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Conserved domains on  [gi|447212601|ref|WP_001289857|]
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MULTISPECIES: gentisate 1,2-dioxygenase [Salmonella]

Protein Classification

gentisate_1_2 family protein( domain architecture ID 11494109)

gentisate_1_2 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
gentisate_1_2 TIGR02272
gentisate 1,2-dioxygenase; This family consists of gentisate 1,2-dioxygenases. This ...
 11-344 0e+00

gentisate 1,2-dioxygenase; This family consists of gentisate 1,2-dioxygenases. This ring-opening enzyme acts in salicylate degradation that goes via gentisate rather than via catechol. It converts gentisate to maleylpyruvate. Some putative gentisate 1,2-dioxygenases are excluded by a relatively high trusted cutoff score because they are too closely related to known examples of 1-hydroxy-2-naphthoate dioxygenase. Therefore some homologs may be bona fide gentisate 1,2-dioxygenases even if they score below the given cutoffs.


:

Pssm-ID: 131325 [Multi-domain]  Cd Length: 335  Bit Score: 676.89  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601   11 SRQQYYQHISGQNLTPLWESLHHLVPQTPNANCAPAYWNYQEIRPLLMESGNVIGAKEAIRRVLVLENPALRGQSSITAT 90
Cdd:TIGR02272   1 EREAFYSKISGQNLTPLWEVLHALVPAEPKSNCAPHHWNYQEIRPLLMEAGDLISAKEAERRVLVLENPGLRGQSSITTS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601   91 LYAGLQLILPGEVAPSHRHNQSALRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLDGLDLPLVN 170
Cdd:TIGR02272  81 LYAGLQLILPGEVAPSHRHTQSALRFIVEGKGAFTAVDGERTTMHPGDFIITPSWTWHDHGNPGDEPMIWLDGLDIPLVQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  171 LLGCGFAEDYPEDQQPVTRKEGDYLPRYAANMLPLRHQRGN-SSPIFNYRYDRSREALHDLTRMGDPDEWEGYKLRYVNP 249
Cdd:TIGR02272 161 LFDCSFAEGYPEDQQPVTRPEGDSLARYGHNMLPVRHKRSDrSSPIFNYPYERSREALDDLTRTGEWDPWHGLKLRYVNP 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  250 VTGGYPMPSMGAFLQLLPKGFASRVARSTDSTIYHVVEGAGQVTIGNETFHFSAKDIFVAPTWHEVSFRSSEDTVLFSFS 329
Cdd:TIGR02272 241 ATGGYPMPTIGAFIQLLPKGFRTATYRSTDATVFCVVEGRGQVRIGDAVFRFSPKDVFVVPSWHPVRFEASDDAVLFSFS 320

                         330
                  ....*....|....*
gi 447212601  330 DKPVQEALGLFREAR 344
Cdd:TIGR02272 321 DRPVQQKLGLFREAR 335
 
Name Accession Description Interval E-value
gentisate_1_2 TIGR02272
gentisate 1,2-dioxygenase; This family consists of gentisate 1,2-dioxygenases. This ...
 11-344 0e+00

gentisate 1,2-dioxygenase; This family consists of gentisate 1,2-dioxygenases. This ring-opening enzyme acts in salicylate degradation that goes via gentisate rather than via catechol. It converts gentisate to maleylpyruvate. Some putative gentisate 1,2-dioxygenases are excluded by a relatively high trusted cutoff score because they are too closely related to known examples of 1-hydroxy-2-naphthoate dioxygenase. Therefore some homologs may be bona fide gentisate 1,2-dioxygenases even if they score below the given cutoffs.


