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Conserved domains on  [gi|446378659|ref|WP_000456514|]
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MULTISPECIES: [50S ribosomal protein L16]-arginine 3-hydroxylase [Salmonella]

Protein Classification

cupin domain-containing protein( domain architecture ID 10006729)

cupin domain-containing protein similar to Escherichia coli 50S ribosomal protein L16 3-hydroxylase (RoxA, also termed YcfD) and Bacillus subtilis YxbC

EC:  1.14.11.47
Gene Ontology:  GO:0043687

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RoxA COG2850
Ribosomal protein L16 Arg81 hydroxylase, contains JmjC domain [Translation, ribosomal ...
 7-276 8.35e-151

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


:

Pssm-ID: 442098  Cd Length: 274  Bit Score: 426.15  E-value: 8.35e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659   7 LNWPDFLERHWQKRPVVLKRGFSNFIDPLSPDELAGLAMESEIDSRLVSHQD-GKWQVSHGPF--ESYDHLGESNWSLLV 83
Cdd:COG2850    1 ISPEQFLRDYWQKKPLLIRGAFPDFVDPLSPDELAGLACEEDVESRLVSNDGqGRWQLRHGPFdeEDFAALPERGWTLLV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659  84 QAVNHWHEPTAALMRPFRALPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVGEK-LQMRQHCPHPDLLQV 162
Cdd:COG2850   81 QGVDHWHPEVAALLRAFRFIPDWRLDDLMISYAPPGGGVGPHFDSYDVFLLQGEGRRRWRIGDQpDDDPELVPDLPLRIL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659 163 DPFEAIIDEELEPGDILYIPPGFPHEGYALENAMNYSVGFRAPNSRELISGFADYVLQRELGNTYYSDPDMPSRKHPADI 242
Cdd:COG2850  161 ADFEPEIDWVLEPGDMLYLPPGFAHDGVALEECMTYSIGFRAPSWAELLSELADYLADDLLGDQRYRDPDLQARADPGEI 240

                        250       260       270
                 ....*....|....*....|....*....|....
gi 446378659 243 LPQEMDKLRNMMLDLINQPAHFQQWLGEFLSQSR 276
Cdd:COG2850  241 PAAALDRLRAMLLDLLDDPELLARWLGEFLTEPK 274
ROXA-like_wH pfam20514
ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, ...
 256-370 5.47e-32

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: 116.78  E-value: 5.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659  256 DLINQPAHFQQWLGEFLSQSRHELDIaPPEPPYQPDEIYDALKQGEVLVRLGGLRVLRIGDEVYANGEKI--DSPHRPAL 333
Cdd:pfam20514   1 ALLADPDLLKHWLGPFLTEPRYELDL-PGEPPPRLDELVEALEDGAVLTRLPNLRLLYTELRLFANGEKFelDELLVAVL 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 446378659  334 EALASHIALTAENFGdALEDPSFLAMLAALVNSGYWF 370
Cdd:pfam20514  80 KSLADARQLHLENLG-ALESPEVRGLLFDLVNQGALQ 115
 
Name Accession Description Interval E-value
RoxA COG2850
Ribosomal protein L16 Arg81 hydroxylase, contains JmjC domain [Translation, ribosomal ...
 7-276 8.35e-151

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


Pssm-ID: 442098  Cd Length: 274  Bit Score: 426.15  E-value: 8.35e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659   7 LNWPDFLERHWQKRPVVLKRGFSNFIDPLSPDELAGLAMESEIDSRLVSHQD-GKWQVSHGPF--ESYDHLGESNWSLLV 83
Cdd:COG2850    1 ISPEQFLRDYWQKKPLLIRGAFPDFVDPLSPDELAGLACEEDVESRLVSNDGqGRWQLRHGPFdeEDFAALPERGWTLLV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659  84 QAVNHWHEPTAALMRPFRALPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVGEK-LQMRQHCPHPDLLQV 162
Cdd:COG2850   81 QGVDHWHPEVAALLRAFRFIPDWRLDDLMISYAPPGGGVGPHFDSYDVFLLQGEGRRRWRIGDQpDDDPELVPDLPLRIL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659 163 DPFEAIIDEELEPGDILYIPPGFPHEGYALENAMNYSVGFRAPNSRELISGFADYVLQRELGNTYYSDPDMPSRKHPADI 242
Cdd:COG2850  161 ADFEPEIDWVLEPGDMLYLPPGFAHDGVALEECMTYSIGFRAPSWAELLSELADYLADDLLGDQRYRDPDLQARADPGEI 240

