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Conserved domains on  [gi|1386813741]
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Chain A, Lysine-specific demethylase 5B,Lysine-specific demethylase 5B

Protein Classification

lysine-specific demethylase family protein( domain architecture ID 10650807)

lysine-specific demethylase family protein is a jumonji C domain-containing (JMJD) protein and may have histone demethylase activity; contains a C5HC2 zinc finger

CATH:  2.60.120.10
EC:  1.14.11.-
Gene Ontology:  GO:0046872|GO:0032452|GO:0006355|GO:0008270
PubMed:  25372754|37832177|35558079|19478949|14697267|17210253|12665246
SCOP:  3001825

Graphical summary

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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 ...
 191-307 4.71e-52

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: 170.94  E-value: 4.71e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813741 191 WLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKklaPELFVSQPDLLHQLVTIMNPNTLMTHE 270
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1386813741 271 VPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNF 307
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 7-48 1.70e-18

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


:

Pssm-ID: 128818  Cd Length: 42  Bit Score: 78.46  E-value: 1.70e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1386813741    7 ECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQP 48
Cdd:smart00545   1 EIPVFYPTMEEFKDPLAYISKIRPQAEKYGICKVVPPKSWKP 42
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
 397-449 1.81e-17

C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.


:

Pssm-ID: 460750  Cd Length: 54  Bit Score: 76.13  E-value: 1.81e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1386813741 397 CVKCKTTCFMSAISCSCKPGLLVCLHHVKELCS-CPPYKYKLRYRYTLDDLYPM 449
Cdd:pfam02928   1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 191-307 4.71e-52

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: 170.94  E-value: 4.71e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813741 191 WLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKklaPELFVSQPDLLHQLVTIMNPNTLMTHE 270
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1386813741 271 VPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNF 307
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 7-48 1.70e-18

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 78.46  E-value: 1.70e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1386813741    7 ECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQP 48
Cdd:smart00545   1 EIPVFYPTMEEFKDPLAYISKIRPQAEKYGICKVVPPKSWKP 42
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
 397-449 1.81e-17

C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.


Pssm-ID: 460750  Cd Length: 54  Bit Score: 76.13  E-value: 1.81e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1386813741 397 CVKCKTTCFMSAISCSCKPGLLVCLHHVKELCS-CPPYKYKLRYRYTLDDLYPM 449
Cdd:pfam02928   1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
JmjN pfam02375
jmjN domain;
9-42 3.60e-14

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 66.16  E-value: 3.60e-14
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1386813741   9 PVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRP 42
Cdd:pfam02375   1 PVFYPTEEEFKDPLKYIEKIRPLGEKYGICKIVP 34
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 164-221 3.03e-13

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: 64.20  E-value: 3.03e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1386813741  164 WNLNNMPvMEQSVLAHITADICGMKL-PWLYVGMCFSSFCWHIEDHwsYSINYLHWGEP 221
Cdd:smart00558   3 WNLAKLP-FKLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDY--DLVNYLHQGAG 58
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 191-307 4.71e-52

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: 170.94  E-value: 4.71e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1386813741 191 WLYVGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKklaPELFVSQPDLLHQLVTIMNPNTLMTHE 270
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLS---DHFGGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1386813741 271 VPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVNF 307
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 7-48 1.70e-18

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 78.46  E-value: 1.70e-18
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1386813741    7 ECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQP 48
Cdd:smart00545   1 EIPVFYPTMEEFKDPLAYISKIRPQAEKYGICKVVPPKSWKP 42
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
 397-449 1.81e-17

C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function.


Pssm-ID: 460750  Cd Length: 54  Bit Score: 76.13  E-value: 1.81e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1386813741 397 CVKCKTTCFMSAISCSCKPGLLVCLHHVKELCS-CPPYKYKLRYRYTLDDLYPM 449
Cdd:pfam02928   1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
JmjN pfam02375
jmjN domain;
9-42 3.60e-14

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 66.16  E-value: 3.60e-14
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1386813741   9 PVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRP 42
Cdd:pfam02375   1 PVFYPTEEEFKDPLKYIEKIRPLGEKYGICKIVP 34
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 164-221 3.03e-13

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: 64.20  E-value: 3.03e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1386813741  164 WNLNNMPvMEQSVLAHITADICGMKL-PWLYVGMCFSSFCWHIEDHwsYSINYLHWGEP 221
Cdd:smart00558   3 WNLAKLP-FKLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDY--DLVNYLHQGAG 58
 
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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