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Conserved domains on  [gi|1246774206|ref|WP_096358970|]
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cupin domain-containing protein [Variibacter gotjawalensis]

Protein Classification

cupin domain-containing protein( domain architecture ID 14401225)

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

CATH:  2.60.120.10
PubMed:  19478949|14697267|9573603
SCOP:  3001825

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
cupin_bxe_c0505 cd06980
uncharacterized protein bxe_c0505, cupin domain; This family includes mostly bacterial ...
 86-192 5.83e-55

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: 169.67  E-value: 5.83e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246774206  86 GLRSYARYRELGIAAATHGLAQAHVVQFIPPCrpEEVSKLHFHDVDFQMVYVLKGWIKSEFAGEGAHVMREGSCWIQPPK 165
Cdd:cd06980     1 GLRAFFEYRDLGIAEATGGRVGAHVIRATGGG--EGPTGWHYHDCDFQMVYVLKGWVKFEFEGGGEVRLEAGDCVYQPPG 78

                          90       100
                  ....*....|....*....|....*..
gi 1246774206 166 VKHKVLDYSDDCEVLEIILPADFDTVE 192
Cdd:cd06980    79 IRHNVLDYSDDLELLEITSPAEFGTVE 105
valS super family cl36437
valyl-tRNA synthetase; Provisional
 5-64 6.41e-06

valyl-tRNA synthetase; Provisional


The actual alignment was detected with superfamily member PRK14900:

Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 45.75  E-value: 6.41e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246774206    5 AKTRKVAKAArsTARKVSARKPAARKTTARKAPARKAPARKSAARKPAAKKAAKPRTRAA 64
Cdd:PRK14900   991 AMKKKVAKKA--PAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAA 1048
 
Name Accession Description Interval E-value
cupin_bxe_c0505 cd06980
uncharacterized protein bxe_c0505, cupin domain; This family includes mostly bacterial ...
 86-192 5.83e-55

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: 169.67  E-value: 5.83e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246774206  86 GLRSYARYRELGIAAATHGLAQAHVVQFIPPCrpEEVSKLHFHDVDFQMVYVLKGWIKSEFAGEGAHVMREGSCWIQPPK 165
Cdd:cd06980     1 GLRAFFEYRDLGIAEATGGRVGAHVIRATGGG--EGPTGWHYHDCDFQMVYVLKGWVKFEFEGGGEVRLEAGDCVYQPPG 78

                          90       100
                  ....*....|....*....|....*..
gi 1246774206 166 VKHKVLDYSDDCEVLEIILPADFDTVE 192
Cdd:cd06980    79 IRHNVLDYSDDLELLEITSPAEFGTVE 105
valS PRK14900
valyl-tRNA synthetase; Provisional
 5-64 6.41e-06

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 45.75  E-value: 6.41e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246774206    5 AKTRKVAKAArsTARKVSARKPAARKTTARKAPARKAPARKSAARKPAAKKAAKPRTRAA 64
Cdd:PRK14900   991 AMKKKVAKKA--PAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAA 1048
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 119-183 8.11e-06

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: 42.25  E-value: 8.11e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1246774206 119 PEEVSKLHFHDVDFQMVYVLKGWIKSEFAGEgAHVMREGSCWIQPPKVKHKVL-DYSDDCEVLEII 183
Cdd:pfam07883   7 PGESSPPHRHPGEDEFFYVLEGEGELTVDGE-EVVLKAGDSVYFPAGVPHRFRnTGDEPARLLDVY 71
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
119-195 1.80e-05

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 42.44  E-value: 1.80e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1246774206 119 PEEVSKLHFHDVDFQMVYVLKGWIKSEFAGEgAHVMREGSCWIQPPKVKHKVLDYSD-DCEVLEIILPADFDTVELEK 195
Cdd:COG0662    36 PGAELSLHVHPHRDEFFYVLEGTGEVTIGDE-EVELKAGDSVYIPAGVPHRLRNPGDePLELLEVQAPAYLGEDDIVR 112
COG1754 COG1754
Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];
5-46 3.71e-05

Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];


Pssm-ID: 441360 [Multi-domain]  Cd Length: 892  Bit Score: 43.65  E-value: 3.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1246774206   5 AKTRKVAKAARSTARKVSARKPAARKTTARKAPARKAPARKS 46
Cdd:COG1754   842 EKRAKGPAKKKKAAKKAAAKKAAAKKTAAKKAAAKKAAAKKA 883
histone_lik_HC2 NF038052
histone H1-like DNA-binding protein Hc2; This model describes highly repetitive, Lys and ...
 4-46 1.87e-04

histone H1-like DNA-binding protein Hc2; This model describes highly repetitive, Lys and Arg-rich histone H1-like protein Hc2, as found in the genus Chlamydia.