Pssm-ID: 131325 [Multi-domain]  Cd Length: 335  Bit Score: 676.89  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601   11 SRQQYYQHISGQNLTPLWESLHHLVPQTPNANCAPAYWNYQEIRPLLMESGNVIGAKEAIRRVLVLENPALRGQSSITAT 90
Cdd:TIGR02272   1 EREAFYSKISGQNLTPLWEVLHALVPAEPKSNCAPHHWNYQEIRPLLMEAGDLISAKEAERRVLVLENPGLRGQSSITTS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601   91 LYAGLQLILPGEVAPSHRHNQSALRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLDGLDLPLVN 170
Cdd:TIGR02272  81 LYAGLQLILPGEVAPSHRHTQSALRFIVEGKGAFTAVDGERTTMHPGDFIITPSWTWHDHGNPGDEPMIWLDGLDIPLVQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  171 LLGCGFAEDYPEDQQPVTRKEGDYLPRYAANMLPLRHQRGN-SSPIFNYRYDRSREALHDLTRMGDPDEWEGYKLRYVNP 249
Cdd:TIGR02272 161 LFDCSFAEGYPEDQQPVTRPEGDSLARYGHNMLPVRHKRSDrSSPIFNYPYERSREALDDLTRTGEWDPWHGLKLRYVNP 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  250 VTGGYPMPSMGAFLQLLPKGFASRVARSTDSTIYHVVEGAGQVTIGNETFHFSAKDIFVAPTWHEVSFRSSEDTVLFSFS 329
Cdd:TIGR02272 241 ATGGYPMPTIGAFIQLLPKGFRTATYRSTDATVFCVVEGRGQVRIGDAVFRFSPKDVFVVPSWHPVRFEASDDAVLFSFS 320

                         330
                  ....*....|....*
gi 447212601  330 DKPVQEALGLFREAR 344
Cdd:TIGR02272 321 DRPVQQKLGLFREAR 335
COG3435 COG3435
Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
34-345 7.60e-180

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


Pssm-ID: 442661 [Multi-domain]  Cd Length: 316  Bit Score: 500.15  E-value: 7.60e-180
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  34 LVPQTPNANCAPAYWNYQEIRPLLMESGNVIGAKEAIRRVLVLENPALRGQSSITATLYAGLQLILPGEVAPSHRHNQSA 113
Cdd:COG3435    1 LVPPEPRPKAVPHLWRYADLRPLLLRAGRLVTAERAERRVLVLENPGLGGKSAATPTLYAGIQLLLPGEVAPAHRHTQSA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601 114 LRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLDGLDLPLVNLLGCGFAEDYPEDQQPVTRKEGD 193
Cdd:COG3435   81 LRFVIEGEGAYTVVDGERVPMERGDFVLTPSWTWHDHGNEGDEPMIWLDGLDIPLVELLEAGFFEDGPDDVQPVTRPEGD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601 194 YLPRYAANML-PLRHQR-GNSSPIFNYRYDRSREALHDLTRMGDPDEWEGYKLRYVNPVTGGYPMPSMGAFLQLLPKGFA 271
Cdd:COG3435  161 SEARYGHGGLrPYEFLRdTVSSPLLHYPWERTREALERLAALEEPDPYGGAALRYVNPATGGDVMPTIGAFMQLLPPGFH 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 447212601 272 SRVARSTDSTIYHVVEGAGQVTIGNETFHFSAKDIFVAPTWHEVSFRS-SEDTVLFSFSDKPVQEALGLFREARY 345
Cdd:COG3435  241 TRPHRHTGSAVYHVVEGSGRSIVGGERFDWGEGDLFVVPSWAWHSHASaDEDAVLFSFSDRPVQEALGLYREERL 315
cupin_GDO-like_N cd02216
gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, ...
 71-178 8.43e-66

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: 202.79  E-value: 8.43e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  71 RRVLVLENPALRGQSSITATLYAGLQLILPGEVAPSHRHNQSALRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDH 150
Cdd:cd02216    1 RRVLLLVNPGLPGTRATTHTLYAGLQLLPPGEVAPAHRHTPNALRFVLEGPGAYTTVDGERCDMEPGDLILTPPGTWHDH 80

