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Conserved domains on  [gi|1478266570|gb|RIL98423|]
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cupin domain-containing protein [Staphylococcus equorum]

Protein Classification

cupin domain-containing protein( domain architecture ID 11465798)

cupin domain-containing protein, part of a functionally diverse superfamily with the active site generally located at the center of a conserved domain forming a beta-barrel fold; similar to gentisate 1,2-dioxygenase that catalyzes the oxygen-dependent ring fission of gentisate between the carboxyl and proximal hydroxyl groups at positions 1 and 2 of the aromatic ring to form maleylpyruvate

CATH:  2.60.120.10
Gene Ontology:  GO:0046872
PubMed:  19478949|14697267|9573603
SCOP:  3001825

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG3435 COG3435
Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
35-348 1.15e-148

Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];


:

Pssm-ID: 442661 [Multi-domain]  Cd Length: 316  Bit Score: 422.34  E-value: 1.15e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570  35 VMNKTPQSHAQAYLWSGELLKKKLSEAAEIFTPDRGgERRAIYFQNPGLTyrqpwGHVSTTQTLYAAVQLLQPGEEAPSH 114
Cdd:COG3435     1 LVPPEPRPKAVPHLWRYADLRPLLLRAGRLVTAERA-ERRVLVLENPGLG-----GKSAATPTLYAGIQLLLPGEVAPAH 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 115 RHTQSALRFITDGEGAYTIVQGERIFMEEGDFLTTPKNLWHGHGHLGDEPMIWMDALDIPTIYNLGGTFFEPYEDGLQQP 194
Cdd:COG3435    75 RHTQSALRFVIEGEGAYTVVDGERVPMERGDFVLTPSWTWHDHGNEGDEPMIWLDGLDIPLVELLEAGFFEDGPDDVQPV 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 195 DVPDNFSEKRYQGGMVRPIGDDKFDVA-PLANYKWDRTVDAINGLM-NFEPDPYDGFTVEYINPSTGKSANPTVGSRMTH 272
Cdd:COG3435   155 TRPEGDSEARYGHGGLRPYEFLRDTVSsPLLHYPWERTREALERLAaLEEPDPYGGAALRYVNPATGGDVMPTIGAFMQL 234

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1478266570 273 LPKGHHTKAHRHTHSVIYCVHRGSGYTVINGTKFNWKKGDYFVVPNWNWHEHV-ASEDSYLFSVNDIPIMNRFELER 348
Cdd:COG3435   235 LPPGFHTRPHRHTGSAVYHVVEGSGRSIVGGERFDWGEGDLFVVPSWAWHSHAsADEDAVLFSFSDRPVQEALGLYR 311
 
Name Accession Description Interval E-value
COG3435 COG3435
Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
35-348 1.15e-148

Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 442661 [Multi-domain]  Cd Length: 316  Bit Score: 422.34  E-value: 1.15e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570  35 VMNKTPQSHAQAYLWSGELLKKKLSEAAEIFTPDRGgERRAIYFQNPGLTyrqpwGHVSTTQTLYAAVQLLQPGEEAPSH 114
Cdd:COG3435     1 LVPPEPRPKAVPHLWRYADLRPLLLRAGRLVTAERA-ERRVLVLENPGLG-----GKSAATPTLYAGIQLLLPGEVAPAH 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 115 RHTQSALRFITDGEGAYTIVQGERIFMEEGDFLTTPKNLWHGHGHLGDEPMIWMDALDIPTIYNLGGTFFEPYEDGLQQP 194
Cdd:COG3435    75 RHTQSALRFVIEGEGAYTVVDGERVPMERGDFVLTPSWTWHDHGNEGDEPMIWLDGLDIPLVELLEAGFFEDGPDDVQPV 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 195 DVPDNFSEKRYQGGMVRPIGDDKFDVA-PLANYKWDRTVDAINGLM-NFEPDPYDGFTVEYINPSTGKSANPTVGSRMTH 272
Cdd:COG3435   155 TRPEGDSEARYGHGGLRPYEFLRDTVSsPLLHYPWERTREALERLAaLEEPDPYGGAALRYVNPATGGDVMPTIGAFMQL 234

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1478266570 273 LPKGHHTKAHRHTHSVIYCVHRGSGYTVINGTKFNWKKGDYFVVPNWNWHEHV-ASEDSYLFSVNDIPIMNRFELER 348
Cdd:COG3435   235 LPPGFHTRPHRHTGSAVYHVVEGSGRSIVGGERFDWGEGDLFVVPSWAWHSHAsADEDAVLFSFSDRPVQEALGLYR 311
cupin_GDO-like_N cd02216
gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, ...
 73-185 5.06e-55

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, N-terminal cupin domain; This family includes the N-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDOs and NDOs in its unique ability to oxidatively cleave many different salicylate, gentisate and 1-hydroxy-2-naphthoate substrates with high catalytic efficiency. The active site of these enzymes is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.


Pssm-ID: 380346 [Multi-domain]  Cd Length: 108  Bit Score: 176.21  E-value: 5.06e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570  73 RRAIYFQNPGLTyrqpwGHVSTTQTLYAAVQLLQPGEEAPSHRHTQSALRFITDGEGAYTIVQGERIFMEEGDFLTTPKN 152
Cdd:cd02216     1 RRVLLLVNPGLP-----GTRATTHTLYAGLQLLPPGEVAPAHRHTPNALRFVLEGPGAYTTVDGERCDMEPGDLILTPPG 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1478266570 153 LWHGHGHLGDEPMIWMDALDIPTIYNLGGTFFE 185
Cdd:cd02216    76 TWHDHGNEGDEPAIWLDGLDAPLVTYLRASFFE 108
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 101-169 4.90e-15

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 69.21  E-value: 4.90e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 101 AVQLLQPGEEAPSHRHTQS-ALRFITDGEGAYTiVQGERIFMEEGDFLTTPKNLWHGHGHLGDEPMIWMD 169
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEdEFFYVLEGEGELT-VDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLD 69
Cupin_1 smart00835
Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' ...
 277-337 8.56e-03

Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.


Pssm-ID: 214845 [Multi-domain]  Cd Length: 146  Bit Score: 36.49  E-value: 8.56e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1478266570  277 HHTkaHRHTHSVIYCVhRGSGYTVI---NGTK---FNWKKGDYFVVPNWNWHEHVASEDSYL----FSVND 337
Cdd:smart00835  45 PHY--HPRATELLYVV-RGEGRVGVvdpNGNKvydARLREGDVFVVPQGHPHFQVNSGDENLefvaFNTND 112
 
Name Accession Description Interval E-value
COG3435 COG3435
Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
35-348 1.15e-148

Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 442661 [Multi-domain]  Cd Length: 316  Bit Score: 422.34  E-value: 1.15e-148
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570  35 VMNKTPQSHAQAYLWSGELLKKKLSEAAEIFTPDRGgERRAIYFQNPGLTyrqpwGHVSTTQTLYAAVQLLQPGEEAPSH 114
Cdd:COG3435     1 LVPPEPRPKAVPHLWRYADLRPLLLRAGRLVTAERA-ERRVLVLENPGLG-----GKSAATPTLYAGIQLLLPGEVAPAH 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 115 RHTQSALRFITDGEGAYTIVQGERIFMEEGDFLTTPKNLWHGHGHLGDEPMIWMDALDIPTIYNLGGTFFEPYEDGLQQP 194
Cdd:COG3435    75 RHTQSALRFVIEGEGAYTVVDGERVPMERGDFVLTPSWTWHDHGNEGDEPMIWLDGLDIPLVELLEAGFFEDGPDDVQPV 154

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 195 DVPDNFSEKRYQGGMVRPIGDDKFDVA-PLANYKWDRTVDAINGLM-NFEPDPYDGFTVEYINPSTGKSANPTVGSRMTH 272
Cdd:COG3435   155 TRPEGDSEARYGHGGLRPYEFLRDTVSsPLLHYPWERTREALERLAaLEEPDPYGGAALRYVNPATGGDVMPTIGAFMQL 234

                         250       260       270       280       290       300       310
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1478266570 273 LPKGHHTKAHRHTHSVIYCVHRGSGYTVINGTKFNWKKGDYFVVPNWNWHEHV-ASEDSYLFSVNDIPIMNRFELER 348
Cdd:COG3435   235 LPPGFHTRPHRHTGSAVYHVVEGSGRSIVGGERFDWGEGDLFVVPSWAWHSHAsADEDAVLFSFSDRPVQEALGLYR 311
cupin_GDO-like_N cd02216
gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, ...
 73-185 5.06e-55

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, N-terminal cupin domain; This family includes the N-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDOs and NDOs in its unique ability to oxidatively cleave many different salicylate, gentisate and 1-hydroxy-2-naphthoate substrates with high catalytic efficiency. The active site of these enzymes is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.


Pssm-ID: 380346 [Multi-domain]  Cd Length: 108  Bit Score: 176.21  E-value: 5.06e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570  73 RRAIYFQNPGLTyrqpwGHVSTTQTLYAAVQLLQPGEEAPSHRHTQSALRFITDGEGAYTIVQGERIFMEEGDFLTTPKN 152
Cdd:cd02216     1 RRVLLLVNPGLP-----GTRATTHTLYAGLQLLPPGEVAPAHRHTPNALRFVLEGPGAYTTVDGERCDMEPGDLILTPPG 75

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1478266570 153 LWHGHGHLGDEPMIWMDALDIPTIYNLGGTFFE 185
Cdd:cd02216    76 TWHDHGNEGDEPAIWLDGLDAPLVTYLRASFFE 108
cupin_GDO-like_C cd06992
gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase ...
 248-344 2.37e-44

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase bicupin aromatic ring-cleaving dioxygenases, C-terminal cupin domain; This model represents the C-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDO's and NDO's in its unique ability to oxidatively cleave many different salicylate, gentisate, and 1-hydroxy-2- naphthoate substrates with high catalytic efficiency. The active site of this enzyme is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.


Pssm-ID: 380397 [Multi-domain]  Cd Length: 99  Bit Score: 148.40  E-value: 2.37e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 248 GFTVEYINPSTGKSANPTVGSRMTHLPKGHHTKAHRHTHSVIYCVHRGSGYTVINGTKFNWKKGDYFVVPNWNWHEHVA- 326
Cdd:cd06992     1 GVALEYVNPTTGGPVMPTIGAFMQLLRAGFSTRPHRSTASAVYHVVEGSGRTVIGGKTFEWEPGDVFVVPSWAWHSHEAd 80

                          90
                  ....*....|....*...
gi 1478266570 327 SEDSYLFSVNDIPIMNRF 344
Cdd:cd06992    81 SEDAVLFSFSDRPVQEAL 98
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 101-169 4.90e-15

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 69.21  E-value: 4.90e-15
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 101 AVQLLQPGEEAPSHRHTQS-ALRFITDGEGAYTiVQGERIFMEEGDFLTTPKNLWHGHGHLGDEPMIWMD 169
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEdEFFYVLEGEGELT-VDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLD 69
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
105-169 7.05e-09

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 52.93  E-value: 7.05e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1478266570 105 LQPGEEAPSHRHTQSALRFITDGEGAYTIvQGERIFMEEGDFLTTPKNLWHGHGHLGDEPMIWMD 169
Cdd:COG1917    30 FEPGARTPWHSHPGEELIYVLEGEGEVEV-GGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLV 93
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 100-167 4.65e-08

