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Conserved domains on  [gi|126137501|ref|XP_001385274|]
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translation initiation factor eIF1A, partial [Scheffersomyces stipitis CBS 6054]

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 ...
 1-127 5.53e-66

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 PTZ00329:

Pssm-ID: 471952  Cd Length: 155  Bit Score: 197.34  E-value: 5.53e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501   1 KGGKNRRRGKNDNSGQKRELIYKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQD 80
Cdd:PTZ00329   7 KGGKNRRRGKNDNEGEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQD 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 126137501  81 DQCDVVHKYNSDEARTLKNVGELPESAKINETDTFgaDDDEDVNFEF 127
Cdd:PTZ00329  87 SKADVILKYTPDEARALKQHGELPETAKINETDIF--DDEGDDGIEF 131
 
Name Accession Description Interval E-value
PTZ00329 PTZ00329
eukaryotic translation initiation factor 1A; Provisional
 1-127 5.53e-66

eukaryotic translation initiation factor 1A; Provisional


Pssm-ID: 185558  Cd Length: 155  Bit Score: 197.34  E-value: 5.53e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501   1 KGGKNRRRGKNDNSGQKRELIYKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQD 80
Cdd:PTZ00329   7 KGGKNRRRGKNDNEGEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQD 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 126137501  81 DQCDVVHKYNSDEARTLKNVGELPESAKINETDTFgaDDDEDVNFEF 127
Cdd:PTZ00329  87 SKADVILKYTPDEARALKQHGELPETAKINETDIF--DDEGDDGIEF 131
eIF-1A TIGR00523
eukaryotic/archaeal initiation factor 1A; Recommended nomenclature: eIF-1A for eukaryotes, ...
 8-105 6.15e-50

eukaryotic/archaeal initiation factor 1A; Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C [Protein synthesis, Translation factors]


Pssm-ID: 273118  Cd Length: 98  Bit Score: 155.02  E-value: 6.15e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501    8 RGKNDNSGQKRELIYKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVH 87
Cdd:TIGR00523   1 RGKQDSDGPRVRLPYKEEGEIYGVITQMLGAGRVKVRCFDGNKRLARIPGKLRKKIWIREGDVVLVKPWEFQDDKCDIVW 80

                          90
                  ....*....|....*...
gi 126137501   88 KYNSDEARTLKNVGELPE 105
Cdd:TIGR00523  81 RYTLTEVEWLKRKGYLKE 98
S1_IF1A cd05793
S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A ...
 27-103 3.19e-42

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: 134.57  E-value: 3.19e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 126137501  27 QEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVHKYNSDEARTLKNVGEL 103
Cdd:cd05793    1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIYKYTPDEVRWLKRKGEL 77
eIF1a smart00652
eukaryotic translation initiation factor 1A;
22-104 3.56e-40

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 129.68  E-value: 3.56e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501    22 YKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVHKYNSDEARTLKNVG 101
Cdd:smart00652   1 FKEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDFQDVKADIIYKYTKDEVRWLKKEG 80


                   ...
gi 126137501   102 ELP 104
Cdd:smart00652  81 ELP 83
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 27-88 1.86e-22

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: 83.97  E-value: 1.86e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 126137501   27 QEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVHK 88
Cdd:pfam01176   1 EVIGKVVEALGNNLFEVELDNGHTRLAHIPGKMRNRIWIKRGDYVLVEPSPYDLTKGRIVYR 62
InfA COG0361
Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; ...
 22-89 7.32e-17

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: 69.75  E-value: 7.32e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501  22 YKEDGQE-YAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRK-KVWMGQGDIILVSLRDFQDDQCDVVHKY 89
Cdd:COG0361    3 KKEDLIEvEGVVEEVLPNARFRVRLENGHERLARISGKMRKnRIRILPGDRVLVEPSPYDLTKGRIVYRY 72
 