                         90       100
                 ....*....|....*....|....*...
gi 447212601 151 GNPGSEPVVWLDGLDLPLVNLLGCGFAE 178
Cdd:cd02216   81 GNEGDEPAIWLDGLDAPLVTYLRASFFE 108
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 94-162 2.29e-19

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: 80.77  E-value: 2.29e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601   94 GLQLILPGEVAPSHRH-NQSALRFIVEGKGAFTaVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLD 162
Cdd:pfam07883   1 GLVTLPPGESSPPHRHpGEDEFFYVLEGEGELT-VDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLD 69
 
Name Accession Description Interval E-value
gentisate_1_2 TIGR02272
gentisate 1,2-dioxygenase; This family consists of gentisate 1,2-dioxygenases. This ...
 11-344 0e+00

gentisate 1,2-dioxygenase; This family consists of gentisate 1,2-dioxygenases. This ring-opening enzyme acts in salicylate degradation that goes via gentisate rather than via catechol. It converts gentisate to maleylpyruvate. Some putative gentisate 1,2-dioxygenases are excluded by a relatively high trusted cutoff score because they are too closely related to known examples of 1-hydroxy-2-naphthoate dioxygenase. Therefore some homologs may be bona fide gentisate 1,2-dioxygenases even if they score below the given cutoffs.


Pssm-ID: 131325 [Multi-domain]  Cd Length: 335  Bit Score: 676.89  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601   11 SRQQYYQHISGQNLTPLWESLHHLVPQTPNANCAPAYWNYQEIRPLLMESGNVIGAKEAIRRVLVLENPALRGQSSITAT 90
Cdd:TIGR02272   1 EREAFYSKISGQNLTPLWEVLHALVPAEPKSNCAPHHWNYQEIRPLLMEAGDLISAKEAERRVLVLENPGLRGQSSITTS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601   91 LYAGLQLILPGEVAPSHRHNQSALRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLDGLDLPLVN 170
Cdd:TIGR02272  81 LYAGLQLILPGEVAPSHRHTQSALRFIVEGKGAFTAVDGERTTMHPGDFIITPSWTWHDHGNPGDEPMIWLDGLDIPLVQ 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  171 LLGCGFAEDYPEDQQPVTRKEGDYLPRYAANMLPLRHQRGN-SSPIFNYRYDRSREALHDLTRMGDPDEWEGYKLRYVNP 249
Cdd:TIGR02272 161 LFDCSFAEGYPEDQQPVTRPEGDSLARYGHNMLPVRHKRSDrSSPIFNYPYERSREALDDLTRTGEWDPWHGLKLRYVNP 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  250 VTGGYPMPSMGAFLQLLPKGFASRVARSTDSTIYHVVEGAGQVTIGNETFHFSAKDIFVAPTWHEVSFRSSEDTVLFSFS 329
Cdd:TIGR02272 241 ATGGYPMPTIGAFIQLLPKGFRTATYRSTDATVFCVVEGRGQVRIGDAVFRFSPKDVFVVPSWHPVRFEASDDAVLFSFS 320

                         330
                  ....*....|....*
gi 447212601  330 DKPVQEALGLFREAR 344
Cdd:TIGR02272 321 DRPVQQKLGLFREAR 335
COG3435 COG3435
Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
34-345 7.60e-180

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


Pssm-ID: 442661 [Multi-domain]  Cd Length: 316  Bit Score: 500.15  E-value: 7.60e-180
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  34 LVPQTPNANCAPAYWNYQEIRPLLMESGNVIGAKEAIRRVLVLENPALRGQSSITATLYAGLQLILPGEVAPSHRHNQSA 113
Cdd:COG3435    1 LVPPEPRPKAVPHLWRYADLRPLLLRAGRLVTAERAERRVLVLENPGLGGKSAATPTLYAGIQLLLPGEVAPAHRHTQSA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601 114 LRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLDGLDLPLVNLLGCGFAEDYPEDQQPVTRKEGD 193
Cdd:COG3435   81 LRFVIEGEGAYTVVDGERVPMERGDFVLTPSWTWHDHGNEGDEPMIWLDGLDIPLVELLEAGFFEDGPDDVQPVTRPEGD 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601 194 YLPRYAANML-PLRHQR-GNSSPIFNYRYDRSREALHDLTRMGDPDEWEGYKLRYVNPVTGGYPMPSMGAFLQLLPKGFA 271
Cdd:COG3435  161 SEARYGHGGLrPYEFLRdTVSSPLLHYPWERTREALERLAALEEPDPYGGAALRYVNPATGGDVMPTIGAFMQLLPPGFH 240