                        250       260       270
                 ....*....|....*....|....*....|....
gi 446378659 243 LPQEMDKLRNMMLDLINQPAHFQQWLGEFLSQSR 276
Cdd:COG2850  241 PAAALDRLRAMLLDLLDDPELLARWLGEFLTEPK 274
JmjC_2 pfam08007
JmjC domain; This entry includes proteins with a JmjC domain that belong to the cupin ...
 95-209 2.05e-57

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: 182.84  E-value: 2.05e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659   95 ALMRPFRALPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVG-EKLQMRQHCPHPDLLQVDPFEAIIDEEL 173
Cdd:pfam08007   1 QLLQPFRFLPDWRIDDIMISFATPGGGVGPHYDDYDVFLLQGEGRKRWRVGaPKVPDLEFYSDPPLRILDDFEPVHDFVL 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 446378659  174 EPGDILYIPPGFPHEGYALENAMNYSVGFRAPNSRE 209
Cdd:pfam08007  81 EPGDMLYLPRGFIHQGVALDESLHYSVGFRAPTAAE 116
ROXA-like_wH pfam20514
ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, ...
 256-370 5.47e-32

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: 116.78  E-value: 5.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659  256 DLINQPAHFQQWLGEFLSQSRHELDIaPPEPPYQPDEIYDALKQGEVLVRLGGLRVLRIGDEVYANGEKI--DSPHRPAL 333
Cdd:pfam20514   1 ALLADPDLLKHWLGPFLTEPRYELDL-PGEPPPRLDELVEALEDGAVLTRLPNLRLLYTELRLFANGEKFelDELLVAVL 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 446378659  334 EALASHIALTAENFGdALEDPSFLAMLAALVNSGYWF 370
Cdd:pfam20514  80 KSLADARQLHLENLG-ALESPEVRGLLFDLVNQGALQ 115
cupin_BLR2406-like cd02210
Bradyrhizobium japonicum BLR2406 and related proteins, cupin domain; This family includes ...
 118-187 7.64e-05

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: 41.35  E-value: 7.64e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446378659 118 PGGGVGPHL-DQYDVFIIQGTGRRRWRVGEKLQMRQhcphpdllqvdpfeaiideELEPGDILYIPPGFPH 187
Cdd:cd02210   20 PGARTGAHHhGEHETAIYVLSGRAETRYGDRLEHRA-------------------EAGPGDFIYIPPGVPH 71
 
Name Accession Description Interval E-value
RoxA COG2850
Ribosomal protein L16 Arg81 hydroxylase, contains JmjC domain [Translation, ribosomal ...
 7-276 8.35e-151

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


Pssm-ID: 442098  Cd Length: 274  Bit Score: 426.15  E-value: 8.35e-151
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659   7 LNWPDFLERHWQKRPVVLKRGFSNFIDPLSPDELAGLAMESEIDSRLVSHQD-GKWQVSHGPF--ESYDHLGESNWSLLV 83
Cdd:COG2850    1 ISPEQFLRDYWQKKPLLIRGAFPDFVDPLSPDELAGLACEEDVESRLVSNDGqGRWQLRHGPFdeEDFAALPERGWTLLV 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659  84 QAVNHWHEPTAALMRPFRALPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVGEK-LQMRQHCPHPDLLQV 162
Cdd:COG2850   81 QGVDHWHPEVAALLRAFRFIPDWRLDDLMISYAPPGGGVGPHFDSYDVFLLQGEGRRRWRIGDQpDDDPELVPDLPLRIL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659 163 DPFEAIIDEELEPGDILYIPPGFPHEGYALENAMNYSVGFRAPNSRELISGFADYVLQRELGNTYYSDPDMPSRKHPADI 242
Cdd:COG2850  161 ADFEPEIDWVLEPGDMLYLPPGFAHDGVALEECMTYSIGFRAPSWAELLSELADYLADDLLGDQRYRDPDLQARADPGEI 240

