NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958659989|ref|XP_038942400|]
View 

lysine-specific demethylase 6B isoform X1 [Rattus norvegicus]

Protein Classification

lysine-specific demethylase( domain architecture ID 10651274)

lysine-specific demethylase is a jumonji C domain-containing (JMJD) family histone demethylase demethylates specific residues of histone, similar to Nakaseomyces glabratus JmjC domain-containing histone demethylation protein 1 hat specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in the histone code

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 1370-1478 8.81e-37

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: 134.73  E-value: 8.81e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659989 1370 QLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHG-------VDYLTGSWWPILddLYASNI 1442
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFggeqpddLLHLNTIISPKQ--LRENGI 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958659989 1443 PVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNV 1478
Cdd:pfam02373   79 PVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 1336-1400 9.05e-08

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: 50.33  E-value: 9.05e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958659989  1336 QLQELLKLPafmrvtSTGNMLSHVGHTILGMNT-VQLYMKVPGSRTPGHQENNNfcSVNINIGPGD 1400
Cdd:smart00558    1 QLWNLAKLP------FKLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYD--LVNYLHQGAG 58
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 90-154 1.40e-03

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 40.56  E-value: 1.40e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958659989   90 LESLHgcvQALLREPAQPVLWEQLGQLYESEHDSEEAICCYHRALRYGGSFAELGPRIGRLQQAQ 154
Cdd:COG4783     58 IVLLH---EALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRAL 119
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 1370-1478 8.81e-37

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: 134.73  E-value: 8.81e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659989 1370 QLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHG-------VDYLTGSWWPILddLYASNI 1442
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFggeqpddLLHLNTIISPKQ--LRENGI 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958659989 1443 PVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNV 1478
Cdd:pfam02373   79 PVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 1336-1400 9.05e-08

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: 50.33  E-value: 9.05e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958659989  1336 QLQELLKLPafmrvtSTGNMLSHVGHTILGMNT-VQLYMKVPGSRTPGHQENNNfcSVNINIGPGD 1400
Cdd:smart00558    1 QLWNLAKLP------FKLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYD--LVNYLHQGAG 58
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 90-154 1.40e-03

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 40.56  E-value: 1.40e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958659989   90 LESLHgcvQALLREPAQPVLWEQLGQLYESEHDSEEAICCYHRALRYGGSFAELGPRIGRLQQAQ 154
Cdd:COG4783     58 IVLLH---EALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRAL 119
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 1370-1478 8.81e-37

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: 134.73  E-value: 8.81e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958659989 1370 QLYMKVPGSRTPGHQENNNFCSVNINIGPGDCEWFAVHEHYWETISAFCDRHG-------VDYLTGSWWPILddLYASNI 1442
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFggeqpddLLHLNTIISPKQ--LRENGI 78

                           90       100       110
                   ....*....|....*....|....*....|....*.
gi 1958659989 1443 PVYRFVQRPGDLVWINAGTVHWVQATGWCNNIAWNV 1478
Cdd:pfam02373   79 PVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 1336-1400 9.05e-08

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: 50.33  E-value: 9.05e-08
                            10        20        30        40        50        60
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958659989  1336 QLQELLKLPafmrvtSTGNMLSHVGHTILGMNT-VQLYMKVPGSRTPGHQENNNfcSVNINIGPGD 1400
Cdd:smart00558    1 QLWNLAKLP------FKLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYD--LVNYLHQGAG 58
BepA COG4783
Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell ...
 90-154 1.40e-03

Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443813 [Multi-domain]  Cd Length: 139  Bit Score: 40.56  E-value: 1.40e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958659989   90 LESLHgcvQALLREPAQPVLWEQLGQLYESEHDSEEAICCYHRALRYGGSFAELGPRIGRLQQAQ 154
Cdd:COG4783     58 IVLLH---EALELDPDEPEARLNLGLALLKAGDYDEALALLEKALKLDPEHPEAYLRLARAYRAL 119
Spy COG3914
Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational ...
 98-154 6.66e-03

Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443119 [Multi-domain]  Cd Length: 658  Bit Score: 41.13  E-value: 6.66e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958659989   98 QALLREPAQPVLWEQLGQLYESEHDSEEAICCYHRALRYGGSFAELGPRIGRLQQAQ 154
Cdd:COG3914    103 RALALNPDNAEALFNLGNLLLALGRLEEALAALRRALALNPDFAEAYLNLGEALRRL 159
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH