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Conserved domains on  [gi|47085971|ref|NP_998350|]
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eukaryotic translation initiation factor 5A-1 [Danio rerio]

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
 1-151 1.92e-79

eukaryotic translation initiation factor 5A; Provisional


The actual alignment was detected with superfamily member PLN03107:

Pssm-ID: 215580  Cd Length: 159  Bit Score: 231.91  E-value: 1.92e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47085971    1 MADPDLDFASGDAGASATYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTNKKYEDICPSTHNM 80
Cdd:PLN03107   1 MSDEEHHFESADAGASKTYPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNC 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 47085971   81 DVPNIKRNDYQLVDISE-GFLSLMMDNGDVREDLRVPDGD--LGKEIENKFAAGEEMLVTVLSAMGEESAVALK 151
Cdd:PLN03107  81 DVPHVNRTDYQLIDISEdGFVSLMDESGNTKDDLKLPTEDdtLAEQIKDGFDEGKDLVVTVMSAMGEEQICALK 154
 
Name Accession Description Interval E-value
PLN03107 PLN03107
eukaryotic translation initiation factor 5A; Provisional
 1-151 1.92e-79

eukaryotic translation initiation factor 5A; Provisional


Pssm-ID: 215580  Cd Length: 159  Bit Score: 231.91  E-value: 1.92e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47085971    1 MADPDLDFASGDAGASATYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTNKKYEDICPSTHNM 80
Cdd:PLN03107   1 MSDEEHHFESADAGASKTYPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNC 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 47085971   81 DVPNIKRNDYQLVDISE-GFLSLMMDNGDVREDLRVPDGD--LGKEIENKFAAGEEMLVTVLSAMGEESAVALK 151
Cdd:PLN03107  81 DVPHVNRTDYQLIDISEdGFVSLMDESGNTKDDLKLPTEDdtLAEQIKDGFDEGKDLVVTVMSAMGEEQICALK 154
eIF_5A TIGR00037
translation elongation factor IF5A; Recent work (2009) changed the view of eIF5A in eukaryotes ...
 15-151 2.98e-54

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: 167.31  E-value: 2.98e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47085971    15 ASATYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTNKKYEDICPSTHNMDVPNIKRNDYQLVD 94
Cdd:TIGR00037   1 MSATKQVEVSALRVGGYVVIDGEPCKIVDISTSKPGKHGHAKARVVAIGIFDGQKREFVSPVTSKVEVPIVDRREAQVLA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 47085971    95 ISEGFLSLMMDNGDVREDLRVPDgdlgkEIENKFAAGEEmlVTVLSAMGEESAVALK 151
Cdd:TIGR00037  81 IMGGMVQLMDLETYETFELPIPE-----ELGDSLEPGFE--VEYIEALGQRKIIRFK 130
S1_eIF5A cd04468
S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. ...
 85-153 4.12e-36

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: 119.18  E-value: 4.12e-36
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 47085971  85 IKRNDYQLVDISEGFLSLMMDNGDVREDLRVPDGDLGKEIENKFAAGEEMLVTVLSAMGEESAVALKPM 153
Cdd:cd04468   1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVTVLSAMGEEQAVAVKEA 69
eIF-5a pfam01287
Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; eIF5A, previously thought to be ...
 84-151 4.72e-32

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: 108.81  E-value: 4.72e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 47085971    84 NIKRNDYQLVDISE-GFLSLMMDNGDVREDLRVPDGDLGKEIENKFAAGEEMLVTVLSAMGEESAVALK 151
Cdd:pfam01287   1 NVKRTEYQLIDISDdGFLSLMDDDGETKEDVKLPEGELGKEIKAKFEEGKDVLVTVLSAMGEEKIIAVK 69
 
Name Accession Description Interval E-value
PLN03107 PLN03107
eukaryotic translation initiation factor 5A; Provisional
 1-151 1.92e-79

eukaryotic translation initiation factor 5A; Provisional


Pssm-ID: 215580  Cd Length: 159  Bit Score: 231.91  E-value: 1.92e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47085971    1 MADPDLDFASGDAGASATYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTNKKYEDICPSTHNM 80
Cdd:PLN03107   1 MSDEEHHFESADAGASKTYPQQAGTIRKGGYIVIKGRPCKVVEVSTSKTGKHGHAKCHFVAIDIFTGKKLEDIVPSSHNC 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 47085971   81 DVPNIKRNDYQLVDISE-GFLSLMMDNGDVREDLRVPDGD--LGKEIENKFAAGEEMLVTVLSAMGEESAVALK 151
Cdd:PLN03107  81 DVPHVNRTDYQLIDISEdGFVSLMDESGNTKDDLKLPTEDdtLAEQIKDGFDEGKDLVVTVMSAMGEEQICALK 154
eIF_5A TIGR00037
translation elongation factor IF5A; Recent work (2009) changed the view of eIF5A in eukaryotes ...
 15-151 2.98e-54