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 447212601 272 SRVARSTDSTIYHVVEGAGQVTIGNETFHFSAKDIFVAPTWHEVSFRS-SEDTVLFSFSDKPVQEALGLFREARY 345
Cdd:COG3435  241 TRPHRHTGSAVYHVVEGSGRSIVGGERFDWGEGDLFVVPSWAWHSHASaDEDAVLFSFSDRPVQEALGLYREERL 315
cupin_GDO-like_N cd02216
gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, ...
 71-178 8.43e-66

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: 202.79  E-value: 8.43e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  71 RRVLVLENPALRGQSSITATLYAGLQLILPGEVAPSHRHNQSALRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDH 150
Cdd:cd02216    1 RRVLLLVNPGLPGTRATTHTLYAGLQLLPPGEVAPAHRHTPNALRFVLEGPGAYTTVDGERCDMEPGDLILTPPGTWHDH 80

                         90       100
                 ....*....|....*....|....*...
gi 447212601 151 GNPGSEPVVWLDGLDLPLVNLLGCGFAE 178
Cdd:cd02216   81 GNEGDEPAIWLDGLDAPLVTYLRASFFE 108
cupin_GDO-like_C cd06992
gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase ...
 241-338 3.61e-52

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: 167.66  E-value: 3.61e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601 241 GYKLRYVNPVTGGYPMPSMGAFLQLLPKGFASRVARSTDSTIYHVVEGAGQVTIGNETFHFSAKDIFVAPTWHEVSFR-S 319
Cdd:cd06992    1 GVALEYVNPTTGGPVMPTIGAFMQLLRAGFSTRPHRSTASAVYHVVEGSGRTVIGGKTFEWEPGDVFVVPSWAWHSHEaD 80

                         90
                 ....*....|....*....
gi 447212601 320 SEDTVLFSFSDKPVQEALG 338
Cdd:cd06992   81 SEDAVLFSFSDRPVQEALG 99
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 94-162 2.29e-19

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: 80.77  E-value: 2.29e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601   94 GLQLILPGEVAPSHRH-NQSALRFIVEGKGAFTaVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLD 162
Cdd:pfam07883   1 GLVTLPPGESSPPHRHpGEDEFFYVLEGEGELT-VDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPARLLD 69
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 93-161 9.35e-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.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 57.11  E-value: 9.35e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447212601  93 AGLQLILPGEVAPSHRH-NQSALRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWL 161
Cdd:cd02208    1 ISVVTLPPGTSSPPHWHpEQDEIFYVLSGEGELTLDDGETVELKAGDIVLIPPGVPHSFVNTSDEPAVFL 70
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
100-162 6.65e-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: 6.65e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447212601 100 PGEVAPSHRHNQSALRFIVEGKGAFTaVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLD 162
Cdd:COG1917   32 PGARTPWHSHPGEELIYVLEGEGEVE-VGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLV 93
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
98-161 1.08e-07

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 49.75  E-value: 1.08e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 447212601  98 ILPGEVAPSHRHNQSA-LRFIVEGKGAFTaVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWL 161
Cdd:COG0662   34 VPPGAELSLHVHPHRDeFFYVLEGTGEVT-IGDEEVELKAGDSVYIPAGVPHRLRNPGDEPLELL 97
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 100-161 6.40e-05

