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Conserved domains on  [gi|1958657144|ref|XP_038941389|]
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eukaryotic translation initiation factor 5A-1 isoform X1 [Rattus norvegicus]

Protein Classification

eukaryotic translation initiation factor 5A family protein( domain architecture ID 1904013)

eukaryotic translation initiation factor 5A (eIF-5A) family protein is a translation factor that promotes translation elongation and termination, particularly upon ribosome stalling at specific amino acid sequence contexts

CATH:  2.40.50.140
Gene Ontology:  GO:0008135|GO:0003723|GO:0006412
PubMed:  17578650|25029904|24402910

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PLN03107 super family cl42976
eukaryotic translation initiation factor 5A; Provisional
 1-150 5.60e-73

eukaryotic translation initiation factor 5A; Provisional


The actual alignment was detected with superfamily member PLN03107:

Pssm-ID: 215580  Cd Length: 159  Bit Score: 215.73  E-value: 5.60e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657144   1 MADDLDFETGDAGASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMD 80
Cdd:PLN03107    2 SDEEHHFESADAGASKTYPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNCD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958657144  81 VPNIKRNDFQLIGI-QDGYLSLLQDSGEVREDLRLPEGD--LGKEIEQKYDCGEEILITVLSAMTEEAAVAIK 150
Cdd:PLN03107   82 VPHVNRTDYQLIDIsEDGFVSLMDESGNTKDDLKLPTEDdtLAEQIKDGFDEGKDLVVTVMSAMGEEQICALK 154
 
Name Accession Description Interval E-value
PLN03107 PLN03107
eukaryotic translation initiation factor 5A; Provisional
 1-150 5.60e-73

eukaryotic translation initiation factor 5A; Provisional


Pssm-ID: 215580  Cd Length: 159  Bit Score: 215.73  E-value: 5.60e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657144   1 MADDLDFETGDAGASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMD 80
Cdd:PLN03107    2 SDEEHHFESADAGASKTYPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNCD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958657144  81 VPNIKRNDFQLIGI-QDGYLSLLQDSGEVREDLRLPEGD--LGKEIEQKYDCGEEILITVLSAMTEEAAVAIK 150
Cdd:PLN03107   82 VPHVNRTDYQLIDIsEDGFVSLMDESGNTKDDLKLPTEDdtLAEQIKDGFDEGKDLVVTVMSAMGEEQICALK 154
eIF_5A TIGR00037
translation elongation factor IF5A; Recent work (2009) changed the view of eIF5A in eukaryotes ...
 14-150 2.04e-50

translation elongation factor IF5A; Recent work (2009) changed the view of eIF5A in eukaryotes and aIF5A in archaea, hypusine-containing proteins, from translation initiation factor to translation elongation factor. [Protein synthesis, Translation factors]


Pssm-ID: 272866 [Multi-domain]  Cd Length: 130  Bit Score: 157.68  E-value: 2.04e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657144  14 ASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIG 93
Cdd:TIGR00037   1 MSATKQVEVSALRVGGYVVIDGEPCKIVDISTSKPGKHGHAKARVVAIGIFDGQKREFVSPVTSKVEVPIVDRREAQVLA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958657144  94 IQDGYLSLLQDSGEVREDLRLPEgDLGKEIEQKYDcgeeilITVLSAMTEEAAVAIK 150
Cdd:TIGR00037  81 IMGGMVQLMDLETYETFELPIPE-ELGDSLEPGFE------VEYIEALGQRKIIRFK 130
S1_eIF5A cd04468
S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. ...
 84-152 1.76e-35

S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed.


Pssm-ID: 239914  Cd Length: 69  Bit Score: 117.64  E-value: 1.76e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958657144  84 IKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKAM 152
Cdd:cd04468     1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVTVLSAMGEEQAVAVKEA 69
eIF-5a pfam01287
Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; eIF5A, previously thought to be ...
 83-150 6.95e-29

Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast.


