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Conserved domains on  [gi|1063681646|ref|NP_001318955|]
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Transcription factor jumonji (jmj) family protein / zinc finger (C5HC2 type) family protein [Arabidopsis thaliana]

Protein Classification

lysine-specific demethylase; lysine-specific demethylase 5C/5D( domain architecture ID 10493105)

lysine-specific demethylase is a jumonji C domain-containing (JMJD) family histone demethylase, such as Arabidopsis thaliana lysine-specific demethylase ELF6 that demethylates 'Lys-27' (H3K27me) of histone H3, thus acting as a positive regulator of gene expression| lysine-specific demethylase 5C/5D is a jumonji C domain-containing (JMJD) family histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code; belongs to the JARID subfamily

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 ...
 394-510 7.63e-51

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: 174.79  E-value: 7.63e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681646  394 WLYIGMCFSSFCWHVEDHHLYSLNYMHWGAPKLWYGVGGKDAVKLEEAMRKHLpdlFEEQPDLLHKLVTQLSPSKLKTAG 473
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1063681646  474 VPVHRCVQHAGEFVLTFPRAYHAGFNSGFNCAEAVNV 510
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 1038-1132 1.89e-29

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


:

Pssm-ID: 197781  Cd Length: 86  Bit Score: 112.39  E-value: 1.89e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681646  1038 LFMVYLESNPSEVFVHMSPTRCWEMVRERVNQEITKQHkagksDLPPLQPSGSpdGFEMFGYSSPAIVQAIEALDVNRVC 1117
Cdd:smart00542    1 LFRVEIESDPGEVFKGESPEKCWEMVLERVQEARIAAD-----LLQLLPEGVS--GEEMFGLSSPAVVKLIEALPGVHQC 73

                            90
                    ....*....|....*
gi 1063681646  1118 TDYWDSrpYSRPQVQ 1132
Cdd:smart00542   74 TNYWFR--YHRSPLL 86
JmjN pfam02375
jmjN domain;
147-179 2.00e-17

jmjN domain;


:

Pssm-ID: 460542  Cd Length: 34  Bit Score: 76.56  E-value: 2.00e-17
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1063681646  147 PVFYPSEEEFEDTLNYIAKIRPEAEKYGICRIV 179
Cdd:pfam02375    1 PVFYPTEEEFKDPLKYIEKIRPLGEKYGICKIV 33
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
 617-669 1.19e-15

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: 71.89  E-value: 1.19e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1063681646  617 CCICFFDLHLSAAGCRCSPEKYSCLTHVKELCS-CPWVTKYFLFRYDIDELNVL 669
Cdd:pfam02928    1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 988-1032 9.15e-13

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


:

Pssm-ID: 128814  Cd Length: 44  Bit Score: 63.46  E-value: 9.15e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 1063681646   988 GCVLSGKSWCSRRAIFPKGFRSRVKYINILDPTNMCFYiSEILDA 1032
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLY-SCVIDE 44
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 394-510 7.63e-51

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: 174.79  E-value: 7.63e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681646  394 WLYIGMCFSSFCWHVEDHHLYSLNYMHWGAPKLWYGVGGKDAVKLEEAMRKHLpdlFEEQPDLLHKLVTQLSPSKLKTAG 473
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1063681646  474 VPVHRCVQHAGEFVLTFPRAYHAGFNSGFNCAEAVNV 510
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 1038-1132 1.89e-29

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 112.39  E-value: 1.89e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681646  1038 LFMVYLESNPSEVFVHMSPTRCWEMVRERVNQEITKQHkagksDLPPLQPSGSpdGFEMFGYSSPAIVQAIEALDVNRVC 1117
Cdd:smart00542    1 LFRVEIESDPGEVFKGESPEKCWEMVLERVQEARIAAD-----LLQLLPEGVS--GEEMFGLSSPAVVKLIEALPGVHQC 73

                            90
                    ....*....|....*
gi 1063681646  1118 TDYWDSrpYSRPQVQ 1132
Cdd:smart00542   74 TNYWFR--YHRSPLL 86
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 1037-1120 3.21e-26

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 103.07  E-value: 3.21e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681646 1037 PLFMVYLESNPSEVFVHMSPTRCWEMVRERVNQeitKQHKAGKsdlpPLQPSGSPDGFEMFGYSSPAIVQAIEALDVNRV 1116
Cdd:pfam05965    2 PLFRVTVEEDPDESFEGSSPTKCWSMVLERVQE---LRREAGL----KLKLPESISGEDMFGLTHPAVVRLIESLPGAEK 74


                   ....
gi 1063681646 1117 CTDY 1120
Cdd:pfam05965   75 CTNY 78
JmjN pfam02375
jmjN domain;
147-179 2.00e-17

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 76.56  E-value: 2.00e-17
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1063681646  147 PVFYPSEEEFEDTLNYIAKIRPEAEKYGICRIV 179
Cdd:pfam02375    1 PVFYPTEEEFKDPLKYIEKIRPLGEKYGICKIV 33
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 146-179 2.91e-16

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: 73.45  E-value: 2.91e-16
                            10        20        30
                    ....*....|....*....|....*....|....
gi 1063681646   146 APVFYPSEEEFEDTLNYIAKIRPEAEKYGICRIV 179
Cdd:smart00545    2 IPVFYPTMEEFKDPLAYISKIRPQAEKYGICKVV 35
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
 617-669 1.19e-15

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: 71.89  E-value: 1.19e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1063681646  617 CCICFFDLHLSAAGCRCSPEKYSCLTHVKELCS-CPWVTKYFLFRYDIDELNVL 669
Cdd:pfam02928    1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 367-424 1.20e-14

