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Conserved domains on  [gi|970414598|ref|NP_001305083|]
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probable JmjC domain-containing histone demethylation protein 2C isoform c [Homo sapiens]

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

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 ...
2200-2299 1.62e-11

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: 63.09  E-value: 1.62e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  2200 DSSEIPGALWHIYAGKDVDKIREFLQKISKEQGLEVLPEHDPIRDQSWYVNKKLRQRLLEEyGVRTCTLIQFLGDAIVLP 2279
Cdd:pfam02373   16 EDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGEQPDDLLHLNTIISPKQLREN-GIPVYRFVQKPGEFVFTF 94
                           90       100
                   ....*....|....*....|
gi 970414598  2280 AGALHQVQNFHSCIQVTEDF 2299
Cdd:pfam02373   95 PGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
2096-2168 1.19e-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: 44.55  E-value: 1.19e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 970414598   2096 YEDLLKSLPLpeycnpegKFNLASHLPGFFVRPDLGPRLcsAYGVVaakdhdIGTTNLHIEVSDVVNILVYVG 2168
Cdd:smart00558    1 QLWNLAKLPF--------KLNLLSDLPEDIPGPDVGPYL--YMGMA------GSTTPWHIDDYDLVNYLHQGA 57
PTZ00121 super family cl31754
MAEBL; Provisional
125-490 2.11e-04

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.06  E-value: 2.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  125 RSIRPNKRKGSDSSIPDEEKMKEEKydyISRGENPKGKNKHLmnkrrKPEEDEKKLNMKRLRTDNVSDFSESSDSENSNK 204
Cdd:PTZ00121 1587 KKAEEARIEEVMKLYEEEKKMKAEE---AKKAEEAKIKAEEL-----KKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEE 1658
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  205 RIIDNSSEQKPENELKNKNTskingEEGKPHNNEKAGEETLKNSQPPWDQIQEDKKHEEAEKRKSVDTQLQEDMIIHSSE 284
Cdd:PTZ00121 1659 NKIKAAEEAKKAEEDKKKAE-----EAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAE 1733
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  285 QSTVSDH----NSNDLLPQECNMDKTHTMELLPKEKFVSRPPTPKCVI-------DITNDTNLEKVAQENSSTFG--LQT 351
Cdd:PTZ00121 1734 EAKKEAEedkkKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIeeeldeeDEKRRMEVDKKIKDIFDNFAniIEG 1813
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  352 LQKMDPNVSDSKHSIANAkFLETAKKDSDQSWVSDVVKVDLTQSSVTNASSGNDHLNMEKEKYvsyisplsavsVMEDKL 431
Cdd:PTZ00121 1814 GKEGNLVINDSKEMEDSA-IKEVADSKNMQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKD-----------LKEDDE 1881
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 970414598  432 HkrspppETIKSKLNTSVDTHKIKSSPSPEVVKPKITHSPDSVKSKATYVNSQATGERR 490
Cdd:PTZ00121 1882 E------EIEEADEIEKIDKDDIEREIPNNNMAGKNNDIIDDKLDKDEYIKRDAEETRE 1934
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
2200-2299 1.62e-11