Pssm-ID: 396035  Cd Length: 69  Bit Score: 100.73  E-value: 6.95e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958657144  83 NIKRNDFQLIGIQ-DGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIK 150
Cdd:pfam01287   1 NVKRTEYQLIDISdDGFLSLMDDDGETKEDVKLPEGELGKEIKAKFEEGKDVLVTVLSAMGEEKIIAVK 69
 
Name Accession Description Interval E-value
PLN03107 PLN03107
eukaryotic translation initiation factor 5A; Provisional
 1-150 5.60e-73

eukaryotic translation initiation factor 5A; Provisional


Pssm-ID: 215580  Cd Length: 159  Bit Score: 215.73  E-value: 5.60e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657144   1 MADDLDFETGDAGASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMD 80
Cdd:PLN03107    2 SDEEHHFESADAGASKTYPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNCD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958657144  81 VPNIKRNDFQLIGI-QDGYLSLLQDSGEVREDLRLPEGD--LGKEIEQKYDCGEEILITVLSAMTEEAAVAIK 150
Cdd:PLN03107   82 VPHVNRTDYQLIDIsEDGFVSLMDESGNTKDDLKLPTEDdtLAEQIKDGFDEGKDLVVTVMSAMGEEQICALK 154
PTZ00328 PTZ00328
eukaryotic initiation factor 5a; Provisional
 3-154 9.60e-52

eukaryotic initiation factor 5a; Provisional


Pssm-ID: 140349 [Multi-domain]  Cd Length: 166  Bit Score: 162.15  E-value: 9.60e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657144   3 DDLDF--ETGDAGASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMD 80
Cdd:PTZ00328    4 EDHDFshQGGGDNASKTYPLPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTHNVE 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657144  81 VPNIKRNDFQLIGIQD-------GYLSLLQDSGEVREDLRL-PEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKAM 152
Cdd:PTZ00328   84 VPFVKTFTYSVLDIQPnedpslpAHLSLMDDEGESREDLDMpPDAALATQIKEQFDSGKEVLVVVVSAMGTEQVLQTKNA 163


                  ..
gi 1958657144 153 AK 154
Cdd:PTZ00328  164 AE 165
eIF_5A TIGR00037
translation elongation factor IF5A; Recent work (2009) changed the view of eIF5A in eukaryotes ...
 14-150 2.04e-50

translation elongation factor IF5A; Recent work (2009) changed the view of eIF5A in eukaryotes and aIF5A in archaea, hypusine-containing proteins, from translation initiation factor to translation elongation factor. [Protein synthesis, Translation factors]


Pssm-ID: 272866 [Multi-domain]  Cd Length: 130  Bit Score: 157.68  E-value: 2.04e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657144  14 ASATFPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIG 93
Cdd:TIGR00037   1 MSATKQVEVSALRVGGYVVIDGEPCKIVDISTSKPGKHGHAKARVVAIGIFDGQKREFVSPVTSKVEVPIVDRREAQVLA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958657144  94 IQDGYLSLLQDSGEVREDLRLPEgDLGKEIEQKYDcgeeilITVLSAMTEEAAVAIK 150
Cdd:TIGR00037  81 IMGGMVQLMDLETYETFELPIPE-ELGDSLEPGFE------VEYIEALGQRKIIRFK 130
S1_eIF5A cd04468
S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. ...
 84-152 1.76e-35

S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed.


Pssm-ID: 239914  Cd Length: 69  Bit Score: 117.64  E-value: 1.76e-35
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958657144  84 IKRNDFQLIGIQDGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIKAM 152
Cdd:cd04468     1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVTVLSAMGEEQAVAVKEA 69
eIF-5a pfam01287
Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; eIF5A, previously thought to be ...
 83-150 6.95e-29

Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast.


Pssm-ID: 396035  Cd Length: 69  Bit Score: 100.73  E-value: 6.95e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958657144  83 NIKRNDFQLIGIQ-DGYLSLLQDSGEVREDLRLPEGDLGKEIEQKYDCGEEILITVLSAMTEEAAVAIK 150
Cdd:pfam01287   1 NVKRTEYQLIDISdDGFLSLMDDDGETKEDVKLPEGELGKEIKAKFEEGKDVLVTVLSAMGEEKIIAVK 69
PRK03999 PRK03999
translation initiation factor IF-5A; Provisional
 25-94 4.20e-19

translation initiation factor IF-5A; Provisional


Pssm-ID: 235193 [Multi-domain]  Cd Length: 129  Bit Score: 77.64  E-value: 4.20e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958657144  25 LRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTGKKYEDICPSTHNMDVPNIKRNDFQLIGI 94
Cdd:PRK03999   11 LKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSI 80
 
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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