Name Accession Description Interval E-value
PTZ00329 PTZ00329
eukaryotic translation initiation factor 1A; Provisional
 1-127 5.53e-66

eukaryotic translation initiation factor 1A; Provisional


Pssm-ID: 185558  Cd Length: 155  Bit Score: 197.34  E-value: 5.53e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501   1 KGGKNRRRGKNDNSGQKRELIYKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQD 80
Cdd:PTZ00329   7 KGGKNRRRGKNDNEGEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQD 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 126137501  81 DQCDVVHKYNSDEARTLKNVGELPESAKINETDTFgaDDDEDVNFEF 127
Cdd:PTZ00329  87 SKADVILKYTPDEARALKQHGELPETAKINETDIF--DDEGDDGIEF 131
PLN00208 PLN00208
translation initiation factor (eIF); Provisional
 1-122 5.82e-57

translation initiation factor (eIF); Provisional


Pssm-ID: 177798  Cd Length: 145  Bit Score: 174.22  E-value: 5.82e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501   1 KGGKNRRRGKNDNSGQKRELIYKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQD 80
Cdd:PLN00208   7 KGGKNRKRGKNEADDEKRELIFKEDGQEYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQD 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 126137501  81 DQCDVVHKYNSDEARTLKNVGELPESAKINETDTFGADDDED 122
Cdd:PLN00208  87 DKADVILKYMPDEARLLKAYGELPENTRLNEGIAGDLDEEED 128
eIF-1A TIGR00523
eukaryotic/archaeal initiation factor 1A; Recommended nomenclature: eIF-1A for eukaryotes, ...
 8-105 6.15e-50

eukaryotic/archaeal initiation factor 1A; Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C [Protein synthesis, Translation factors]


Pssm-ID: 273118  Cd Length: 98  Bit Score: 155.02  E-value: 6.15e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501    8 RGKNDNSGQKRELIYKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVH 87
Cdd:TIGR00523   1 RGKQDSDGPRVRLPYKEEGEIYGVITQMLGAGRVKVRCFDGNKRLARIPGKLRKKIWIREGDVVLVKPWEFQDDKCDIVW 80

                          90
                  ....*....|....*...
gi 126137501   88 KYNSDEARTLKNVGELPE 105
Cdd:TIGR00523  81 RYTLTEVEWLKRKGYLKE 98
S1_IF1A cd05793
S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A ...
 27-103 3.19e-42

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: 134.57  E-value: 3.19e-42
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 126137501  27 QEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVHKYNSDEARTLKNVGEL 103
Cdd:cd05793    1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIYKYTPDEVRWLKRKGEL 77
eIF1a smart00652
eukaryotic translation initiation factor 1A;
22-104 3.56e-40

eukaryotic translation initiation factor 1A;


Pssm-ID: 128900  Cd Length: 83  Bit Score: 129.68  E-value: 3.56e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501    22 YKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVHKYNSDEARTLKNVG 101
Cdd:smart00652   1 FKEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDFQDVKADIIYKYTKDEVRWLKKEG 80


                   ...
gi 126137501   102 ELP 104
Cdd:smart00652  81 ELP 83
S1_IF1A_like cd04456
S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is ...
 27-103 5.15e-28

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: 98.78  E-value: 5.15e-28
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 126137501  27 QEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQ-CDVVHKYNSDEARTLKNVGEL 103
Cdd:cd04456    1 QQIVRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEEGEDVkADIIFVYCKDHVRSLKKEGFL 78
PRK04012 PRK04012
translation initiation factor IF-1A; Provisional
 6-105 1.47e-27

translation initiation factor IF-1A; Provisional


Pssm-ID: 179708  Cd Length: 100  Bit Score: 98.10  E-value: 1.47e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501   6 RRRGKNDNSGQKRELIYKEDGQEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDV 85
Cdd:PRK04012   1 MKKKQDDEEVTRVRLPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADI 80

                         90       100
                 ....*....|....*....|
gi 126137501  86 VHKYNSDEARTLKNVGELPE 105
Cdd:PRK04012  81 IWRYTKPQVDWLRRKGYISE 100
eIF-1a pfam01176
Translation initiation factor 1A / IF-1; This family includes both the eukaryotic translation ...
 27-88 1.86e-22

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: 83.97  E-value: 1.86e-22
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 126137501   27 QEYAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVHK 88
Cdd:pfam01176   1 EVIGKVVEALGNNLFEVELDNGHTRLAHIPGKMRNRIWIKRGDYVLVEPSPYDLTKGRIVYR 62
InfA COG0361
Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]; ...
 22-89 7.32e-17

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: 69.75  E-value: 7.32e-17
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 126137501  22 YKEDGQE-YAQITKMLGNGRIEVSCFDGIKRMGHIRGKLRK-KVWMGQGDIILVSLRDFQDDQCDVVHKY 89
Cdd:COG0361    3 KKEDLIEvEGVVEEVLPNARFRVRLENGHERLARISGKMRKnRIRILPGDRVLVEPSPYDLTKGRIVYRY 72
 
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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