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: 69.20  E-value: 1.20e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063681646   367 WNLNNFPRlPGSLLKYEGSDISGVLV-PWLYIGMCFSSFCWHVEDHHLysLNYMHWGAP 424
Cdd:smart00558    3 WNLAKLPF-KLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 988-1032 9.15e-13

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 63.46  E-value: 9.15e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 1063681646   988 GCVLSGKSWCSRRAIFPKGFRSRVKYINILDPTNMCFYiSEILDA 1032
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLY-SCVIDE 44
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 996-1029 3.71e-08

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 50.58  E-value: 3.71e-08
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1063681646  996 WCSRRAIFPKGFRSRVKYINILDPTNMCFYISEI 1029
Cdd:pfam05964   18 FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 394-510 7.63e-51

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: 174.79  E-value: 7.63e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681646  394 WLYIGMCFSSFCWHVEDHHLYSLNYMHWGAPKLWYGVGGKDAVKLEEAMRKHLpdlFEEQPDLLHKLVTQLSPSKLKTAG 473
Cdd:pfam02373    1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHF---GGEQPDDLLHLNTIISPKQLRENG 77

                           90       100       110
                   ....*....|....*....|....*....|....*..
gi 1063681646  474 VPVHRCVQHAGEFVLTFPRAYHAGFNSGFNCAEAVNV 510
Cdd:pfam02373   78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
FYRC smart00542
FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region ...
 1038-1132 1.89e-29

FY-rich domain, C-terminal region; is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 197781  Cd Length: 86  Bit Score: 112.39  E-value: 1.89e-29
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681646  1038 LFMVYLESNPSEVFVHMSPTRCWEMVRERVNQEITKQHkagksDLPPLQPSGSpdGFEMFGYSSPAIVQAIEALDVNRVC 1117
Cdd:smart00542    1 LFRVEIESDPGEVFKGESPEKCWEMVLERVQEARIAAD-----LLQLLPEGVS--GEEMFGLSSPAVVKLIEALPGVHQC 73

                            90
                    ....*....|....*
gi 1063681646  1118 TDYWDSrpYSRPQVQ 1132
Cdd:smart00542   74 TNYWFR--YHRSPLL 86
FYRC pfam05965
F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 1037-1120 3.21e-26

F/Y rich C-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542.


Pssm-ID: 461788  Cd Length: 83  Bit Score: 103.07  E-value: 3.21e-26
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063681646 1037 PLFMVYLESNPSEVFVHMSPTRCWEMVRERVNQeitKQHKAGKsdlpPLQPSGSPDGFEMFGYSSPAIVQAIEALDVNRV 1116
Cdd:pfam05965    2 PLFRVTVEEDPDESFEGSSPTKCWSMVLERVQE---LRREAGL----KLKLPESISGEDMFGLTHPAVVRLIESLPGAEK 74


                   ....
gi 1063681646 1117 CTDY 1120
Cdd:pfam05965   75 CTNY 78
JmjN pfam02375
jmjN domain;
147-179 2.00e-17

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 76.56  E-value: 2.00e-17
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1063681646  147 PVFYPSEEEFEDTLNYIAKIRPEAEKYGICRIV 179
Cdd:pfam02375    1 PVFYPTEEEFKDPLKYIEKIRPLGEKYGICKIV 33
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 146-179 2.91e-16

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: 73.45  E-value: 2.91e-16
                            10        20        30
                    ....*....|....*....|....*....|....
gi 1063681646   146 APVFYPSEEEFEDTLNYIAKIRPEAEKYGICRIV 179
Cdd:smart00545    2 IPVFYPTMEEFKDPLAYISKIRPQAEKYGICKVV 35
zf-C5HC2 pfam02928
C5HC2 zinc finger; Predicted zinc finger with eight potential zinc ligand binding residues. ...
 617-669 1.19e-15

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: 71.89  E-value: 1.19e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1063681646  617 CCICFFDLHLSAAGCRCSPEKYSCLTHVKELCS-CPWVTKYFLFRYDIDELNVL 669
Cdd:pfam02928    1 CSFCKAYCYLSAVTCSKCSGKVVCLRHAKELCSdCPPSKRTLLYRYTDDELEAL 54
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 367-424 1.20e-14

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: 69.20  E-value: 1.20e-14
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*....
gi 1063681646   367 WNLNNFPRlPGSLLKYEGSDISGVLV-PWLYIGMCFSSFCWHVEDHHLysLNYMHWGAP 424
Cdd:smart00558    3 WNLAKLPF-KLNLLSDLPEDIPGPDVgPYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
FYRN smart00541
FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region ...
 988-1032 9.15e-13

FY-rich domain, N-terminal region; is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.


Pssm-ID: 128814  Cd Length: 44  Bit Score: 63.46  E-value: 9.15e-13
                            10        20        30        40
                    ....*....|....*....|....*....|....*....|....*
gi 1063681646   988 GCVLSGKSWCSRRAIFPKGFRSRVKYINILDPTNMCFYiSEILDA 1032
Cdd:smart00541    1 LLPIQGKLFHSESAIFPVGYKSTRKYWSVKDPNRRCLY-SCVIDE 44
FYRN pfam05964
F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It ...
 996-1029 3.71e-08

F/Y-rich N-terminus; This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541.


Pssm-ID: 461787  Cd Length: 51  Bit Score: 50.58  E-value: 3.71e-08
                           10        20        30
                   ....*....|....*....|....*....|....
gi 1063681646  996 WCSRRAIFPKGFRSRVKYINILDPTNMCFYISEI 1029
Cdd:pfam05964   18 FHTERYIYPVGYKSTRLYWSTKDPRKRCRYTCEI 51
 
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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