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Conserved domains on  [gi|1278000705|gb|PIV89923|]
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translation initiation factor IF-1A [Candidatus Huberarchaeum crystalense]

Protein Classification

S1 domain-containing protein( domain architecture ID 237)

S1 domain-containing protein may bind RNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
S1_like super family cl09927
S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of ...
 22-109 1.03e-23

S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.


The actual alignment was detected with superfamily member PRK04012:

Pssm-ID: 471952  Cd Length: 100  Bit Score: 86.93  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278000705  22 LRLPKSNEVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVYSYNDVGKSKL 101
Cdd:PRK04012   15 LPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMK-KRMWIREGDVVIVAPWDFQDE-KADIIWRYTKPQVDWL 92


                  ....*...
gi 1278000705 102 EERKLLDF 109
Cdd:PRK04012   93 RRKGYISE 100
 
Name Accession Description Interval E-value
PRK04012 PRK04012
translation initiation factor IF-1A; Provisional
 22-109 1.03e-23

translation initiation factor IF-1A; Provisional


Pssm-ID: 179708  Cd Length: 100  Bit Score: 86.93  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278000705  22 LRLPKSNEVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVYSYNDVGKSKL 101
Cdd:PRK04012   15 LPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMK-KRMWIREGDVVIVAPWDFQDE-KADIIWRYTKPQVDWL 92


                  ....*...
gi 1278000705 102 EERKLLDF 109
Cdd:PRK04012   93 RRKGYISE 100
S1_IF1A cd05793
S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A ...
 29-107 1.46e-18

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: 73.33  E-value: 1.46e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278000705  29 EVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVYSYNDVGKSKLEERKLL 107
Cdd:cd05793     1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMR-KRVWINEGDIVLVAPWDFQDD-KADIIYKYTPDEVRWLKRKGEL 77
InfA COG0361
Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; ...
 28-93 2.00e-18

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: 72.83  E-value: 2.00e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278000705  28 NEVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKFKKMWVRENSIVIVEIPPIQGNiKGEIVYSY 93
Cdd:COG0361     8 IEVEGVVEEVLPNARFRVRLENGHERLARISGKMRKNRIRILPGDRVLVEPSPYDLT-KGRIVYRY 72
eIF1a smart00652
eukaryotic translation initiation factor 1A;
25-95 3.93e-17

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 69.97  E-value: 3.93e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278000705   25 PKSNEVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVYSYND 95
Cdd:smart00652   2 KEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMR-KKVWIRRGDIVLVDPWDFQDV-KADIIYKYTK 70
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 29-91 6.74e-16

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: 65.87  E-value: 6.74e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278000705  29 EVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVY 91
Cdd:pfam01176   1 EVIGKVVEALGNNLFEVELDNGHTRLAHIPGKMR-NRIWIKRGDYVLVEPSPYDLT-KGRIVY 61
 
Name Accession Description Interval E-value
PRK04012 PRK04012
translation initiation factor IF-1A; Provisional
 22-109 1.03e-23

translation initiation factor IF-1A; Provisional


Pssm-ID: 179708  Cd Length: 100  Bit Score: 86.93  E-value: 1.03e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278000705  22 LRLPKSNEVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVYSYNDVGKSKL 101
Cdd:PRK04012   15 LPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMK-KRMWIREGDVVIVAPWDFQDE-KADIIWRYTKPQVDWL 92


                  ....*...
gi 1278000705 102 EERKLLDF 109
Cdd:PRK04012   93 RRKGYISE 100
S1_IF1A cd05793
S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A ...
 29-107 1.46e-18

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: 73.33  E-value: 1.46e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1278000705  29 EVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVYSYNDVGKSKLEERKLL 107
Cdd:cd05793     1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMR-KRVWINEGDIVLVAPWDFQDD-KADIIYKYTPDEVRWLKRKGEL 77
InfA COG0361
Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; ...
 28-93 2.00e-18

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: 72.83  E-value: 2.00e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278000705  28 NEVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKFKKMWVRENSIVIVEIPPIQGNiKGEIVYSY 93
Cdd:COG0361     8 IEVEGVVEEVLPNARFRVRLENGHERLARISGKMRKNRIRILPGDRVLVEPSPYDLT-KGRIVYRY 72
eIF1a smart00652
eukaryotic translation initiation factor 1A;
25-95 3.93e-17

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 69.97  E-value: 3.93e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1278000705   25 PKSNEVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVYSYND 95
Cdd:smart00652   2 KEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMR-KKVWIRRGDIVLVDPWDFQDV-KADIIYKYTK 70
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 29-91 6.74e-16

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: 65.87  E-value: 6.74e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278000705  29 EVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVY 91
Cdd:pfam01176   1 EVIGKVVEALGNNLFEVELDNGHTRLAHIPGKMR-NRIWIKRGDYVLVEPSPYDLT-KGRIVY 61
S1_IF1A_like cd04456
S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is ...
 29-94 4.35e-13

S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. 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: 239903  Cd Length: 78  Bit Score: 59.49  E-value: 4.35e-13
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1278000705  29 EVLGIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNIKGEIVYSYN 94
Cdd:cd04456     1 QQIVRVLRMLGNNRHEVECADGQRRLVSIPGKLR-KNIWIKRGDFLIVDPIEEGEDVKADIIFVYC 65
PLN00208 PLN00208
translation initiation factor (eIF); Provisional
 34-93 8.78e-05

translation initiation factor (eIF); Provisional


Pssm-ID: 177798  Cd Length: 145  Bit Score: 39.40  E-value: 8.78e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278000705  34 VIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQGNiKGEIVYSY 93
Cdd:PLN00208   38 VLRMLGNGRCEALCIDGTKRLCHIRGKMR-KKVWIAAGDIILVGLRDYQDD-KADVILKY 95
S1_YloQ_GTPase cd04466
S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. ...
 32-80 2.12e-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: 36.77  E-value: 2.12e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1278000705  32 GIVIQRLANkHFYVKCSDGKVRLCRMPGSFKFKKM------WVR-----ENSIVIVEIPP 80
Cdd:cd04466     3 GLIIKAIGG-FYYVETEDGKIYECRLRGKFRKDKNppavgdRVEfepedDGEGVIEEILP 61
PTZ00329 PTZ00329
eukaryotic translation initiation factor 1A; Provisional
 32-94 8.22e-04

eukaryotic translation initiation factor 1A; Provisional


Pssm-ID: 185558  Cd Length: 155  Bit Score: 36.71  E-value: 8.22e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1278000705  32 GIVIQRLANKHFYVKCSDGKVRLCRMPGSFKfKKMWVRENSIVIVEIPPIQgNIKGEIVYSYN 94
Cdd:PTZ00329   36 AQVLRMLGNGRLEAYCFDGVKRLCHIRGKMR-KRVWINIGDIILVSLRDFQ-DSKADVILKYT 96
 
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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