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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1373345191  53 ASVLRIPPNSWSPIHHNSEQDAIINVVSGTGTLVVKEGfkgelRHHELHPGDFAFVPAWTEHQARNDSDQDLVWVIT 129
Cdd:cd02208     1 ISVVTLPPGTSSPPHWHPEQDEIFYVLSGEGELTLDDG-----ETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLVV 72

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1373345191  53 ASVLRIPPNSWSPIHHNSEQDAIINVVSGTGTLVVKEGfkgelRHHELHPGDFAFVPAWTEHQARNDSDQDLVWVIT 129
Cdd:cd02208     1 ISVVTLPPGTSSPPHWHPEQDEIFYVLSGEGELTLDDG-----ETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLVV 72

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1373345191  55 VLRIPPNSWSPIHHNSEQDAIINVVSGTGTLVVKEgfkgelRHHELHPGDFAFVPAWTEHQARNDSDQDLVWV 127
Cdd:pfam07883   2 LVTLPPGESSPPHRHPGEDEFFYVLEGEGELTVDG------EEVVLKAGDSVYFPAGVPHRFRNTGDEPARLL 68

(S)-ureidoglycine aminohydrolase;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1373345191  78 VVSGTGTLVVkEGfkgelRHHELHPGDFAFVPAWTEHQARNDSDQD--LVWV 127
Cdd:PRK11171   89 VVEGEITLTL-EG-----KTHALSEGGYAYLPPGSDWTLRNAGAEDarFHWI 134

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1373345191  53 ASVLRIPPNSWSPIHHNSEQDAIINVVSGTGTLVVKEGfkgelRHHELHPGDFAFVPAWTEHQARNDSDQDLVWVIT 129
Cdd:cd02208     1 ISVVTLPPGTSSPPHWHPEQDEIFYVLSGEGELTLDDG-----ETVELKAGDIVLIPPGVPHSFVNTSDEPAVFLVV 72

Uncharacterized conserved protein, RmlC-like cupin domain [General function prediction only];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373345191  50 KMCASVLRIPPNSWSPIHHNSEQDAIINVVSGTGTLVVKEGfkgeLRHH-ELHPGDFAFVPAWTEHQARNDSD-QDLVWV 127
Cdd:COG4101    45 GLWMGLVTIPPGARAKAHHHGEHETAIYVLSGRAETRYGER----LEHRvVTEPGDFIFIPPGVPHQEINLSDtEPAVAV 120

                  ....*.
gi 1373345191 128 ITQSGP 133
Cdd:COG4101   121 IARTDP 126

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373345191  22 VTHADQLKPmlDNEGRSIRDSAIVGKCDKMCASVLRIPPNSWSPIHHN-SEQDAIINVVSGTGTLVVKEGfkgelrHHEL 100
Cdd:COG3837     1 IVNLDDLPG--PEAGRRYRRLGDALGLTRLGVNLITLPPGASSSPYHAhSAEEEFVYVLEGELTLRIGGE------EYVL 72

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1373345191 101 HPGDFAFVPAWTEHQARNDSDQDLV--WVITQS 131
Cdd:COG3837    73 EPGDSVGFPAGVPHRLRNRGDEPARylVVGTRA 105

Silicibacter pomeroyi SPO2919 and related proteins, uncharacterized sugar phosphate isomerase with a cupin domain; This family includes proteins similar to sugar phosphate isomerase SPO2919 from Silicibacter pomeroyi and Afe_0303 from Acidithiobacillus ferrooxidans, but are as yet uncharacterized. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1373345191  53 ASVLRIPPNSWS-PIHHNSEQDAIINVVSGTGTLVVkegfKGElrHHELHPGDFAFVPAWTE--HQARNDSDQDLV 125
Cdd:cd02224    19 VNLERLPPGARSsPRHWHSAEEEFVYVLSGEGTLRL----DGE--EVLPRPGDFVGFPAGTGvaHQLINRSDEPLV 88

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1373345191  57 RIPPNSWSPIHHNSEQDAIInVVSGTGTLVVkegfkgELRHHELHPGDFAFVPAWTEHQARNDSDQDL----VW 126
Cdd:cd06988     8 VVRPGTTSTPHSHHEYEIFI-VISGKGIVVV------DGEREPVKAGDVVYIPPGTEHYVKNDGDEDFefysIW 74

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.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1373345191   51 MCASVLRIPPNSWSPIHHNSEQDAIINVVSGTGTL-VVKEGfKGELRHHELHPGDFAFVPAWTEHQARNDSDQDLVWVI 128
Cdd:smart00835  30 ISAARVNLEPGGMLPPHYHPRATELLYVVRGEGRVgVVDPN-GNKVYDARLREGDVFVVPQGHPHFQVNSGDENLEFVA 107

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).

