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Conserved domains on  [gi|1958644502|ref|XP_038964265|]
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probable RNA-binding protein EIF1AD isoform X1 [Rattus norvegicus]

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 ...
 1-50 6.71e-29

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 cd05792:

Pssm-ID: 471952  Cd Length: 78  Bit Score: 99.81  E-value: 6.71e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958644502   1 MPSKYRKNIWIKRGDFLIVDPIEEGEKVKAEISFVLCKNHVRSLQKEGHW 50
Cdd:cd05792    29 MPTKFRKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTRDHVKYIKEEGLW 78
 
Name Accession Description Interval E-value
S1_eIF1AD_like cd05792
S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD) ...
 1-50 6.71e-29

S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.


Pssm-ID: 240218  Cd Length: 78  Bit Score: 99.81  E-value: 6.71e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958644502   1 MPSKYRKNIWIKRGDFLIVDPIEEGEKVKAEISFVLCKNHVRSLQKEGHW 50
Cdd:cd05792    29 MPTKFRKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTRDHVKYIKEEGLW 78
eIF1a smart00652
eukaryotic translation initiation factor 1A;
1-51 1.05e-22

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 84.23  E-value: 1.05e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958644502    1 MPSKYRKNIWIKRGDFLIVDPIEEGeKVKAEISFVLCKNHVRSLQKEGHWP 51
Cdd:smart00652  34 IPGKMRKKVWIRRGDIVLVDPWDFQ-DVKADIIYKYTKDEVRWLKKEGELP 83
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 1-35 1.23e-09

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: 50.08  E-value: 1.23e-09
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958644502   1 MPSKYRKNIWIKRGDFLIVDPIEEgEKVKAEISFV 35
Cdd:pfam01176  29 IPGKMRNRIWIKRGDYVLVEPSPY-DLTKGRIVYR 62
PRK04012 PRK04012
translation initiation factor IF-1A; Provisional
 2-52 2.86e-04

translation initiation factor IF-1A; Provisional


Pssm-ID: 179708  Cd Length: 100  Bit Score: 37.24  E-value: 2.86e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958644502   2 PSKYRKNIWIKRGDFLIVDPIEEGEKvKAEISFVLCKNHVRSLQKEGHWPE 52
Cdd:PRK04012   51 PGKMKKRMWIREGDVVIVAPWDFQDE-KADIIWRYTKPQVDWLRRKGYISE 100
 
Name Accession Description Interval E-value
S1_eIF1AD_like cd05792
S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD) ...
 1-50 6.71e-29

S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A 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.


Pssm-ID: 240218  Cd Length: 78  Bit Score: 99.81  E-value: 6.71e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958644502   1 MPSKYRKNIWIKRGDFLIVDPIEEGEKVKAEISFVLCKNHVRSLQKEGHW 50
Cdd:cd05792    29 MPTKFRKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTRDHVKYIKEEGLW 78
S1_IF1A_like cd04456
S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is ...
 1-50 1.83e-25

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: 91.07  E-value: 1.83e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1958644502   1 MPSKYRKNIWIKRGDFLIVDPIEEGEKVKAEISFVLCKNHVRSLQKEGHW 50
Cdd:cd04456    29 IPGKLRKNIWIKRGDFLIVDPIEEGEDVKADIIFVYCKDHVRSLKKEGFL 78
eIF1a smart00652
eukaryotic translation initiation factor 1A;
1-51 1.05e-22

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 84.23  E-value: 1.05e-22
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1958644502    1 MPSKYRKNIWIKRGDFLIVDPIEEGeKVKAEISFVLCKNHVRSLQKEGHWP 51
Cdd:smart00652  34 IPGKMRKKVWIRRGDIVLVDPWDFQ-DVKADIIYKYTKDEVRWLKKEGELP 83
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 1-35 1.23e-09

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: 50.08  E-value: 1.23e-09
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1958644502   1 MPSKYRKNIWIKRGDFLIVDPIEEgEKVKAEISFV 35
Cdd:pfam01176  29 IPGKMRNRIWIKRGDYVLVEPSPY-DLTKGRIVYR 62
PRK04012 PRK04012
translation initiation factor IF-1A; Provisional
 2-52 2.86e-04

translation initiation factor IF-1A; Provisional


Pssm-ID: 179708  Cd Length: 100  Bit Score: 37.24  E-value: 2.86e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958644502   2 PSKYRKNIWIKRGDFLIVDPIEEGEKvKAEISFVLCKNHVRSLQKEGHWPE 52
Cdd:PRK04012   51 PGKMKKRMWIREGDVVIVAPWDFQDE-KADIIWRYTKPQVDWLRRKGYISE 100
S1_IF1A cd05793
S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A ...
 2-49 3.99e-03

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: 33.65  E-value: 3.99e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1958644502   2 PSKYRKNIWIKRGDFLIVDPIEEGEKvKAEISFVLCKNHVRSLQKEGH 49
Cdd:cd05793    30 RGKMRKRVWINEGDIVLVAPWDFQDD-KADIIYKYTPDEVRWLKRKGE 76
 
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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