                        250       260       270
                 ....*....|....*....|....*....|....
gi 446378659 243 LPQEMDKLRNMMLDLINQPAHFQQWLGEFLSQSR 276
Cdd:COG2850  241 PAAALDRLRAMLLDLLDDPELLARWLGEFLTEPK 274
JmjC_2 pfam08007
JmjC domain; This entry includes proteins with a JmjC domain that belong to the cupin ...
 95-209 2.05e-57

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: 182.84  E-value: 2.05e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659   95 ALMRPFRALPDWRIDDLMISFSVPGGGVGPHLDQYDVFIIQGTGRRRWRVG-EKLQMRQHCPHPDLLQVDPFEAIIDEEL 173
Cdd:pfam08007   1 QLLQPFRFLPDWRIDDIMISFATPGGGVGPHYDDYDVFLLQGEGRKRWRVGaPKVPDLEFYSDPPLRILDDFEPVHDFVL 80

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 446378659  174 EPGDILYIPPGFPHEGYALENAMNYSVGFRAPNSRE 209
Cdd:pfam08007  81 EPGDMLYLPRGFIHQGVALDESLHYSVGFRAPTAAE 116
ROXA-like_wH pfam20514
ROXA-like winged helix; This entry represents the winged helix domain of ribosomal oxygenases, ...
 256-370 5.47e-32

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: 116.78  E-value: 5.47e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446378659  256 DLINQPAHFQQWLGEFLSQSRHELDIaPPEPPYQPDEIYDALKQGEVLVRLGGLRVLRIGDEVYANGEKI--DSPHRPAL 333
Cdd:pfam20514   1 ALLADPDLLKHWLGPFLTEPRYELDL-PGEPPPRLDELVEALEDGAVLTRLPNLRLLYTELRLFANGEKFelDELLVAVL 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 446378659  334 EALASHIALTAENFGdALEDPSFLAMLAALVNSGYWF 370
Cdd:pfam20514  80 KSLADARQLHLENLG-ALESPEVRGLLFDLVNQGALQ 115
cupin_BLR2406-like cd02210
Bradyrhizobium japonicum BLR2406 and related proteins, cupin domain; This family includes ...
 118-187 7.64e-05

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: 41.35  E-value: 7.64e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446378659 118 PGGGVGPHL-DQYDVFIIQGTGRRRWRVGEKLQMRQhcphpdllqvdpfeaiideELEPGDILYIPPGFPH 187
Cdd:cd02210   20 PGARTGAHHhGEHETAIYVLSGRAETRYGDRLEHRA-------------------EAGPGDFIYIPPGVPH 71
cupin_KdgF cd02238
pectin degradation protein KdgF and related proteins, cupin domain; This family includes ...
 165-195 1.16e-04

pectin degradation protein KdgF and related proteins, cupin domain; This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380366 [Multi-domain]  Cd Length: 104  Bit Score: 40.92  E-value: 1.16e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 446378659 165 FEAIIDEE---LEPGDILYIPPGFPHEGYALENA 195
Cdd:cd02238   58 FEFTIGGEtriLKPGDSYYIPPNVPHGAEALEDS 91
RmlC COG4101
Uncharacterized conserved protein, RmlC-like cupin domain [General function prediction only];
118-188 3.06e-03

Uncharacterized conserved protein, RmlC-like cupin domain [General function prediction only];


Pssm-ID: 443277  Cd Length: 146  Bit Score: 37.64  E-value: 3.06e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446378659 118 PGGGVGPHL-DQYD--VFIIQGTGRRRWrvGEKLQMRqhcphpdllqvdpfeaiidEELEPGDILYIPPGFPHE 188
Cdd:COG4101   55 PGARAKAHHhGEHEtaIYVLSGRAETRY--GERLEHR-------------------VVTEPGDFIFIPPGVPHQ 107
OxdD COG2140
Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate ...
 118-187 6.62e-03

Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate transport and metabolism]; Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily is part of the Pathway/BioSystem: Glycolysis


Pssm-ID: 441743 [Multi-domain]  Cd Length: 115  Bit Score: 36.10  E-value: 6.62e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446378659 118 PGGGVGP--HLDQYDV-FIIQGTGRrrwrvgeklqmrqhcphpdLLQVDPFEAIIDEELEPGDILYIPPGFPH 187
Cdd:COG2140   12 PGGVREEhwHPNAAEWyYVLSGEAR-------------------MTVQDPPGRARTVDVGPGDVVYVPPGYGH 65
 
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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