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Conserved domains on  [gi|2756281847|ref|XP_066160270|]
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lysine-specific demethylase JMJ29 isoform X3 [Oryza sativa Japonica Group]

Protein Classification

lysine-specific demethylase( domain architecture ID 15468173)

lysine-specific demethylase is a jumonji C domain-containing (JMJD) family histone demethylase demethylates specific residues of histone, similar to human lysine-specific demethylases 3A and 3B that specifically demethylate 'Lys-9' of histone H3, thereby playing a central role in the histone code

CATH:  2.60.120.10
EC:  1.14.11.-
Gene Ontology:  GO:0046872|GO:0141052|GO:0006355
PubMed:  25372754|37832177|35558079|19478949|14697267
SCOP:  3001825

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
cupin_RmlC-like super family cl40423
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 773-873 2.42e-15

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


The actual alignment was detected with superfamily member pfam02373:

Pssm-ID: 477354  Cd Length: 114  Bit Score: 72.72  E-value: 2.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2756281847 773 NKGGALWDIFRREDVPKLKLYLDKHSKEfrhiycsavqKVCNPV------HDETFYLTEEHkRKLKEEHGIEPWTFVQKL 846
Cdd:pfam02373  19 GLYSINYLHFGAPKVWYIIPPEYAEKFE----------KVLSDHfggeqpDDLLHLNTIIS-PKQLRENGIPVYRFVQKP 87

                          90       100
                  ....*....|....*....|....*..
gi 2756281847 847 GEAVFIPAGCPHQVRNLKSCTKIALDF 873
Cdd:pfam02373  88 GEFVFTFPGWYHQVFNLGFNIAEAVNF 114
zf-4CXXC_R1 super family cl20401
Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor ...
 168-226 1.74e-07

Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type.


The actual alignment was detected with superfamily member pfam10497:

Pssm-ID: 463117  Cd Length: 99  Bit Score: 49.95  E-value: 1.74e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2756281847 168 SCHQCKRVKPRPEEMVRCQLCGDK--VFCAACIKNKYPE-MQQAEVRD--KCPFCRNICNCTRC 226
Cdd:pfam10497   8 TCHQCRQKTLDTKTSCRNSQCKGVrgQFCGDCLRNRYGEnVEEALANPdwICPKCRGICNCSFC 71
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 648-717 2.32e-03

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


:

Pssm-ID: 214721  Cd Length: 58  Bit Score: 37.23  E-value: 2.32e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2756281847  648 MNSLPFqpytnlksgLLNVSTLLPDDILKLDMGPKSYIaygyaqelGRGDSVTKLHCDLSDAVNVLMHTA 717
Cdd:smart00558   5 LAKLPF---------KLNLLSDLPEDIPGPDVGPYLYM--------GMAGSTTPWHIDDYDLVNYLHQGA 57
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 773-873 2.42e-15

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: 72.72  E-value: 2.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2756281847 773 NKGGALWDIFRREDVPKLKLYLDKHSKEfrhiycsavqKVCNPV------HDETFYLTEEHkRKLKEEHGIEPWTFVQKL 846
Cdd:pfam02373  19 GLYSINYLHFGAPKVWYIIPPEYAEKFE----------KVLSDHfggeqpDDLLHLNTIIS-PKQLRENGIPVYRFVQKP 87

                          90       100
                  ....*....|....*....|....*..
gi 2756281847 847 GEAVFIPAGCPHQVRNLKSCTKIALDF 873
Cdd:pfam02373  88 GEFVFTFPGWYHQVFNLGFNIAEAVNF 114
zf-4CXXC_R1 pfam10497
Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor ...
 168-226 1.74e-07

Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type.


Pssm-ID: 463117  Cd Length: 99  Bit Score: 49.95  E-value: 1.74e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2756281847 168 SCHQCKRVKPRPEEMVRCQLCGDK--VFCAACIKNKYPE-MQQAEVRD--KCPFCRNICNCTRC 226
Cdd:pfam10497   8 TCHQCRQKTLDTKTSCRNSQCKGVrgQFCGDCLRNRYGEnVEEALANPdwICPKCRGICNCSFC 71
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 648-717 2.32e-03

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 37.23  E-value: 2.32e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2756281847  648 MNSLPFqpytnlksgLLNVSTLLPDDILKLDMGPKSYIaygyaqelGRGDSVTKLHCDLSDAVNVLMHTA 717
Cdd:smart00558   5 LAKLPF---------KLNLLSDLPEDIPGPDVGPYLYM--------GMAGSTTPWHIDDYDLVNYLHQGA 57
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
817-877 6.80e-03

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 37.14  E-value: 6.80e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2756281847 817 HDETFYLTEEhkrKLKEEHGIEPWTFVQklGEAVFIPAGCPHQVRNLKSCTKIALDFVSPE 877
Cdd:COG1917    43 GEELIYVLEG---EGEVEVGGEEYELKP--GDVVFIPPGVPHAFRNLGDEPAVLLVVFSPG 98
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 773-873 2.42e-15

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: 72.72  E-value: 2.42e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2756281847 773 NKGGALWDIFRREDVPKLKLYLDKHSKEfrhiycsavqKVCNPV------HDETFYLTEEHkRKLKEEHGIEPWTFVQKL 846
Cdd:pfam02373  19 GLYSINYLHFGAPKVWYIIPPEYAEKFE----------KVLSDHfggeqpDDLLHLNTIIS-PKQLRENGIPVYRFVQKP 87

                          90       100
                  ....*....|....*....|....*..
gi 2756281847 847 GEAVFIPAGCPHQVRNLKSCTKIALDF 873
Cdd:pfam02373  88 GEFVFTFPGWYHQVFNLGFNIAEAVNF 114
zf-4CXXC_R1 pfam10497
Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor ...
 168-226 1.74e-07

Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type.


Pssm-ID: 463117  Cd Length: 99  Bit Score: 49.95  E-value: 1.74e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2756281847 168 SCHQCKRVKPRPEEMVRCQLCGDK--VFCAACIKNKYPE-MQQAEVRD--KCPFCRNICNCTRC 226
Cdd:pfam10497   8 TCHQCRQKTLDTKTSCRNSQCKGVrgQFCGDCLRNRYGEnVEEALANPdwICPKCRGICNCSFC 71
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 648-717 2.32e-03

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 37.23  E-value: 2.32e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2756281847  648 MNSLPFqpytnlksgLLNVSTLLPDDILKLDMGPKSYIaygyaqelGRGDSVTKLHCDLSDAVNVLMHTA 717
Cdd:smart00558   5 LAKLPF---------KLNLLSDLPEDIPGPDVGPYLYM--------GMAGSTTPWHIDDYDLVNYLHQGA 57
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
817-877 6.80e-03

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 37.14  E-value: 6.80e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2756281847 817 HDETFYLTEEhkrKLKEEHGIEPWTFVQklGEAVFIPAGCPHQVRNLKSCTKIALDFVSPE 877
Cdd:COG1917    43 GEELIYVLEG---EGEVEVGGEEYELKP--GDVVFIPPGVPHAFRNLGDEPAVLLVVFSPG 98
 
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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