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Conserved domains on  [gi|1347653426|gb|PPR62353|]
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hypothetical protein CFH10_00857 [Alphaproteobacteria bacterium MarineAlpha4_Bin2]

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 ...
 26-120 3.92e-28

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 cd02233:

Pssm-ID: 477354 [Multi-domain]  Cd Length: 106  Bit Score: 99.16  E-value: 3.92e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1347653426  26 GEVRRSRqvIIEPSESENYNCSVVNFTKGSTTGWHIHDCDQILVVVHGIGLVASEGEEEQEITVGDVVHIKAGENHWHGA 105
Cdd:cd02233     3 GTVWLDP--LFPADEPSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                          90
                  ....*....|....*
gi 1347653426 106 KADTVMGHITVTLKG 120
Cdd:cd02233    81 APDSAMTHLAITEAL 95
 
Name Accession Description Interval E-value
cupin_HNL-like cd02233
Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This ...
 26-120 3.92e-28

Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This family includes archaeal, eukaryotic, and bacterial proteins homologous to hydroxynitrile lyase from Granulicella tundricola (GtHNL), a novel class of HNLs that does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs. HNLs comprise a diverse group of enzymes that vary in terms of their substrate specificity, enantioselectivity and the need for a co-factor. In plants, they catalyze the reversible cleavage of cyanohydrins, yielding HCN and aldehydes or ketones. Also included in this family is TM1010 from Thermotoga maritima, a protein of unknown function. Some but not all members of this family have N- or C-terminal carboxymuconolactone decarboxylase domains in addition to the cupin domain. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380361 [Multi-domain]  Cd Length: 106  Bit Score: 99.16  E-value: 3.92e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1347653426  26 GEVRRSRqvIIEPSESENYNCSVVNFTKGSTTGWHIHDCDQILVVVHGIGLVASEGEEEQEITVGDVVHIKAGENHWHGA 105
Cdd:cd02233     3 GTVWLDP--LFPADEPSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                          90
                  ....*....|....*
gi 1347653426 106 KADTVMGHITVTLKG 120
Cdd:cd02233    81 APDSAMTHLAITEAL 95
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
48-116 8.91e-12

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 57.17  E-value: 8.91e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1347653426  48 VVNFTKGSTTGWHIHDCDQILVVVHGIGLVaSEGEEEQEITVGDVVHIKAGENHWHGAKADTVMGHITV 116
Cdd:COG1917    27 RVTFEPGARTPWHSHPGEELIYVLEGEGEV-EVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVV 94
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 48-111 2.96e-04

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: 36.85  E-value: 2.96e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1347653426  48 VVNFTKGSTTGWHIH-DCDQILVVVHGIGLVaSEGEEEQEITVGDVVHIKAGENHWHGAKADTVM 111
Cdd:pfam07883   2 LVTLPPGESSPPHRHpGEDEFFYVLEGEGEL-TVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPA 65
 
Name Accession Description Interval E-value
cupin_HNL-like cd02233
Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This ...
 26-120 3.92e-28

Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain; This family includes archaeal, eukaryotic, and bacterial proteins homologous to hydroxynitrile lyase from Granulicella tundricola (GtHNL), a novel class of HNLs that does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs. HNLs comprise a diverse group of enzymes that vary in terms of their substrate specificity, enantioselectivity and the need for a co-factor. In plants, they catalyze the reversible cleavage of cyanohydrins, yielding HCN and aldehydes or ketones. Also included in this family is TM1010 from Thermotoga maritima, a protein of unknown function. Some but not all members of this family have N- or C-terminal carboxymuconolactone decarboxylase domains in addition to the cupin domain. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.


