEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKvWIR--RGDIVLVDPWDFQDVKADIIYKY 68
 
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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