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Conserved domains on  [gi|1958744847|ref|XP_038953206|]
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lysine-specific demethylase 3B isoform X2 [Rattus norvegicus]

Protein Classification

lysine-specific demethylase( domain architecture ID 16112604)

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 ...
 1400-1505 2.17e-20

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: 88.12  E-value: 2.17e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958744847 1400 TKQRIHDGKEKPG-ALWHIYAAKDAEKIRELLRKVGEEqGQENP-PDHDPIHDQSWYLDQILRKRLfEEYGVQGWAIVQF 1477
Cdd:pfam02373    9 STTPWHIEDQGLYsINYLHFGAPKVWYIIPPEYAEKFE-KVLSDhFGGEQPDDLLHLNTIISPKQL-RENGIPVYRFVQK 86

                           90       100
                   ....*....|....*....|....*...
gi 1958744847 1478 LGDAVFIPAGAPHQVHNLYSCIKVAEDF 1505
Cdd:pfam02373   87 PGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 1303-1375 5.34e-05

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: 42.24  E-value: 5.34e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958744847  1303 FEDLMENLPLpeytkrdgRLNLASRLPSYFVRPDLGPKMYnaYGLItaedrrVGTTNLHLDVSDAVNVMVYVG 1375
Cdd:smart00558    1 QLWNLAKLPF--------KLNLLSDLPEDIPGPDVGPYLY--MGMA------GSTTPWHIDDYDLVNYLHQGA 57
PRK11901 super family cl36081
hypothetical protein; Reviewed
 473-558 6.33e-03

hypothetical protein; Reviewed


The actual alignment was detected with superfamily member PRK11901:

Pssm-ID: 237015 [Multi-domain]  Cd Length: 327  Bit Score: 40.44  E-value: 6.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958744847  473 PSWPESHSSADSASLAKKkplfITTDSSKLVSGvlGSALSTGGPSLSAMGNGRSSSPTSSLTQPIEMPTLSSSPTEERPT 552
Cdd:PRK11901    61 PTEHESQQSSNNAGAEKN----IDLSGSSSLSS--GNQSSPSAANNTSDGHDASGVKNTAPPQDISAPPISPTPTQAAPP 134


                   ....*..
gi 1958744847  553 VGP-GQQ 558
Cdd:PRK11901   135 QTPnGQQ 141
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 1400-1505 2.17e-20

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: 88.12  E-value: 2.17e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958744847 1400 TKQRIHDGKEKPG-ALWHIYAAKDAEKIRELLRKVGEEqGQENP-PDHDPIHDQSWYLDQILRKRLfEEYGVQGWAIVQF 1477
Cdd:pfam02373    9 STTPWHIEDQGLYsINYLHFGAPKVWYIIPPEYAEKFE-KVLSDhFGGEQPDDLLHLNTIISPKQL-RENGIPVYRFVQK 86

                           90       100
                   ....*....|....*....|....*...
gi 1958744847 1478 LGDAVFIPAGAPHQVHNLYSCIKVAEDF 1505
Cdd:pfam02373   87 PGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
cupin_Bh2720-like cd02223
Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, ...
 1432-1497 2.56e-05

Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, archaeal, and eukaryotic proteins similar to Bh2720, a Bacillus halodurans protein of unknown function with a cupin beta-barrel fold.


Pssm-ID: 380352 [Multi-domain]  Cd Length: 98  Bit Score: 44.46  E-value: 2.56e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958744847 1432 KVGEEQGQEnppdhdpIHDQSwylDQILRkrlFEEyGvQGWAIV---QFL---GDAVFIPAGAPHQVHN-------LYS 1497
Cdd:cd02223     19 PPGEDIGLE-------VHDDV---DQFLR---IEE-G-EGKAIMggfESEvkdGDAIIVPAGTWHNVINtgneplkLYT 82
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 1303-1375 5.34e-05