Pssm-ID: 380361 [Multi-domain]  Cd Length: 106  Bit Score: 99.16  E-value: 3.92e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1347653426  26 GEVRRSRqvIIEPSESENYNCSVVNFTKGSTTGWHIHDCDQILVVVHGIGLVASEGEEEQEITVGDVVHIKAGENHWHGA 105
Cdd:cd02233     3 GTVWLDP--LFPADEPSRVSVANVTFEPGARTAWHTHPGGQILIVTSGVGWVQEEGGPPQELRPGDVVWIPPGVKHWHGA 80

                          90
                  ....*....|....*
gi 1347653426 106 KADTVMGHITVTLKG 120
Cdd:cd02233    81 APDSAMTHLAITEAL 95
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
48-116 8.91e-12

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 57.17  E-value: 8.91e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1347653426  48 VVNFTKGSTTGWHIHDCDQILVVVHGIGLVaSEGEEEQEITVGDVVHIKAGENHWHGAKADTVMGHITV 116
Cdd:COG1917    27 RVTFEPGARTPWHSHPGEELIYVLEGEGEV-EVGGEEYELKPGDVVFIPPGVPHAFRNLGDEPAVLLVV 94
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
1-102 6.63e-06

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 42.05  E-value: 6.63e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1347653426   1 MKVVTLQDIPEIDLGEAVPIAgwdggevrrsrqviiepSESENYNCSVVNFTKGSTTGWHIH-DCDQILVVVHGIGLVAS 79
Cdd:COG0662     1 MQDVNIEELKAIGWGSYEVLG-----------------EGGERLSVKRITVPPGAELSLHVHpHRDEFFYVLEGTGEVTI 63

                          90       100
                  ....*....|....*....|...
gi 1347653426  80 eGEEEQEITVGDVVHIKAGENHW 102
Cdd:COG0662    64 -GDEEVELKAGDSVYIPAGVPHR 85
cupin_DddK cd06988
Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain; This family includes ...
 54-101 1.15e-05

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: 40.68  E-value: 1.15e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1347653426  54 GSTTGWHIHDCDQILVVVHGIGLVASEGEEEqEITVGDVVHIKAGENH 101
Cdd:cd06988    12 GTTSTPHSHHEYEIFIVISGKGIVVVDGERE-PVKAGDVVYIPPGTEH 58
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 31-102 1.63e-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: 40.51  E-value: 1.63e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1347653426  31 SRQVIIEPSE-SENYNCSVVNFTKGSTTGWHIHDCDQILVVVHGIGLVASEGEEeQEITVGDVVHIKAGENHW 102
Cdd:cd02222     3 TIRVLIGPEDgAPNFAMRYFEIEPGGHTPLHTHPWEHEVYVLRGKGVVVIGGEE-YPVKPGDVVYIPPNEPHQ 74
cupin_Bh2720-like cd02223
Bacillus halodurans Bh2720 and related proteins, cupin domain; This family includes bacterial, ...
 54-101 7.97e-05

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: 38.68  E-value: 7.97e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1347653426  54 GSTTGWHIHDC-DQILVVVHGIGLvASEGEEEQEITVGDVVHIKAGENH 101
Cdd:cd02223    21 GEDIGLEVHDDvDQFLRIEEGEGK-AIMGGFESEVKDGDAIIVPAGTWH 68
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 48-111 2.96e-04

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: 36.85  E-value: 2.96e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1347653426  48 VVNFTKGSTTGWHIH-DCDQILVVVHGIGLVaSEGEEEQEITVGDVVHIKAGENHWHGAKADTVM 111
Cdd:pfam07883   2 LVTLPPGESSPPHRHpGEDEFFYVLEGEGEL-TVDGEEVVLKAGDSVYFPAGVPHRFRNTGDEPA 65
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 54-102 4.59e-04