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: 63.09  E-value: 1.62e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  2200 DSSEIPGALWHIYAGKDVDKIREFLQKISKEQGLEVLPEHDPIRDQSWYVNKKLRQRLLEEyGVRTCTLIQFLGDAIVLP 2279
Cdd:pfam02373   16 EDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGEQPDDLLHLNTIISPKQLREN-GIPVYRFVQKPGEFVFTF 94
                           90       100
                   ....*....|....*....|
gi 970414598  2280 AGALHQVQNFHSCIQVTEDF 2299
Cdd:pfam02373   95 PGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
2096-2168 1.19e-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: 44.55  E-value: 1.19e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 970414598   2096 YEDLLKSLPLpeycnpegKFNLASHLPGFFVRPDLGPRLcsAYGVVaakdhdIGTTNLHIEVSDVVNILVYVG 2168
Cdd:smart00558    1 QLWNLAKLPF--------KLNLLSDLPEDIPGPDVGPYL--YMGMA------GSTTPWHIDDYDLVNYLHQGA 57
PTZ00121 PTZ00121
MAEBL; Provisional
125-490 2.11e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.06  E-value: 2.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  125 RSIRPNKRKGSDSSIPDEEKMKEEKydyISRGENPKGKNKHLmnkrrKPEEDEKKLNMKRLRTDNVSDFSESSDSENSNK 204
Cdd:PTZ00121 1587 KKAEEARIEEVMKLYEEEKKMKAEE---AKKAEEAKIKAEEL-----KKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEE 1658
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  205 RIIDNSSEQKPENELKNKNTskingEEGKPHNNEKAGEETLKNSQPPWDQIQEDKKHEEAEKRKSVDTQLQEDMIIHSSE 284
Cdd:PTZ00121 1659 NKIKAAEEAKKAEEDKKKAE-----EAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAE 1733
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  285 QSTVSDH----NSNDLLPQECNMDKTHTMELLPKEKFVSRPPTPKCVI-------DITNDTNLEKVAQENSSTFG--LQT 351
Cdd:PTZ00121 1734 EAKKEAEedkkKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIeeeldeeDEKRRMEVDKKIKDIFDNFAniIEG 1813
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  352 LQKMDPNVSDSKHSIANAkFLETAKKDSDQSWVSDVVKVDLTQSSVTNASSGNDHLNMEKEKYvsyisplsavsVMEDKL 431
Cdd:PTZ00121 1814 GKEGNLVINDSKEMEDSA-IKEVADSKNMQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKD-----------LKEDDE 1881
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 970414598  432 HkrspppETIKSKLNTSVDTHKIKSSPSPEVVKPKITHSPDSVKSKATYVNSQATGERR 490
Cdd:PTZ00121 1882 E------EIEEADEIEKIDKDDIEREIPNNNMAGKNNDIIDDKLDKDEYIKRDAEETRE 1934
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
2200-2299 1.62e-11

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: 63.09  E-value: 1.62e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  2200 DSSEIPGALWHIYAGKDVDKIREFLQKISKEQGLEVLPEHDPIRDQSWYVNKKLRQRLLEEyGVRTCTLIQFLGDAIVLP 2279
Cdd:pfam02373   16 EDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFGGEQPDDLLHLNTIISPKQLREN-GIPVYRFVQKPGEFVFTF 94
                           90       100
                   ....*....|....*....|
gi 970414598  2280 AGALHQVQNFHSCIQVTEDF 2299
Cdd:pfam02373   95 PGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
2096-2168 1.19e-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: 44.55  E-value: 1.19e-05
                            10        20        30        40        50        60        70
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 970414598   2096 YEDLLKSLPLpeycnpegKFNLASHLPGFFVRPDLGPRLcsAYGVVaakdhdIGTTNLHIEVSDVVNILVYVG 2168
Cdd:smart00558    1 QLWNLAKLPF--------KLNLLSDLPEDIPGPDVGPYL--YMGMA------GSTTPWHIDDYDLVNYLHQGA 57
PTZ00121 PTZ00121
MAEBL; Provisional
125-490 2.11e-04

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 47.06  E-value: 2.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  125 RSIRPNKRKGSDSSIPDEEKMKEEKydyISRGENPKGKNKHLmnkrrKPEEDEKKLNMKRLRTDNVSDFSESSDSENSNK 204
Cdd:PTZ00121 1587 KKAEEARIEEVMKLYEEEKKMKAEE---AKKAEEAKIKAEEL-----KKAEEEKKKVEQLKKKEAEEKKKAEELKKAEEE 1658
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  205 RIIDNSSEQKPENELKNKNTskingEEGKPHNNEKAGEETLKNSQPPWDQIQEDKKHEEAEKRKSVDTQLQEDMIIHSSE 284
Cdd:PTZ00121 1659 NKIKAAEEAKKAEEDKKKAE-----EAKKAEEDEKKAAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAE 1733
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  285 QSTVSDH----NSNDLLPQECNMDKTHTMELLPKEKFVSRPPTPKCVI-------DITNDTNLEKVAQENSSTFG--LQT 351
Cdd:PTZ00121 1734 EAKKEAEedkkKAEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIeeeldeeDEKRRMEVDKKIKDIFDNFAniIEG 1813
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970414598  352 LQKMDPNVSDSKHSIANAkFLETAKKDSDQSWVSDVVKVDLTQSSVTNASSGNDHLNMEKEKYvsyisplsavsVMEDKL 431
Cdd:PTZ00121 1814 GKEGNLVINDSKEMEDSA-IKEVADSKNMQLEEADAFEKHKFNKNNENGEDGNKEADFNKEKD-----------LKEDDE 1881
                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 970414598  432 HkrspppETIKSKLNTSVDTHKIKSSPSPEVVKPKITHSPDSVKSKATYVNSQATGERR 490
Cdd:PTZ00121 1882 E------EIEEADEIEKIDKDDIEREIPNNNMAGKNNDIIDDKLDKDEYIKRDAEETRE 1934
 
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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