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: 41.28  E-value: 6.40e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 447212601 100 PGEVAPSHRHNQSALRFIVEGKGAFTaVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWL 161
Cdd:cd02222   26 PGGHTPLHTHPWEHEVYVLRGKGVVV-IGGEEYPVKPGDVVYIPPNEPHQFRNTGDEPLGFL 86
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 100-162 3.28e-04

Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380393 [Multi-domain]  Cd Length: 76  Bit Score: 38.76  E-value: 3.28e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 447212601 100 PGEVAPSHRHNQSALRFIVEGKGAFTaVDGERTPMHTGDFILTPQWRWHDHGNPGSEP----VVWLD 162
Cdd:cd06988   11 PGTTSTPHSHHEYEIFIVISGKGIVV-VDGEREPVKAGDVVYIPPGTEHYVKNDGDEDfefySIWWD 76
cupin_CV2614-like cd02236
Chromobacterium violaceum CV2614 and related proteins, cupin domain; This family includes ...
 83-161 4.41e-04

Chromobacterium violaceum CV2614 and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to CV2614, a Chromobacterium violaceum protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380364 [Multi-domain]  Cd Length: 102  Bit Score: 39.01  E-value: 4.41e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 447212601  83 GQSSITATLYAglqlILPGEVAPSHRHNQSALRFIVEGKGAFTAVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWL 161
Cdd:cd02236   18 GQPEITVLRIT----IPPGAELPWHTHPVPNAGYVLSGELTVEYEDGKKRTFKAGDAFVEAVNTWHRGRNGGDEPVELL 92
cupin_yp_001338853-like cd07008
Klebsiella pneumoniae yp_001338853.1 and related proteins, cupin domain; This family includes ...
 99-159 1.41e-03

Klebsiella pneumoniae yp_001338853.1 and related proteins, cupin domain; This family includes bacterial proteins homologous to Klebsiella pneumoniae yp_001338853.1, an uncharacterized conserved protein with double-stranded beta-helix domain. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380411 [Multi-domain]  Cd Length: 101  Bit Score: 37.62  E-value: 1.41e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447212601  99 LPGEVAPSHRHNQSALRFIV-EGKGAFTAVDGERTPMHTGDFILTPqwRWHDHG--NPGSEPVV 159
Cdd:cd07008   35 KPGQEIAAHIHPHGQDTWIVlSGEGEYLLGDGQTVPIKAGDIVIAP--AGQVHGarNTGDEPLV 96
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
257-328 1.86e-03

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 37.14  E-value: 1.86e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 447212601 257 PSMGAFLQLLPKGFASRVARSTDSTIYHVVEGAGQVTIGNETFHFSAKDIFVAP--TWHEVSFRSSEDTVLFSF 328
Cdd:COG1917   21 DELEVVRVTFEPGARTPWHSHPGEELIYVLEGEGEVEVGGEEYELKPGDVVFIPpgVPHAFRNLGDEPAVLLVV 94
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 262-327 1.90e-03

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: 36.47  E-value: 1.90e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 447212601  262 FLQLLPKGFASRVARSTDST-IYHVVEGAGQVTIGNETFHFSAKDIFVAP--TWHEVSFRSSEDTVLFS 327
Cdd:pfam07883   1 GLVTLPPGESSPPHRHPGEDeFFYVLEGEGELTVDGEEVVLKAGDSVYFPagVPHRFRNTGDEPARLLD 69
cupin_TTHA0104 cd06122
Thermus thermophilus TTHA0104 and related proteins, cupin domain; This family contains ...
 88-161 2.39e-03

Thermus thermophilus TTHA0104 and related proteins, cupin domain; This family contains bacterial proteins including TTHA0104 (also called TT1209), a putative antibiotic synthesis protein from Thermus thermophilus. TTHA0104 is a cupin-like protein. The 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).