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: 42.24  E-value: 5.34e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958744847  1303 FEDLMENLPLpeytkrdgRLNLASRLPSYFVRPDLGPKMYnaYGLItaedrrVGTTNLHLDVSDAVNVMVYVG 1375
Cdd:smart00558    1 QLWNLAKLPF--------KLNLLSDLPEDIPGPDVGPYLY--MGMA------GSTTPWHIDDYDLVNYLHQGA 57
PRK11901 PRK11901
hypothetical protein; Reviewed
 473-558 6.33e-03

hypothetical protein; Reviewed


Pssm-ID: 237015 [Multi-domain]  Cd Length: 327  Bit Score: 40.44  E-value: 6.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958744847  473 PSWPESHSSADSASLAKKkplfITTDSSKLVSGvlGSALSTGGPSLSAMGNGRSSSPTSSLTQPIEMPTLSSSPTEERPT 552
Cdd:PRK11901    61 PTEHESQQSSNNAGAEKN----IDLSGSSSLSS--GNQSSPSAANNTSDGHDASGVKNTAPPQDISAPPISPTPTQAAPP 134


                   ....*..
gi 1958744847  553 VGP-GQQ 558
Cdd:PRK11901   135 QTPnGQQ 141
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 1400-1505 2.17e-20

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: 88.12  E-value: 2.17e-20
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958744847 1400 TKQRIHDGKEKPG-ALWHIYAAKDAEKIRELLRKVGEEqGQENP-PDHDPIHDQSWYLDQILRKRLfEEYGVQGWAIVQF 1477
Cdd:pfam02373    9 STTPWHIEDQGLYsINYLHFGAPKVWYIIPPEYAEKFE-KVLSDhFGGEQPDDLLHLNTIISPKQL-RENGIPVYRFVQK 86

                           90       100
                   ....*....|....*....|....*...
gi 1958744847 1478 LGDAVFIPAGAPHQVHNLYSCIKVAEDF 1505
Cdd:pfam02373   87 PGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
cupin_Bh2720-like cd02223
Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, ...
 1432-1497 2.56e-05

Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, archaeal, and eukaryotic proteins similar to Bh2720, a Bacillus halodurans protein of unknown function with a cupin beta-barrel fold.


Pssm-ID: 380352 [Multi-domain]  Cd Length: 98  Bit Score: 44.46  E-value: 2.56e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958744847 1432 KVGEEQGQEnppdhdpIHDQSwylDQILRkrlFEEyGvQGWAIV---QFL---GDAVFIPAGAPHQVHN-------LYS 1497
Cdd:cd02223     19 PPGEDIGLE-------VHDDV---DQFLR---IEE-G-EGKAIMggfESEvkdGDAIIVPAGTWHNVINtgneplkLYT 82
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 1303-1375 5.34e-05

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: 42.24  E-value: 5.34e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958744847  1303 FEDLMENLPLpeytkrdgRLNLASRLPSYFVRPDLGPKMYnaYGLItaedrrVGTTNLHLDVSDAVNVMVYVG 1375
Cdd:smart00558    1 QLWNLAKLPF--------KLNLLSDLPEDIPGPDVGPYLY--MGMA------GSTTPWHIDDYDLVNYLHQGA 57
PRK11901 PRK11901
hypothetical protein; Reviewed
 473-558 6.33e-03

hypothetical protein; Reviewed


Pssm-ID: 237015 [Multi-domain]  Cd Length: 327  Bit Score: 40.44  E-value: 6.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958744847  473 PSWPESHSSADSASLAKKkplfITTDSSKLVSGvlGSALSTGGPSLSAMGNGRSSSPTSSLTQPIEMPTLSSSPTEERPT 552
Cdd:PRK11901    61 PTEHESQQSSNNAGAEKN----IDLSGSSSLSS--GNQSSPSAANNTSDGHDASGVKNTAPPQDISAPPISPTPTQAAPP 134


                   ....*..
gi 1958744847  553 VGP-GQQ 558
Cdd:PRK11901   135 QTPnGQQ 141
 
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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