Pssm-ID: 468327 [Multi-domain]  Cd Length: 201  Bit Score: 40.66  E-value: 1.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1246774206   4 KAKTRKVAK----AARSTARK-VSARKPAARKTTARKAPARKAPARKS 46
Cdd:NF038052   32 KAPVRKVAAkktvARKTVAKKtVAARKPVAKKATAKKAPVRKVAAKKT 79
 
Name Accession Description Interval E-value
cupin_bxe_c0505 cd06980
uncharacterized protein bxe_c0505, cupin domain; This family includes mostly bacterial ...
 86-192 5.83e-55

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: 169.67  E-value: 5.83e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246774206  86 GLRSYARYRELGIAAATHGLAQAHVVQFIPPCrpEEVSKLHFHDVDFQMVYVLKGWIKSEFAGEGAHVMREGSCWIQPPK 165
Cdd:cd06980     1 GLRAFFEYRDLGIAEATGGRVGAHVIRATGGG--EGPTGWHYHDCDFQMVYVLKGWVKFEFEGGGEVRLEAGDCVYQPPG 78

                          90       100
                  ....*....|....*....|....*..
gi 1246774206 166 VKHKVLDYSDDCEVLEIILPADFDTVE 192
Cdd:cd06980    79 IRHNVLDYSDDLELLEITSPAEFGTVE 105
valS PRK14900
valyl-tRNA synthetase; Provisional
 5-64 6.41e-06

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 45.75  E-value: 6.41e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246774206    5 AKTRKVAKAArsTARKVSARKPAARKTTARKAPARKAPARKSAARKPAAKKAAKPRTRAA 64
Cdd:PRK14900   991 AMKKKVAKKA--PAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAAKKAAKKPARKAA 1048
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 119-183 8.11e-06

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: 42.25  E-value: 8.11e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1246774206 119 PEEVSKLHFHDVDFQMVYVLKGWIKSEFAGEgAHVMREGSCWIQPPKVKHKVL-DYSDDCEVLEII 183
Cdd:pfam07883   7 PGESSPPHRHPGEDEFFYVLEGEGELTVDGE-EVVLKAGDSVYFPAGVPHRFRnTGDEPARLLDVY 71
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 119-183 8.80e-06

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: 42.08  E-value: 8.80e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1246774206 119 PEEVSKLHFHDVDFQMVYVLKGWIKSEFAGEGAHVMREGSCWIQPPKVKHKVLDYSD-DCEVLEII 183
Cdd:cd02208     8 PGTSSPPHWHPEQDEIFYVLSGEGELTLDDGETVELKAGDIVLIPPGVPHSFVNTSDePAVFLVVS 73
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
119-195 1.80e-05

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 42.44  E-value: 1.80e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1246774206 119 PEEVSKLHFHDVDFQMVYVLKGWIKSEFAGEgAHVMREGSCWIQPPKVKHKVLDYSD-DCEVLEIILPADFDTVELEK 195
Cdd:COG0662    36 PGAELSLHVHPHRDEFFYVLEGTGEVTIGDE-EVELKAGDSVYIPAGVPHRLRNPGDePLELLEVQAPAYLGEDDIVR 112
valS PRK14900
valyl-tRNA synthetase; Provisional
 10-80 2.33e-05

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 44.21  E-value: 2.33e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1246774206   10 VAKAARSTARKVSARKPAARKTTARKAPARKAPARKSAARKPAAKKAAKPRTRAALAKRPPQTFVASHLGA 80
Cdd:PRK14900   974 VRKTVRRSVKKAAATRAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAAKKAAKKPA 1044
COG1754 COG1754
Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];
5-46 3.71e-05

Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];


Pssm-ID: 441360 [Multi-domain]  Cd Length: 892  Bit Score: 43.65  E-value: 3.71e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1246774206   5 AKTRKVAKAARSTARKVSARKPAARKTTARKAPARKAPARKS 46
Cdd:COG1754   842 EKRAKGPAKKKKAAKKAAAKKAAAKKTAAKKAAAKKAAAKKA 883
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
119-186 4.71e-05