Pssm-ID: 380377 [Multi-domain]  Cd Length: 102  Bit Score: 37.15  E-value: 2.39e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 447212601  88 TATLYAGLQLILPGEVAPSHRHN-QSALRFIVEGKGAFTaVDGERTPMHTGDFILTPQWRwhDHG--NPGSEPVVWL 161
Cdd:cd06122   24 SERLFCDLYCLEPGQSQKVHAHAgSDKVYFVLEGEGRFT-VGDEERELGAGEAVLAPAGV--PHGvrNTGAERLVLL 97
cupin_TTHA0104 cd06122
Thermus thermophilus TTHA0104 and related proteins, cupin domain; This family contains ...
 282-328 2.63e-03

Thermus thermophilus TTHA0104 and related proteins, cupin domain; This family contains bacterial proteins including TTHA0104 (also called TT1209), a putative antibiotic synthesis protein from Thermus thermophilus. TTHA0104 is a cupin-like protein. The 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).


Pssm-ID: 380377 [Multi-domain]  Cd Length: 102  Bit Score: 36.77  E-value: 2.63e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 447212601 282 IYHVVEGAGQVTIGNETFHFSAKDIFVAP--TWHEVSFRSSEDTVLFSF 328
Cdd:cd06122   51 VYFVLEGEGRFTVGDEERELGAGEAVLAPagVPHGVRNTGAERLVLLVF 99
cupin_TM1287-like cd02221
Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial ...
 107-162 4.11e-03

Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial proteins homologous to TM1287 decarboxylase, a Thermotoga maritima manganese-containing cupin thought to catalyze the conversion of oxalate to formate and carbon dioxide, due to its similarity to oxalate decarboxylase (OXDC) from Bacillus subtilis. TM1287 shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold and forms a homodimer.


Pssm-ID: 380350 [Multi-domain]  Cd Length: 93  Bit Score: 35.91  E-value: 4.11e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 447212601 107 HRH-NQSALRFIVEGKGAFTaVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWLD 162
Cdd:cd02221   35 HQHeGEFEIYYILSGEGLYT-DNGKEYEVKAGDVTFTRDGESHGIENTGDEDLVFIA 90
cupin_Bh2720-like cd02223
Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, ...
 90-157 5.45e-03

Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, archaeal, and eukaryotic proteins similar to Bh2720, a Bacillus halodurans protein of unknown function with a cupin beta-barrel fold.


Pssm-ID: 380352 [Multi-domain]  Cd Length: 98  Bit Score: 35.98  E-value: 5.45e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447212601  90 TLYAG--LQLIL----PGEVAPS--HRHNQSALRfIVEGKGaFTAVDGERTPMHTGDFILTPQWRWHDHGNPGSEP 157
Cdd:cd02223    4 VLWTGknLQLVLmsipPGEDIGLevHDDVDQFLR-IEEGEG-KAIMGGFESEVKDGDAIIVPAGTWHNVINTGNEP 77
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
100-161 6.86e-03

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 36.15  E-value: 6.86e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 447212601 100 PGEVAP---SHRHNQSALrFIVEGKGAFTaVDGERTPMHTGDFILTPQWRWHDHGNPGSEPVVWL 161
Cdd:COG3837   37 PGASSSpyhAHSAEEEFV-YVLEGELTLR-IGGEEYVLEPGDSVGFPAGVPHRLRNRGDEPARYL 99
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 281-329 8.11e-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: 34.77  E-value: 8.11e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 447212601 281 TIYHVVEGAGQVTIG-NETFHFSAKDIFVAPTWHEVSFR--SSEDTVLFSFS 329
Cdd:cd02208   22 EIFYVLSGEGELTLDdGETVELKAGDIVLIPPGVPHSFVntSDEPAVFLVVS 73
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
282-328 9.85e-03

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 35.50  E-value: 9.85e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 447212601 282 IYHVVEGAGQVTIGNETFHFSAKDIFVAP--TWHEVSFRSSEDTVLFSF 328
Cdd:COG0662   51 FFYVLEGTGEVTIGDEEVELKAGDSVYIPagVPHRLRNPGDEPLELLEV 99
 
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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