NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1625649091|ref|NP_001357023|]
View 

lysine-specific demethylase 4B isoform 3 [Homo sapiens]

Protein Classification

JmjN and JmjC domain-containing protein( domain architecture ID 10650725)

JmjN and JmjC domain-containing protein

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 ...
 176-292 1.66e-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: 171.33  E-value: 1.66e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1625649091 176 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFpgsSQGCDAFLRHKMTLISPIILKKYG 255
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1625649091 256 IPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 292
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 15-56 2.53e-15

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: 69.60  E-value: 2.53e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1625649091   15 IMTFRPTMEEFKDFNKYVAYIESQgAHRAGLAKIIPPKEWKP 56
Cdd:smart00545   2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 176-292 1.66e-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: 171.33  E-value: 1.66e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1625649091 176 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFpgsSQGCDAFLRHKMTLISPIILKKYG 255
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1625649091 256 IPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 292
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 15-56 2.53e-15

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: 69.60  E-value: 2.53e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1625649091   15 IMTFRPTMEEFKDFNKYVAYIESQgAHRAGLAKIIPPKEWKP 56
Cdd:smart00545   2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
JmjN pfam02375
jmjN domain;
16-50 3.89e-13

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 63.08  E-value: 3.89e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1625649091  16 MTFRPTMEEFKDFNKYVAYIESQGAhRAGLAKIIP 50
Cdd:pfam02375   1 PVFYPTEEEFKDPLKYIEKIRPLGE-KYGICKIVP 34
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 149-206 3.41e-12

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: 61.11  E-value: 3.41e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1625649091  149 WNIGSLRTILDMVeRECGTIIEGVNT-PYLYFGMWKTTFAWHTEDMDLysINYLHFGEP 206
Cdd:smart00558   3 WNLAKLPFKLNLL-SDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 176-292 1.66e-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: 171.33  E-value: 1.66e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1625649091 176 YLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAIGFFpgsSQGCDAFLRHKMTLISPIILKKYG 255
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1625649091 256 IPFSRITQEAGEFMITFPYGYHAGFNHGFNCAESTNF 292
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 15-56 2.53e-15

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: 69.60  E-value: 2.53e-15
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 1625649091   15 IMTFRPTMEEFKDFNKYVAYIESQgAHRAGLAKIIPPKEWKP 56
Cdd:smart00545   2 IPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
JmjN pfam02375
jmjN domain;
16-50 3.89e-13

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 63.08  E-value: 3.89e-13
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1625649091  16 MTFRPTMEEFKDFNKYVAYIESQGAhRAGLAKIIP 50
Cdd:pfam02375   1 PVFYPTEEEFKDPLKYIEKIRPLGE-KYGICKIVP 34
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 149-206 3.41e-12

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: 61.11  E-value: 3.41e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1625649091  149 WNIGSLRTILDMVeRECGTIIEGVNT-PYLYFGMWKTTFAWHTEDMDLysINYLHFGEP 206
Cdd:smart00558   3 WNLAKLPFKLNLL-SDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH