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Conserved domains on  [gi|966924422|ref|XP_014984097|]
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ribosomal oxygenase 2 isoform X1 [Macaca mulatta]

Protein Classification

cupin domain-containing protein( domain architecture ID 10547114)

cupin domain-containing protein similar to human ribosomal oxygenase 1, also called histone lysine demethylase NO66, that acts as both a histone lysine demethylase and a ribosomal histidine hydroxylase, and plays a central role in the histone code

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
JmjC_2 pfam08007
JmjC domain; This entry includes proteins with a JmjC domain that belong to the cupin ...
136-261 7.38e-47

JmjC domain; This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66, Ribosomal oxygenase 1/2, and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases.


:

Pssm-ID: 462340  Cd Length: 116  Bit Score: 157.80  E-value: 7.38e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  136 QFHQPQRFKDElWRIQEKLECYfgslvgsnvyITPAGsqGLPPHYDDVEVFILQLEGEKHWRLYHPTVPLAREYSVEAEE 215
Cdd:pfam08007   1 QLLQPFRFLPD-WRIDDIMISF----------ATPGG--GVGPHYDDYDVFLLQGEGRKRWRVGAPKVPDLEFYSDPPLR 67
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 966924422  216 RIG--RPVHEFMLKPGDLLYFPRGTIHQADTPA-GLAHSTHVTISTYQN 261
Cdd:pfam08007  68 ILDdfEPVHDFVLEPGDMLYLPRGFIHQGVALDeSLHYSVGFRAPTAAE 116
ROXA-like_wH pfam20514
ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, ...
332-428 8.77e-18

ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, including ROXA from E.coli, which is reminiscent of WH-domains involved in protein-protein and protein-nucleic acid interactions. However, this domain has an overall negative charge suggesting they do not directly bind nucleic acids.


:

Pssm-ID: 466663  Cd Length: 115  Bit Score: 79.04  E-value: 8.77e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  332 KDFIMHRLPPYSAGDGAELSTPGGKLPRLDSVVRLQfKDHIVLTVLPDQD------------QSDEAQEKMVYIYHSLKN 399
Cdd:pfam20514   6 PDLLKHWLGPFLTEPRYELDLPGEPPPRLDELVEAL-EDGAVLTRLPNLRllytelrlfangEKFELDELLVAVLKSLAD 84
                          90       100       110
                  ....*....|....*....|....*....|.
gi 966924422  400 RRETHMM--GNEEETESHGLRFPLSHLDALK 428
Cdd:pfam20514  85 ARQLHLEnlGALESPEVRGLLFDLVNQGALQ 115
 
Name Accession Description Interval E-value
JmjC_2 pfam08007
JmjC domain; This entry includes proteins with a JmjC domain that belong to the cupin ...
136-261 7.38e-47

JmjC domain; This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66, Ribosomal oxygenase 1/2, and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases.


Pssm-ID: 462340  Cd Length: 116  Bit Score: 157.80  E-value: 7.38e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  136 QFHQPQRFKDElWRIQEKLECYfgslvgsnvyITPAGsqGLPPHYDDVEVFILQLEGEKHWRLYHPTVPLAREYSVEAEE 215
Cdd:pfam08007   1 QLLQPFRFLPD-WRIDDIMISF----------ATPGG--GVGPHYDDYDVFLLQGEGRKRWRVGAPKVPDLEFYSDPPLR 67
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 966924422  216 RIG--RPVHEFMLKPGDLLYFPRGTIHQADTPA-GLAHSTHVTISTYQN 261
Cdd:pfam08007  68 ILDdfEPVHDFVLEPGDMLYLPRGFIHQGVALDeSLHYSVGFRAPTAAE 116
RoxA COG2850
Ribosomal protein L16 Arg81 hydroxylase, contains JmjC domain [Translation, ribosomal ...
46-274 5.41e-28

Ribosomal protein L16 Arg81 hydroxylase, contains JmjC domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442098  Cd Length: 274  Bit Score: 112.22  E-value: 5.41e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  46 ISPiktETFFKEFWEQKPLLIRRDDPalatYYGSLFKLTDLKSLCSRgmyygRDVNvCRCV--NGKKKVLNKDG---KAH 120
Cdd:COG2850    1 ISP---EQFLRDYWQKKPLLIRGAFP----DFVDPLSPDELAGLACE-----EDVE-SRLVsnDGQGRWQLRHGpfdEED 67
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422 121 FlqlrKDLDQKRATI------QFHQP-----QRFKDEL-WRIQEklecyfgslvgsNVYITPAGSQGLPPHYDDVEVFIL 188
Cdd:COG2850   68 F----AALPERGWTLlvqgvdHWHPEvaallRAFRFIPdWRLDD------------LMISYAPPGGGVGPHFDSYDVFLL 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422 189 QLEGEKHWRLYHPTVPLArEYSVEAEERI---GRPVHEFMLKPGDLLYFPRGTIHQadtpaGLAHSTHVTIS------TY 259
Cdd:COG2850  132 QGEGRRRWRIGDQPDDDP-ELVPDLPLRIladFEPEIDWVLEPGDMLYLPPGFAHD-----GVALEECMTYSigfrapSW 205
                        250
                 ....*....|....*..
gi 966924422 260 QN--NSWGDFLLDTISG 274
Cdd:COG2850  206 AEllSELADYLADDLLG 222
ROXA-like_wH pfam20514
ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, ...
332-428 8.77e-18

ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, including ROXA from E.coli, which is reminiscent of WH-domains involved in protein-protein and protein-nucleic acid interactions. However, this domain has an overall negative charge suggesting they do not directly bind nucleic acids.


Pssm-ID: 466663  Cd Length: 115  Bit Score: 79.04  E-value: 8.77e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  332 KDFIMHRLPPYSAGDGAELSTPGGKLPRLDSVVRLQfKDHIVLTVLPDQD------------QSDEAQEKMVYIYHSLKN 399
Cdd:pfam20514   6 PDLLKHWLGPFLTEPRYELDLPGEPPPRLDELVEAL-EDGAVLTRLPNLRllytelrlfangEKFELDELLVAVLKSLAD 84
                          90       100       110
                  ....*....|....*....|....*....|.
gi 966924422  400 RRETHMM--GNEEETESHGLRFPLSHLDALK 428
Cdd:pfam20514  85 ARQLHLEnlGALESPEVRGLLFDLVNQGALQ 115
cupin_BLR2406-like cd02210
Bradyrhizobium japonicum BLR2406 and related proteins, cupin domain; This family includes ...
159-242 1.33e-03

Bradyrhizobium japonicum BLR2406 and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to BLR2406, a Bradyrhizobium japonicum protein of unknown function with a cupin beta barrel domain. Proteins in this subfamily appear to align closest to RmlC carbohydrate epimerase which is involved in dTDP-L-rhamnose production, and belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380340 [Multi-domain]  Cd Length: 98  Bit Score: 37.88  E-value: 1.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422 159 GSLVGS-----NVYITPAGSQGLPPHYDDVEVFILQLEGEKHWRlYHPTVplarEYSVEAEerigrpvhefmlkPGDLLY 233
Cdd:cd02210    3 AETVGAkglwmGVVTIPPGARTGAHHHGEHETAIYVLSGRAETR-YGDRL----EHRAEAG-------------PGDFIY 64

                 ....*....
gi 966924422 234 FPRGTIHQA 242
Cdd:cd02210   65 IPPGVPHQE 73
 
Name Accession Description Interval E-value
JmjC_2 pfam08007
JmjC domain; This entry includes proteins with a JmjC domain that belong to the cupin ...
136-261 7.38e-47

JmjC domain; This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66, Ribosomal oxygenase 1/2, and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases.


Pssm-ID: 462340  Cd Length: 116  Bit Score: 157.80  E-value: 7.38e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  136 QFHQPQRFKDElWRIQEKLECYfgslvgsnvyITPAGsqGLPPHYDDVEVFILQLEGEKHWRLYHPTVPLAREYSVEAEE 215
Cdd:pfam08007   1 QLLQPFRFLPD-WRIDDIMISF----------ATPGG--GVGPHYDDYDVFLLQGEGRKRWRVGAPKVPDLEFYSDPPLR 67
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 966924422  216 RIG--RPVHEFMLKPGDLLYFPRGTIHQADTPA-GLAHSTHVTISTYQN 261
Cdd:pfam08007  68 ILDdfEPVHDFVLEPGDMLYLPRGFIHQGVALDeSLHYSVGFRAPTAAE 116
RoxA COG2850
Ribosomal protein L16 Arg81 hydroxylase, contains JmjC domain [Translation, ribosomal ...
46-274 5.41e-28

Ribosomal protein L16 Arg81 hydroxylase, contains JmjC domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442098  Cd Length: 274  Bit Score: 112.22  E-value: 5.41e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  46 ISPiktETFFKEFWEQKPLLIRRDDPalatYYGSLFKLTDLKSLCSRgmyygRDVNvCRCV--NGKKKVLNKDG---KAH 120
Cdd:COG2850    1 ISP---EQFLRDYWQKKPLLIRGAFP----DFVDPLSPDELAGLACE-----EDVE-SRLVsnDGQGRWQLRHGpfdEED 67
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422 121 FlqlrKDLDQKRATI------QFHQP-----QRFKDEL-WRIQEklecyfgslvgsNVYITPAGSQGLPPHYDDVEVFIL 188
Cdd:COG2850   68 F----AALPERGWTLlvqgvdHWHPEvaallRAFRFIPdWRLDD------------LMISYAPPGGGVGPHFDSYDVFLL 131
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422 189 QLEGEKHWRLYHPTVPLArEYSVEAEERI---GRPVHEFMLKPGDLLYFPRGTIHQadtpaGLAHSTHVTIS------TY 259
Cdd:COG2850  132 QGEGRRRWRIGDQPDDDP-ELVPDLPLRIladFEPEIDWVLEPGDMLYLPPGFAHD-----GVALEECMTYSigfrapSW 205
                        250
                 ....*....|....*..
gi 966924422 260 QN--NSWGDFLLDTISG 274
Cdd:COG2850  206 AEllSELADYLADDLLG 222
ROXA-like_wH pfam20514
ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, ...
332-428 8.77e-18

ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, including ROXA from E.coli, which is reminiscent of WH-domains involved in protein-protein and protein-nucleic acid interactions. However, this domain has an overall negative charge suggesting they do not directly bind nucleic acids.


Pssm-ID: 466663  Cd Length: 115  Bit Score: 79.04  E-value: 8.77e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  332 KDFIMHRLPPYSAGDGAELSTPGGKLPRLDSVVRLQfKDHIVLTVLPDQD------------QSDEAQEKMVYIYHSLKN 399
Cdd:pfam20514   6 PDLLKHWLGPFLTEPRYELDLPGEPPPRLDELVEAL-EDGAVLTRLPNLRllytelrlfangEKFELDELLVAVLKSLAD 84
                          90       100       110
                  ....*....|....*....|....*....|.
gi 966924422  400 RRETHMM--GNEEETESHGLRFPLSHLDALK 428
Cdd:pfam20514  85 ARQLHLEnlGALESPEVRGLLFDLVNQGALQ 115
cupin_BLR2406-like cd02210
Bradyrhizobium japonicum BLR2406 and related proteins, cupin domain; This family includes ...
159-242 1.33e-03

Bradyrhizobium japonicum BLR2406 and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to BLR2406, a Bradyrhizobium japonicum protein of unknown function with a cupin beta barrel domain. Proteins in this subfamily appear to align closest to RmlC carbohydrate epimerase which is involved in dTDP-L-rhamnose production, and belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380340 [Multi-domain]  Cd Length: 98  Bit Score: 37.88  E-value: 1.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422 159 GSLVGS-----NVYITPAGSQGLPPHYDDVEVFILQLEGEKHWRlYHPTVplarEYSVEAEerigrpvhefmlkPGDLLY 233
Cdd:cd02210    3 AETVGAkglwmGVVTIPPGARTGAHHHGEHETAIYVLSGRAETR-YGDRL----EHRAEAG-------------PGDFIY 64

                 ....*....
gi 966924422 234 FPRGTIHQA 242
Cdd:cd02210   65 IPPGVPHQE 73
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
174-240 5.92e-03

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 36.37  E-value: 5.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 966924422 174 QGLPPHYDDVEVFILQLEGEkhwrlyhptvplareysveAEERIGRPVHEfmLKPGDLLYFPRGTIH 240
Cdd:COG1917   34 ARTPWHSHPGEELIYVLEGE-------------------GEVEVGGEEYE--LKPGDVVFIPPGVPH 79
Cupin_8 pfam13621
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
120-244 9.88e-03

Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.


Pssm-ID: 463936  Cd Length: 251  Bit Score: 37.73  E-value: 9.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966924422  120 HFL-QLRKDLDQKRATIQFHQPQRFKDELWRIQEK------LECYFGSLVGSNVYITPAGSQGlPPHYDDVEVFILQLEG 192
Cdd:pfam13621  81 EFLdRLEAGEDTDTAPYAYLQSDNLRSEFPELLEDndlpfaTEAFGGEPDAVNLWMGNGRSVT-SLHYDHYENLYCVVRG 159
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 966924422  193 EKHWRLYHPT-VPLAREYSVEaEERIGRPV----------------------HEFMLKPGDLLYFPRGTIHQADT 244
Cdd:pfam13621 160 RKRFTLFPPSdVPNLYPGPLE-PTPEGQVFslvdplapdferfprfrdaarpLVVTLNPGDVLYLPALWWHHVES 233
 
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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