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


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 40.60  E-value: 4.71e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1246774206 119 PEEVSKLHFHDVDfQMVYVLKGWIKSEFAGEgAHVMREGSCWIQPPKVKHKVLDYSDD-CEVLEIILPA 186
Cdd:COG1917    32 PGARTPWHSHPGE-ELIYVLEGEGEVEVGGE-EYELKPGDVVFIPPGVPHAFRNLGDEpAVLLVVFSPG 98
valS PRK14900
valyl-tRNA synthetase; Provisional
 4-69 4.81e-05

valyl-tRNA synthetase; Provisional


Pssm-ID: 237855 [Multi-domain]  Cd Length: 1052  Bit Score: 43.44  E-value: 4.81e-05
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1246774206    4 KAKTRKVAK---AARSTARKVSARKPAARKTTARKAPARKAPARKSAARKPAAKKAAKPRTRAALAKRP 69
Cdd:PRK14900   975 RKTVRRSVKkaaATRAAMKKKVAKKAPAKKAAAKKAAAKKAAAKKKVAKKAPAKKVARKPAAKKAAKKP 1043
histone_lik_HC2 NF038052
histone H1-like DNA-binding protein Hc2; This model describes highly repetitive, Lys and ...
 4-46 1.87e-04

histone H1-like DNA-binding protein Hc2; This model describes highly repetitive, Lys and Arg-rich histone H1-like protein Hc2, as found in the genus Chlamydia.


Pssm-ID: 468327 [Multi-domain]  Cd Length: 201  Bit Score: 40.66  E-value: 1.87e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1246774206   4 KAKTRKVAK----AARSTARK-VSARKPAARKTTARKAPARKAPARKS 46
Cdd:NF038052   32 KAPVRKVAAkktvARKTVAKKtVAARKPVAKKATAKKAPVRKVAAKKT 79
cupin_BLR7677-like cd02234
Bradyrhizobium japonicum BLR7677 and related proteins, cupin domain; This family includes ...
 119-170 7.60e-04

Bradyrhizobium japonicum BLR7677 and related proteins, cupin domain; This family includes bacterial and fungal proteins homologous to BLR7677, a Bradyrhizobium japonicum 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: 380362 [Multi-domain]  Cd Length: 103  Bit Score: 37.48  E-value: 7.60e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1246774206 119 PEEVSKLHFHDvDFQMVYVLKGWIKSEFAGEGAHVMREGSCWIQPPKVKHKV 170
Cdd:cd02234    28 PGAASPPHRHP-GFVFAYVLEGEVRSQVNGGPPRVYKAGESFYEPPGAHHRV 78
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
91-189 1.11e-03

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 37.30  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1246774206  91 ARYRELGIAAATHGLAQAHVVqfIPPcrPEEVSKLHFHDVDFQMVYVLKG----WIksefaGEGAHVMREGSCWIQPPKV 166
Cdd:COG3837    14 RRYRRLGDALGLTRLGVNLIT--LPP--GASSSPYHAHSAEEEFVYVLEGeltlRI-----GGEEYVLEPGDSVGFPAGV 84

                          90       100
                  ....*....|....*....|....*...
gi 1246774206 167 KHKVLDYSD-DCEVLEII----LPADFD 189
Cdd:COG3837    85 PHRLRNRGDePARYLVVGtrapYPDSFD 112
PRK08173 PRK08173
DNA topoisomerase III; Validated
 3-46 3.60e-03

DNA topoisomerase III; Validated


Pssm-ID: 236172 [Multi-domain]  Cd Length: 862  Bit Score: 37.72  E-value: 3.60e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1246774206   3 AKAKTRKVAKAARSTARKVSARKPAARKTTARKAPARKAPARKS 46
Cdd:PRK08173  818 PKAAAAKKTAAKATAAAATKAEKAAAKKAPAKKTAAKKTAARKT 861
COG1754 COG1754
Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];
11-53 6.14e-03

Uncharacterized C-terminal domain of topoisomerase IA [Function unknown];


Pssm-ID: 441360 [Multi-domain]  Cd Length: 892  Bit Score: 36.72  E-value: 6.14e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1246774206  11 AKAARS-TARKVSARKPAARKTTARKAPARKAPARKSAARKPAA 53
Cdd:COG1754   842 EKRAKGpAKKKKAAKKAAAKKAAAKKTAAKKAAAKKAAAKKAAA 885
PRK13808 PRK13808
adenylate kinase; Provisional
 6-72 8.70e-03

adenylate kinase; Provisional


Pssm-ID: 172341 [Multi-domain]  Cd Length: 333  Bit Score: 36.02  E-value: 8.70e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1246774206   6 KTRKVAKAARSTARKVSARKPAARKTTARKAPARKAPARKSAARKPAAKKAAKPRTRAALAKRPPQT 72
Cdd:PRK13808  201 KAAKTPAAKSGAKKASAKAKSAAKKVSKKKAAKTAVSAKKAAKTAAKAAKKAKKTAKKALKKAAKAV 267
 
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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