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: 36.73  E-value: 4.59e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1347653426  54 GSTTGWHIHDC-DQILVVVHGIGLVASEGEEeQEITVGDVVHIKAGENHW 102
Cdd:cd02214    29 GESTLPHRLKGsEEVYYILEGEGTMEIDGEP-REVGPGDAVLIPPGAVQR 77
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 47-109 4.75e-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.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 36.31  E-value: 4.75e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1347653426  47 SVVNFTKGSTTGWHIHD-CDQILVVVHGIGLVASEGEEEQEITVGDVVHIKAGENHWHGAKADT 109
Cdd:cd02208     2 SVVTLPPGTSSPPHWHPeQDEIFYVLSGEGELTLDDGETVELKAGDIVLIPPGVPHSFVNTSDE 65
cupin_BLL4011-like cd02235
Bradyrhizobium diazoefficiens BLL4011 and related proteins, cupin domain; This family includes ...
 48-101 8.80e-04

Bradyrhizobium diazoefficiens BLL4011 and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to BLL4011, a Bradyrhizobium diazoefficiens 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: 380363 [Multi-domain]  Cd Length: 100  Bit Score: 36.02  E-value: 8.80e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1347653426  48 VVNFTKGSTTGWHIHDCDQILVVVHGIGLVASEGEEEQEITVGDVVHIKAGENH 101
Cdd:cd02235    23 RVEIPPGAVAGRHTHPGEESGYVLEGSLELEVDGQPPVTLKAGDSFFIPAGTVH 76
cupin_TTHA0104 cd06122
Thermus thermophilus TTHA0104 and related proteins, cupin domain; This family contains ...
 40-101 2.84e-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: 34.84  E-value: 2.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1347653426  40 ESENYNCSVVNFTKGSTTGWHIH-DCDQILVVVHGIGLVaSEGEEEQEITVGDVVHIKAGENH 101
Cdd:cd06122    23 ESERLFCDLYCLEPGQSQKVHAHaGSDKVYFVLEGEGRF-TVGDEERELGAGEAVLAPAGVPH 84
cupin_bxe_c0505 cd06980
uncharacterized protein bxe_c0505, cupin domain; This family includes mostly bacterial ...
 56-101 4.83e-03

uncharacterized protein bxe_c0505, cupin domain; This family includes mostly bacterial proteins homologous to bxe_c0505, a Burkholderia xenovorans 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: 380385 [Multi-domain]  Cd Length: 105  Bit Score: 34.08  E-value: 4.83e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1347653426  56 TTGWHIHDCD-QILVVVHGIGLVASEGEEEQEITVGDVVHIKAGENH 101
Cdd:cd06980    35 PTGWHYHDCDfQMVYVLKGWVKFEFEGGGEVRLEAGDCVYQPPGIRH 81
cupin_7S_vicilin-like_N cd02244
7S vicilin seed storage globulin, N-terminal cupin domain; This family contains the N-terminal ...
 63-98 7.30e-03

7S vicilin seed storage globulin, N-terminal cupin domain; This family contains the N-terminal domains of plant 7S seed storage proteins such as vicilin, and includes beta-conglycinin, phaseolin, canavalin, conglutin-beta, a chromatin protein in Pisum sativum called P54, and a sucrose binding protein in soybean called SBP. These 7S globulins also include soybean allergen beta-conglycinin, peanut allergen conarachin (Ara h 1), walnut allergen Jug r 2, and lentil allergen Len c 1. Proteins in this family perform various functions, including a role in sucrose binding, desiccation, defense against microbes and oxidative stress. The vicilin peptides formed by trypsin or chymotrypsin digestion exhibit antihypertensive effects. These plant seed storage globulins have tandem cupin-like beta-barrel folds (referred to as a bicupin). Storage proteins are the cause of well-known allergic reactions to peanuts and cereals. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.


Pssm-ID: 380371  Cd Length: 178  Bit Score: 34.41  E-value: 7.30e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1347653426  63 DCDQILVVVHG---IGLVASEGEEEQEITVGDVVHIKAG 98
Cdd:cd02244    47 DADMVFYVHTGrgtITWVDEDKRESYNLERGDVYRIPAG 85
 
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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