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Conserved domains on  [gi|71989247|ref|NP_001023785|]
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Translation initiation factor eIF2B subunit delta [Caenorhabditis elegans]

Protein Classification

IF-2B domain-containing protein( domain architecture ID 1002306)

IF-2B domain-containing protein may function as an eukaryotic initiation factor 2B alpha, beta or delta subunit, but could also be functioning as an enzyme such as a 5-methylthioribose-1-phosphate isomerase

CATH:  3.40.50.10470
Gene Ontology:  GO:0044237
PubMed:  15215245

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IF-2B super family cl29528
Initiation factor 2 subunit family; This family includes initiation factor 2B alpha, beta and ...
 269-481 5.02e-13

Initiation factor 2 subunit family; This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterized as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The crystal structure of Ypr118w, a non-essential, low-copy number gene product from Saccharomyces cerevisiae, reveals a dimeric protein with two domains and a putative active site cleft.


The actual alignment was detected with superfamily member pfam01008:

Pssm-ID: 395798 [Multi-domain]  Cd Length: 281  Bit Score: 69.24  E-value: 5.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71989247   269 PLPFALGNTVRLLKRTIKRLEESTNMKCEEELQVYLEDTLAINFCHAYKAISQLLVRKIQQFKKVVVFDWCPVVNHVLLE 348
Cdd:pfam01008  47 PTAVSLGNAIDRLLRIVLALHSSSDVEEAKESLIEAADEFIDEIEEARRKIGAIAAELIKDGDTILTHCNSGTVLGVLRA 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71989247   349 AKQQIPDMQLSVIDANSNGRGTRHVKSFVDQGYNVKYVTMKGASWASLASGVLILGCSAIFANGAVAARKGALAVVLCAN 428
Cdd:pfam01008 127 AHKEGKRFRVIVTESRPRLQGRLTAKELVQAGIPVTLITDSAVGYVMQEVDKVIVGADRILANGGIANKIGTYQLALLAK 206

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71989247   429 HYNIPVIVVAEHFKFIDKGQ---------------VYQRVALLGRQNIECIQ-------SDLVTAVVTDLRILGP 481
Cdd:pfam01008 207 AHNVPFYVVAETYKFDPRFPldedifieerdpeevLYRTGVRIAPPNLKVRNpafdytpPELITLIITEVGVLPP 281
 
Name Accession Description Interval E-value
IF-2B pfam01008
Initiation factor 2 subunit family; This family includes initiation factor 2B alpha, beta and ...
 269-481 5.02e-13

Initiation factor 2 subunit family; This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterized as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The crystal structure of Ypr118w, a non-essential, low-copy number gene product from Saccharomyces cerevisiae, reveals a dimeric protein with two domains and a putative active site cleft.


Pssm-ID: 395798 [Multi-domain]  Cd Length: 281  Bit Score: 69.24  E-value: 5.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71989247   269 PLPFALGNTVRLLKRTIKRLEESTNMKCEEELQVYLEDTLAINFCHAYKAISQLLVRKIQQFKKVVVFDWCPVVNHVLLE 348
Cdd:pfam01008  47 PTAVSLGNAIDRLLRIVLALHSSSDVEEAKESLIEAADEFIDEIEEARRKIGAIAAELIKDGDTILTHCNSGTVLGVLRA 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71989247   349 AKQQIPDMQLSVIDANSNGRGTRHVKSFVDQGYNVKYVTMKGASWASLASGVLILGCSAIFANGAVAARKGALAVVLCAN 428
Cdd:pfam01008 127 AHKEGKRFRVIVTESRPRLQGRLTAKELVQAGIPVTLITDSAVGYVMQEVDKVIVGADRILANGGIANKIGTYQLALLAK 206

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71989247   429 HYNIPVIVVAEHFKFIDKGQ---------------VYQRVALLGRQNIECIQ-------SDLVTAVVTDLRILGP 481
Cdd:pfam01008 207 AHNVPFYVVAETYKFDPRFPldedifieerdpeevLYRTGVRIAPPNLKVRNpafdytpPELITLIITEVGVLPP 281
GCD2 COG1184
Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ...
 402-489 8.52e-07

Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440797 [Multi-domain]  Cd Length: 304  Bit Score: 50.62  E-value: 8.52e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71989247 402 ILGCSAIFANGAVAARKGALAVVLCANHYNIPVIVVAEHFKFIDKGqvYQRVAL-------LGRQNIECIQ--------- 465
Cdd:COG1184 191 VVGADTITADGAVVNKIGTSPLALAAREAGVPVTVAAETYKFSPET--FELVEIeerdpseVYDEEPEGVTvrnpafdvt 268

                        90       100
                ....*....|....*....|....*
gi 71989247 466 -SDLVTAVVTDLRILGPTSAPAVLK 489
Cdd:COG1184 269 pPDLIDAIITERGVLPPEAIYTVIR 293
PRK08535 PRK08535
ribose 1,5-bisphosphate isomerase;
402-443 7.47e-03

ribose 1,5-bisphosphate isomerase;


Pssm-ID: 236282 [Multi-domain]  Cd Length: 310  Bit Score: 38.34  E-value: 7.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 71989247  402 ILGCSAIFANGAVAARKGALAVVLCANHYNIPVIVVAEHFKF 443
Cdd:PRK08535 193 VVGADAITANGAVINKIGTSQIALAAHEARVPFMVAAETYKF 234
 
Name Accession Description Interval E-value
IF-2B pfam01008
Initiation factor 2 subunit family; This family includes initiation factor 2B alpha, beta and ...
 269-481 5.02e-13

Initiation factor 2 subunit family; This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterized as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The crystal structure of Ypr118w, a non-essential, low-copy number gene product from Saccharomyces cerevisiae, reveals a dimeric protein with two domains and a putative active site cleft.


Pssm-ID: 395798 [Multi-domain]  Cd Length: 281  Bit Score: 69.24  E-value: 5.02e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71989247   269 PLPFALGNTVRLLKRTIKRLEESTNMKCEEELQVYLEDTLAINFCHAYKAISQLLVRKIQQFKKVVVFDWCPVVNHVLLE 348
Cdd:pfam01008  47 PTAVSLGNAIDRLLRIVLALHSSSDVEEAKESLIEAADEFIDEIEEARRKIGAIAAELIKDGDTILTHCNSGTVLGVLRA 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71989247   349 AKQQIPDMQLSVIDANSNGRGTRHVKSFVDQGYNVKYVTMKGASWASLASGVLILGCSAIFANGAVAARKGALAVVLCAN 428
Cdd:pfam01008 127 AHKEGKRFRVIVTESRPRLQGRLTAKELVQAGIPVTLITDSAVGYVMQEVDKVIVGADRILANGGIANKIGTYQLALLAK 206

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 71989247   429 HYNIPVIVVAEHFKFIDKGQ---------------VYQRVALLGRQNIECIQ-------SDLVTAVVTDLRILGP 481
Cdd:pfam01008 207 AHNVPFYVVAETYKFDPRFPldedifieerdpeevLYRTGVRIAPPNLKVRNpafdytpPELITLIITEVGVLPP 281
GCD2 COG1184
Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ...
 402-489 8.52e-07

Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]; Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family is part of the Pathway/BioSystem: Translation factors


Pssm-ID: 440797 [Multi-domain]  Cd Length: 304  Bit Score: 50.62  E-value: 8.52e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 71989247 402 ILGCSAIFANGAVAARKGALAVVLCANHYNIPVIVVAEHFKFIDKGqvYQRVAL-------LGRQNIECIQ--------- 465
Cdd:COG1184 191 VVGADTITADGAVVNKIGTSPLALAAREAGVPVTVAAETYKFSPET--FELVEIeerdpseVYDEEPEGVTvrnpafdvt 268

                        90       100
                ....*....|....*....|....*
gi 71989247 466 -SDLVTAVVTDLRILGPTSAPAVLK 489
Cdd:COG1184 269 pPDLIDAIITERGVLPPEAIYTVIR 293
PRK08535 PRK08535
ribose 1,5-bisphosphate isomerase;
402-443 7.47e-03

ribose 1,5-bisphosphate isomerase;


Pssm-ID: 236282 [Multi-domain]  Cd Length: 310  Bit Score: 38.34  E-value: 7.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 71989247  402 ILGCSAIFANGAVAARKGALAVVLCANHYNIPVIVVAEHFKF 443
Cdd:PRK08535 193 VVGADAITANGAVINKIGTSQIALAAHEARVPFMVAAETYKF 234
 
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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