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: 167.31  E-value: 2.98e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47085971    15 ASATYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTNKKYEDICPSTHNMDVPNIKRNDYQLVD 94
Cdd:TIGR00037   1 MSATKQVEVSALRVGGYVVIDGEPCKIVDISTSKPGKHGHAKARVVAIGIFDGQKREFVSPVTSKVEVPIVDRREAQVLA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 47085971    95 ISEGFLSLMMDNGDVREDLRVPDgdlgkEIENKFAAGEEmlVTVLSAMGEESAVALK 151
Cdd:TIGR00037  81 IMGGMVQLMDLETYETFELPIPE-----ELGDSLEPGFE--VEYIEALGQRKIIRFK 130
PTZ00328 PTZ00328
eukaryotic initiation factor 5a; Provisional
 1-151 9.19e-54

eukaryotic initiation factor 5a; Provisional


Pssm-ID: 140349 [Multi-domain]  Cd Length: 166  Bit Score: 167.54  E-value: 9.19e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47085971    1 MADPDLDFAS--GDAGASATYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTNKKYEDICPSTH 78
Cdd:PTZ00328   1 MSDEDHDFSHqgGGDNASKTYPLPAGALKKGGYVCINGRPCKVIDLSVSKTGKHGHAKVSIVATDIFTGNRLEDQAPSTH 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47085971   79 NMDVPNIKRNDYQLVDISE-------GFLSLMMDNGDVREDLRV-PDGDLGKEIENKFAAGEEMLVTVLSAMGEESAVAL 150
Cdd:PTZ00328  81 NVEVPFVKTFTYSVLDIQPnedpslpAHLSLMDDEGESREDLDMpPDAALATQIKEQFDSGKEVLVVVVSAMGTEQVLQT 160


                 .
gi 47085971  151 K 151
Cdd:PTZ00328 161 K 161
S1_eIF5A cd04468
S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. ...
 85-153 4.12e-36

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: 119.18  E-value: 4.12e-36
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 47085971  85 IKRNDYQLVDISEGFLSLMMDNGDVREDLRVPDGDLGKEIENKFAAGEEMLVTVLSAMGEESAVALKPM 153
Cdd:cd04468   1 VKRTEYQLIDIDDGFLSLMDDDGETREDLKLPEGELGKEIREKFDEGKDVLVTVLSAMGEEQAVAVKEA 69
eIF-5a pfam01287
Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; eIF5A, previously thought to be ...
 84-151 4.72e-32

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: 108.81  E-value: 4.72e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 47085971    84 NIKRNDYQLVDISE-GFLSLMMDNGDVREDLRVPDGDLGKEIENKFAAGEEMLVTVLSAMGEESAVALK 151
Cdd:pfam01287   1 NVKRTEYQLIDISDdGFLSLMDDDGETKEDVKLPEGELGKEIKAKFEEGKDVLVTVLSAMGEEKIIAVK 69
PRK03999 PRK03999
translation initiation factor IF-5A; Provisional
 17-143 1.99e-22

translation initiation factor IF-5A; Provisional


Pssm-ID: 235193 [Multi-domain]  Cd Length: 129  Bit Score: 86.12  E-value: 1.99e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47085971   17 ATYPMQCSALRKNGFVVLKGRPCKIVEMSTSKTGKHGHAKVHLVGIDIFTNKKYEDICPSTHNMDVPNIKRNDYQLVDIS 96
Cdd:PRK03999   2 SKKQVEVGELKEGSYVVIDGEPCKIVEISKSKPGKHGSAKARIVAIGIFDGQKRSLVQPVDAKVEVPIIEKKTGQVLSIM 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 47085971   97 EGFLSLM-MDNGDVREdLRVPDgdlgkEIENKFAAGEEmlVTVLSAMG 143
Cdd:PRK03999  82 GDVVQLMdLETYETFE-IPIPE-----ELKDKLEPGVE--VEYWEAMG 121
S1_Hex1 cd04469
S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin ...
 90-151 3.18e-03

S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.


Pssm-ID: 239915  Cd Length: 75  Bit Score: 34.71  E-value: 3.18e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 47085971  90 YQLVDISEGFLSLMMDNGDVREDLRVPD-GDLGKEIENKFAAGEEML-VTVLSAMGEESAVALK 151
Cdd:cd04469   5 YRVLDIQDGSIVAMTETGDVKQGLPVIDqSNLWTRLKTAFESGRGSVrVLVVNDGGRELVVDMK 68
 
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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