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.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 49.79  E-value: 4.65e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1478266570 100 AAVQLLQPGEEAPSHRHT-QSALRFITDGEGAYTIVQGERIFMEEGDFLTTPKNLWHGHGHLGDEPMIW 167
Cdd:cd02208     1 ISVVTLPPGTSSPPHWHPeQDEIFYVLSGEGELTLDDGETVELKAGDIVLIPPGVPHSFVNTSDEPAVF 69
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
239-330 2.33e-06

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 45.61  E-value: 2.33e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 239 MNFEPDPYDGFTVEYINPstgksANPTVGSRMTHLPKGHHTKAHRHTHSVIYCVHRGSGYTVINGTKFNWKKGDYFVVPN 318
Cdd:COG1917     1 MRLAEIALTGVSVRVLAD-----GEDELEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPP 75

                          90
                  ....*....|..
gi 1478266570 319 WNWHEHVASEDS 330
Cdd:COG1917    76 GVPHAFRNLGDE 87
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
86-168 5.74e-05

Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 42.05  E-value: 5.74e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570  86 RQPWGHVSTTQTLYAAVQL----LQPGEEAPSHRHTQSA-LRFITDGEGAYTIvQGERIFMEEGDFLTTPKNLWHGHGHL 160
Cdd:COG0662    11 AIGWGSYEVLGEGGERLSVkritVPPGAELSLHVHPHRDeFFYVLEGTGEVTI-GDEEVELKAGDSVYIPAGVPHRLRNP 89


                  ....*...
gi 1478266570 161 GDEPMIWM 168
Cdd:COG0662    90 GDEPLELL 97
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 270-329 8.39e-05

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 40.32  E-value: 8.39e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1478266570 270 MTHLPKGHHTKAHRHTHS--VIYcVHRGSGYTVINGTKFNWKKGDYFVVPNWNWHEHVASED 329
Cdd:pfam07883   2 LVTLPPGESSPPHRHPGEdeFFY-VLEGEGELTVDGEEVVLKAGDSVYFPAGVPHRFRNTGD 62
cupin_ARD cd02232
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ...
 114-155 3.07e-04

acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization


Pssm-ID: 380360  Cd Length: 134  Bit Score: 40.22  E-value: 3.07e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1478266570 114 HRHTQSALRFITDGEGAYTIVQGE----RIFMEEGDFLTTPKNLWH 155
Cdd:cd02232    65 HLHEDDEVRFILDGSGYFDVRDKDdewiRILVEKGDLIVVPAGIYH 110
CENP-C_C pfam11699
Mif2/CENP-C like; CENP-C_C is a C-terminal family of fungal and eukaryote proteins necessary ...
 263-320 8.05e-04

Mif2/CENP-C like; CENP-C_C is a C-terminal family of fungal and eukaryote proteins necessary for centromere formation. CENP-C is the inner-kinetochore centromere (CEN) binding protein. In the budding-yeast, Mif2, the yeast homolog, binds in the CDEIII region of the centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins. Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerization domain of a bacterial transcription factor. The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast. This C-terminal domain is the region via which CENP-C localizes to centromeres throughout the cell cycle 2,3].


Pssm-ID: 403028 [Multi-domain]  Cd Length: 85  Bit Score: 38.07  E-value: 8.05e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1478266570 263 NPTVGSRMTHLPKGHhTKAHRHTH--SVIYCVHRGSGYTVINGTKFNWKKGDYFVVPNWN 320
Cdd:pfam11699   9 TPFFASGILDLPPGA-EKKPKNSKkmTMVFYVIQGRVEVTVHKTSFIIGKGSVFQVPRGN 67
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
105-167 1.30e-03

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 38.07  E-value: 1.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1478266570 105 LQPGEEAPS-HRHTQSA-LRFITDGEGAYTIvQGERIFMEEGDFLTTPKNLWHGHGHLGDEPMIW 167
Cdd:COG3837    35 LPPGASSSPyHAHSAEEeFVYVLEGELTLRI-GGEEYVLEPGDSVGFPAGVPHRLRNRGDEPARY 98
Adi1 COG1791
Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and ...
 114-155 1.98e-03

Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism];


Pssm-ID: 441396  Cd Length: 180  Bit Score: 38.64  E-value: 1.98e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1478266570 114 HRHTQSALRFITDGEGAYTIVQGERIFM---EEGDFLTTPKNLWH 155
Cdd:COG1791    96 HTHTEDEVRFFVAGEGLFGLHLGGKVYEvlcEAGDLISVPAGTEH 140
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 270-332 2.64e-03

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.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 36.31  E-value: 2.64e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1478266570 270 MTHLPKGHHTKAHRHTHS--VIYcVHRGSGYTVINGT-KFNWKKGDYFVVPNWNWHEHVASEDSYL 332
Cdd:cd02208     3 VVTLPPGTSSPPHWHPEQdeIFY-VLSGEGELTLDDGeTVELKAGDIVLIPPGVPHSFVNTSDEPA 67
cupin_TcmJ-like cd06991
TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of ...
 95-165 3.55e-03

TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of the tetracenomycin (TCM) polyketide synthase (PKS) type II complex in Streptomyces glaucescens. TcmJ is a quinone-forming monooxygenase involved in the modification of aromatic polyketides synthesized by polyketide synthases of types II and III. Orthologs of TcmJ include the Streptomyces BenD (benastatin biosynthetic pathway), the Streptomyces olivaceus ElmJ (polyketide antibiotic elloramycin biosynthetic pathway), the Actinomadura hibisca PdmL (pradimicin biosynthetic pathway), the Streptomyces cyaneus CurC (curamycin biosynthetic pathway), the Streptomyces rishiriensis Lct30 (lactonamycin biosynthetic pathway), and the Streptomyces WhiE II (spore pigment polyketide biosynthetic pathway). Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380396 [Multi-domain]  Cd Length: 105  Bit Score: 36.50  E-value: 3.55e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1478266570  95 TQTLYAAVQLLQPGEEAPSHRHTQSALR-FITDGEGAYTIvQGERIFMEEGDFLTTPKNLWHGHGHLGDEPM 165
Cdd:cd06991    16 ATSGFMGTLTLAPGERVSEHYHPYSEEFlYVVRGRLVVRV-DGEPVVLEAGEALLVPRGVRHRLENAGDEPA 86
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 269-322 4.53e-03

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380351 [Multi-domain]  Cd Length: 91  Bit Score: 35.89  E-value: 4.53e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1478266570 269 RMTHLPKGHHTKAHRHTHS-VIYcVHRGSGYTVINGTKFNWKKGDYFVVPNWNWH 322
Cdd:cd02222    20 RYFEIEPGGHTPLHTHPWEhEVY-VLRGKGVVVIGGEEYPVKPGDVVYIPPNEPH 73
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 273-317 7.39e-03

Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion.


Pssm-ID: 380344 [Multi-domain]  Cd Length: 100  Bit Score: 35.57  E-value: 7.39e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1478266570 273 LPKGHHTKAHRHTHSV-IYCVHRGSGYTVINGTKFNWKKGDYFVVP 317
Cdd:cd02214    26 VPPGESTLPHRLKGSEeVYYILEGEGTMEIDGEPREVGPGDAVLIP 71
Cupin_1 smart00835
Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' ...
 277-337 8.56e-03

Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant.


Pssm-ID: 214845 [Multi-domain]  Cd Length: 146  Bit Score: 36.49  E-value: 8.56e-03
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1478266570  277 HHTkaHRHTHSVIYCVhRGSGYTVI---NGTK---FNWKKGDYFVVPNWNWHEHVASEDSYL----FSVND 337
Cdd:smart00835  45 PHY--HPRATELLYVV-RGEGRVGVvdpNGNKvydARLREGDVFVVPQGHPHFQVNSGDENLefvaFNTND 112
 
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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