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Conserved domains on  [gi|186506962|ref|NP_001118488|]
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Nucleic acid-binding, OB-fold-like protein [Arabidopsis thaliana]

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 ...
 1-68 1.66e-17

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 smart00652:

Pssm-ID: 471952  Cd Length: 83  Bit Score: 71.51  E-value: 1.66e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186506962     1 MDAKGENSLALFPAKFRESMWIRRGSFVVID--HTGKEKAQesgskvtsIVCKVLfFEQVRLLQKSPEWP 68
Cdd:smart00652  23 MCADGKERLARIPGKMRKKVWIRRGDIVLVDpwDFQDVKAD--------IIYKYT-KDEVRWLKKEGELP 83
 
Name Accession Description Interval E-value
eIF1a smart00652
eukaryotic translation initiation factor 1A;
1-68 1.66e-17

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 71.51  E-value: 1.66e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186506962     1 MDAKGENSLALFPAKFRESMWIRRGSFVVID--HTGKEKAQesgskvtsIVCKVLfFEQVRLLQKSPEWP 68
Cdd:smart00652  23 MCADGKERLARIPGKMRKKVWIRRGDIVLVDpwDFQDVKAD--------IIYKYT-KDEVRWLKKEGELP 83
S1_eIF1AD_like cd05792
S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD) ...
 2-67 2.42e-10

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: 52.82  E-value: 2.42e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 186506962   2 DAKGENSLALFPAKFRESMWIRRGSFVVIDHTgkekaqESGSKVTSIVCKVLFFEQVRLLQKSPEW 67
Cdd:cd05792   19 TPNGSRYLVSMPTKFRKNIWIKRGDFVLVEPI------EEGDKVKAEIVKILTRDHVKYIKEEGLW 78
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 5-31 3.45e-03

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: 33.90  E-value: 3.45e-03
                          10        20
                  ....*....|....*....|....*..
gi 186506962    5 GENSLALFPAKFRESMWIRRGSFVVID 31
Cdd:pfam01176  22 GHTRLAHIPGKMRNRIWIKRGDYVLVE 48
 
Name Accession Description Interval E-value
eIF1a smart00652
eukaryotic translation initiation factor 1A;
1-68 1.66e-17

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 71.51  E-value: 1.66e-17
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186506962     1 MDAKGENSLALFPAKFRESMWIRRGSFVVID--HTGKEKAQesgskvtsIVCKVLfFEQVRLLQKSPEWP 68
Cdd:smart00652  23 MCADGKERLARIPGKMRKKVWIRRGDIVLVDpwDFQDVKAD--------IIYKYT-KDEVRWLKKEGELP 83
S1_eIF1AD_like cd05792
S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD) ...
 2-67 2.42e-10

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: 52.82  E-value: 2.42e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 186506962   2 DAKGENSLALFPAKFRESMWIRRGSFVVIDHTgkekaqESGSKVTSIVCKVLFFEQVRLLQKSPEW 67
Cdd:cd05792   19 TPNGSRYLVSMPTKFRKNIWIKRGDFVLVEPI------EEGDKVKAEIVKILTRDHVKYIKEEGLW 78
S1_IF1A_like cd04456
S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is ...
 1-67 1.10e-04

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: 38.30  E-value: 1.10e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 186506962   1 MDAKGENSLALFPAKFRESMWIRRGSFVVIDHtgKEKAQESGSKVTSIVCKvlffEQVRLLQKSPEW 67
Cdd:cd04456   18 ECADGQRRLVSIPGKLRKNIWIKRGDFLIVDP--IEEGEDVKADIIFVYCK----DHVRSLKKEGFL 78
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 5-31 3.45e-03

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: 33.90  E-value: 3.45e-03
                          10        20
                  ....*....|....*....|....*..
gi 186506962    5 GENSLALFPAKFRESMWIRRGSFVVID 31
Cdd:pfam01176  22 GHTRLAHIPGKMRNRIWIKRGDYVLVE 48
 
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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