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Conserved domains on  [gi|1958656963|ref|XP_038941317|]
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2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform X1 [Rattus norvegicus]

Protein Classification

cupin domain-containing protein( domain architecture ID 1562428)

cupin domain-containing protein, part of a functionally diverse superfamily with the active site generally located at the center of a conserved domain forming a beta-barrel fold

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Cupin_8 super family cl46322
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
43-276 1.06e-15

Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.


The actual alignment was detected with superfamily member pfam13621:

Pssm-ID: 463936  Cd Length: 251  Bit Score: 76.25  E-value: 1.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963  43 ADFVKGFLLPNLPCVFSSAfTEGWGSRRRWVTSEGkpdFEYLLQKYGDAVVPVA-----NCGVREYNS-----NPKEH-M 111
Cdd:pfam13621   2 AEFFREYVAKNKPVVIRGA-VKDWPAVQKWTDSSL---LDYLKDKYGDVEVTVEvtpdgRADRLFYNDdftfvNPKEErM 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963 112 PFRDYIsywkEYIQGGYSSPRGC-LYLKDwhLCRDSLVDDLEDIFTLPvyFSSDWLNEFWDVLNV-------------DD 177
Cdd:pfam13621  78 PFGEFL----DRLEAGEDTDTAPyAYLQS--DNLRSEFPELLEDNDLP--FATEAFGGEPDAVNLwmgngrsvtslhyDH 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963 178 YRFVYagpkgtcwsVNICGKKKWLFFPPGQEEAL--RDCRGNLPYDVTST---ELLDTHLYPRIQQDSLPIEVIQEPGEM 252
Cdd:pfam13621 150 YENLY---------CVVRGRKRFTLFPPSDVPNLypGPLEPTPEGQVFSLvdpLAPDFERFPRFRDAARPLVVTLNPGDV 220
                         250       260
                  ....*....|....*....|....*
gi 1958656963 253 VFVPSGWHHQVYNLED-TISINHNW 276
Cdd:pfam13621 221 LYLPALWWHHVESLDPfNIAVNYWY 245
 
Name Accession Description Interval E-value
Cupin_8 pfam13621
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
43-276 1.06e-15

Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.


Pssm-ID: 463936  Cd Length: 251  Bit Score: 76.25  E-value: 1.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963  43 ADFVKGFLLPNLPCVFSSAfTEGWGSRRRWVTSEGkpdFEYLLQKYGDAVVPVA-----NCGVREYNS-----NPKEH-M 111
Cdd:pfam13621   2 AEFFREYVAKNKPVVIRGA-VKDWPAVQKWTDSSL---LDYLKDKYGDVEVTVEvtpdgRADRLFYNDdftfvNPKEErM 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963 112 PFRDYIsywkEYIQGGYSSPRGC-LYLKDwhLCRDSLVDDLEDIFTLPvyFSSDWLNEFWDVLNV-------------DD 177
Cdd:pfam13621  78 PFGEFL----DRLEAGEDTDTAPyAYLQS--DNLRSEFPELLEDNDLP--FATEAFGGEPDAVNLwmgngrsvtslhyDH 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963 178 YRFVYagpkgtcwsVNICGKKKWLFFPPGQEEAL--RDCRGNLPYDVTST---ELLDTHLYPRIQQDSLPIEVIQEPGEM 252
Cdd:pfam13621 150 YENLY---------CVVRGRKRFTLFPPSDVPNLypGPLEPTPEGQVFSLvdpLAPDFERFPRFRDAARPLVVTLNPGDV 220
                         250       260
                  ....*....|....*....|....*
gi 1958656963 253 VFVPSGWHHQVYNLED-TISINHNW 276
Cdd:pfam13621 221 LYLPALWWHHVESLDPfNIAVNYWY 245
 
Name Accession Description Interval E-value
Cupin_8 pfam13621
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
43-276 1.06e-15

Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.


Pssm-ID: 463936  Cd Length: 251  Bit Score: 76.25  E-value: 1.06e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963  43 ADFVKGFLLPNLPCVFSSAfTEGWGSRRRWVTSEGkpdFEYLLQKYGDAVVPVA-----NCGVREYNS-----NPKEH-M 111
Cdd:pfam13621   2 AEFFREYVAKNKPVVIRGA-VKDWPAVQKWTDSSL---LDYLKDKYGDVEVTVEvtpdgRADRLFYNDdftfvNPKEErM 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963 112 PFRDYIsywkEYIQGGYSSPRGC-LYLKDwhLCRDSLVDDLEDIFTLPvyFSSDWLNEFWDVLNV-------------DD 177
Cdd:pfam13621  78 PFGEFL----DRLEAGEDTDTAPyAYLQS--DNLRSEFPELLEDNDLP--FATEAFGGEPDAVNLwmgngrsvtslhyDH 149
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963 178 YRFVYagpkgtcwsVNICGKKKWLFFPPGQEEAL--RDCRGNLPYDVTST---ELLDTHLYPRIQQDSLPIEVIQEPGEM 252
Cdd:pfam13621 150 YENLY---------CVVRGRKRFTLFPPSDVPNLypGPLEPTPEGQVFSLvdpLAPDFERFPRFRDAARPLVVTLNPGDV 220
                         250       260
                  ....*....|....*....|....*
gi 1958656963 253 VFVPSGWHHQVYNLED-TISINHNW 276
Cdd:pfam13621 221 LYLPALWWHHVESLDPfNIAVNYWY 245
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
180-276 3.51e-14

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 68.48  E-value: 3.51e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958656963 180 FVYAGPKGTC-------------WSVNICGKKKWLFFPPGQEEAL-RDCRGNLPYDVTSTELLDTHLYPRIQQDSLPIEV 245
Cdd:pfam02373   1 WLYLGMPFSTtpwhiedqglysiNYLHFGAPKVWYIIPPEYAEKFeKVLSDHFGGEQPDDLLHLNTIISPKQLRENGIPV 80
                          90       100       110
                  ....*....|....*....|....*....|....
gi 1958656963 246 I---QEPGEMVFVPSGWHHQVYNLEDTISINHNW 276
Cdd:pfam02373  81 YrfvQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
 
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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