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Conserved domains on  [gi|1084463925|gb|OGN30019|]
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MAG: hypothetical protein A3A33_01700 [Candidatus Yanofskybacteria bacterium RIFCSPLOWO2_01_FULL_49_25]

Protein Classification

cupin domain-containing protein( domain architecture ID 1562428)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
cupin_RmlC-like super family cl40423
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 37-131 4.10e-04

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.


The actual alignment was detected with superfamily member TIGR04366:

Pssm-ID: 477354  Cd Length: 132  Bit Score: 37.92  E-value: 4.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084463925  37 PLQVGLIEHRHGKKVLPHIHRNlfydvntTQEFIYVEKGRnILITLFDIKWTEIKKIKMAAGDSILFV----GGGHSLDI 112
Cdd:TIGR04366  33 PVQRMLIALEPGTYVRPHRHPH-------KSETFIVLEGE-LDVLLFDDDGEVTERVVLSPGGGTFGVeippGTWHTLVA 104

                          90       100
                  ....*....|....*....|.
gi 1084463925 113 -PPNCRLFEIKQGPY-PGDAK 131
Cdd:TIGR04366 105 lSEGTVIFEVKEGPYdPLADK 125
 
Name Accession Description Interval E-value
cupin_WbuC TIGR04366
cupin fold metalloprotein, WbuC family; Members of this family show sequence similarity to ...
 37-131 4.10e-04

cupin fold metalloprotein, WbuC family; Members of this family show sequence similarity to cupin fold proteins (see pfam07883), including conserved His residues likely to serve as metal-binding ligands. Many members occur in bacterial O-antigen biosynthesis regions. Some members have acquired the gene symbol wbuC (e.g. Jarvis, et al, 2011), but publications using this term do not ascribe a function.


Pssm-ID: 275159  Cd Length: 132  Bit Score: 37.92  E-value: 4.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084463925  37 PLQVGLIEHRHGKKVLPHIHRNlfydvntTQEFIYVEKGRnILITLFDIKWTEIKKIKMAAGDSILFV----GGGHSLDI 112
Cdd:TIGR04366  33 PVQRMLIALEPGTYVRPHRHPH-------KSETFIVLEGE-LDVLLFDDDGEVTERVVLSPGGGTFGVeippGTWHTLVA 104

                          90       100
                  ....*....|....*....|.
gi 1084463925 113 -PPNCRLFEIKQGPY-PGDAK 131
Cdd:TIGR04366 105 lSEGTVIFEVKEGPYdPLADK 125
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
26-129 4.87e-04

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 37.43  E-value: 4.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084463925  26 GSIRFLTPQSFPLQVGLIEHRHGKKVLPHIHRNlfydvntTQEFIYVEKGRnILITLFDikwteiKKIKMAAGDSILF-V 104
Cdd:COG0662    15 GSYEVLGEGGERLSVKRITVPPGAELSLHVHPH-------RDEFFYVLEGT-GEVTIGD------EEVELKAGDSVYIpA 80

                          90       100
                  ....*....|....*....|....*....
gi 1084463925 105 GGGHSL----DIPpnCRLFEIKQGPYPGD 129
Cdd:COG0662    81 GVPHRLrnpgDEP--LELLEVQAPAYLGE 107
cupin_WbuC-like cd07005
Escherichia coli WbuC and related proteins, cupin domain; This family includes bacterial ...
 37-131 1.06e-03

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


Pssm-ID: 380408  Cd Length: 114  Bit Score: 36.34  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084463925  37 PLQVGLIEHRHGKKVLPHIHRNlfydvNTTQEFIYVEKGRnILITLFDIKWTEIKKIKMAAGDSILFVggghslDIPPN- 115
Cdd:cd07005    15 PVQRMLNALQPGTYVRPHRHPD-----PPKWELFVVLRGR-IAVLIFDDDGTVTERVILGAGGGVFGI------EIPPGt 82

                          90       100
                  ....*....|....*....|....*..
gi 1084463925 116 -----CR-----LFEIKQGPY-PGDAK 131
Cdd:cd07005    83 whtvvALepdtvIFEVKEGPYdPATDK 109
 
Name Accession Description Interval E-value
cupin_WbuC TIGR04366
cupin fold metalloprotein, WbuC family; Members of this family show sequence similarity to ...
 37-131 4.10e-04

cupin fold metalloprotein, WbuC family; Members of this family show sequence similarity to cupin fold proteins (see pfam07883), including conserved His residues likely to serve as metal-binding ligands. Many members occur in bacterial O-antigen biosynthesis regions. Some members have acquired the gene symbol wbuC (e.g. Jarvis, et al, 2011), but publications using this term do not ascribe a function.


Pssm-ID: 275159  Cd Length: 132  Bit Score: 37.92  E-value: 4.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084463925  37 PLQVGLIEHRHGKKVLPHIHRNlfydvntTQEFIYVEKGRnILITLFDIKWTEIKKIKMAAGDSILFV----GGGHSLDI 112
Cdd:TIGR04366  33 PVQRMLIALEPGTYVRPHRHPH-------KSETFIVLEGE-LDVLLFDDDGEVTERVVLSPGGGTFGVeippGTWHTLVA 104

                          90       100
                  ....*....|....*....|.
gi 1084463925 113 -PPNCRLFEIKQGPY-PGDAK 131
Cdd:TIGR04366 105 lSEGTVIFEVKEGPYdPLADK 125
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
26-129 4.87e-04

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 37.43  E-value: 4.87e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084463925  26 GSIRFLTPQSFPLQVGLIEHRHGKKVLPHIHRNlfydvntTQEFIYVEKGRnILITLFDikwteiKKIKMAAGDSILF-V 104
Cdd:COG0662    15 GSYEVLGEGGERLSVKRITVPPGAELSLHVHPH-------RDEFFYVLEGT-GEVTIGD------EEVELKAGDSVYIpA 80

                          90       100
                  ....*....|....*....|....*....
gi 1084463925 105 GGGHSL----DIPpnCRLFEIKQGPYPGD 129
Cdd:COG0662    81 GVPHRLrnpgDEP--LELLEVQAPAYLGE 107
cupin_WbuC-like cd07005
Escherichia coli WbuC and related proteins, cupin domain; This family includes bacterial ...
 37-131 1.06e-03

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


Pssm-ID: 380408  Cd Length: 114  Bit Score: 36.34  E-value: 1.06e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1084463925  37 PLQVGLIEHRHGKKVLPHIHRNlfydvNTTQEFIYVEKGRnILITLFDIKWTEIKKIKMAAGDSILFVggghslDIPPN- 115
Cdd:cd07005    15 PVQRMLNALQPGTYVRPHRHPD-----PPKWELFVVLRGR-IAVLIFDDDGTVTERVILGAGGGVFGI------EIPPGt 82

                          90       100
                  ....*....|....*....|....*..
gi 1084463925 116 -----CR-----LFEIKQGPY-PGDAK 131
Cdd:cd07005    83 whtvvALepdtvIFEVKEGPYdPATDK 109
 
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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