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1373345191  65 PIHHNSEQDAIINVVSGTGTLVVKEgfkgelRHHELHPGDFAFVPAWTEHQARNDSDQDLV 125
Cdd:cd06122    41 KVHAHAGSDKVYFVLEGEGRFTVGD------EERELGAGEAVLAPAGVPHGVRNTGAERLV 95

Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate transport and metabolism]; Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily is part of the Pathway/BioSystem: Glycolysis

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1373345191  50 KMCASVLRIPPNSWSPIHHNSEQDAIINVVSGTGTLVVKEGFkGELRHHELHPGDFAFVPAWTEHQARNDSDQDLV 125
Cdd:COG2140     2 TLAGGLTVLEPGGVREEHWHPNAAEWYYVLSGEARMTVQDPP-GRARTVDVGPGDVVYVPPGYGHYIINTGDEPLV 76

XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain; This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373345191  50 KMCASVLRIPPN--SWSPIHHNSEQdaIINVVSGTGTLVVKEgfkgelRHHELHPGDFAFVPAWTEHQARNDSDQD--LV 125
Cdd:cd02209    15 KMEPFLVTLPPGgsGGEPYSHEGEE--FGYVLEGELELTVGG------ETYVLEAGDSIYFDSDVPHRYRNPGDEParVL 86

                  ....
gi 1373345191 126 WVIT 129
Cdd:cd02209    87 WVIT 90

Xanthomonas campestris XcTcmJ and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to plant pathogen Xanthomonas campestris tetracenomycin polyketide synthesis protein XcTcmJ, a protein encoded by the tcmJ gene. XcTcmJ is annotated as being involved in tetracenomycin polyketide biosynthesis. Also included is Xc5357 from a different strain of X. campestris. Structure studies show that binding of zinc induces conformational changes and serves a functional role in this cupin protein. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1373345191  67 HHNSEQdaIINVVSGTGTLVVkEGfkgelRHHELHPGDFAFVPAWTEHQARNDSDQDL 124
Cdd:cd07006    30 HRGSDQ--WLYVVSGSGEAIV-EG-----ERVALKPGSLLLIEAGETHEIRNTGDEPL 79

(S)-ureidoglycine aminohydrolase;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1373345191  78 VVSGTGTLVVkEGfkgelRHHELHPGDFAFVPAWTEHQARNDSDQD--LVWV 127
Cdd:PRK11171   89 VVEGEITLTL-EG-----KTHALSEGGYAYLPPGSDWTLRNAGAEDarFHWI 134

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1373345191  51 MCASVLRIPPN-SWSPIHHNSEqdAIINVVSGTGTLVVkegfkGELRHhELHPGDFAFVPAWTEHQArNDSDQDLV 125
Cdd:COG3435   228 IGAFMQLLPPGfHTRPHRHTGS--AVYHVVEGSGRSIV-----GGERF-DWGEGDLFVVPSWAWHSH-ASADEDAV 294

Oxalate decarboxylase (OxDC), cupin domain; Oxalate decarboxylase (OxDC; EC 4.1.1.2) is a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds and both domains are included in this alignment. Each OxDC cupin domain contains one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues. Members of this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373345191  51 MCASVLRIPPNSWSPIHHNSEQDAIINVVSGTGTLVVKEGfKGELRHHELHPGDFAFVPAWTEHQARNDSDQDLVWVITQ 130
Cdd:cd02240    27 LSSALVRVAPGAMRELHWHPNTAEWQYVISGSARVTVFDE-DGRFETFNLGAGDVGYVPSGSGHHIENIGDEDAEFLLIF 105

                          90       100
                  ....*....|....*....|.
gi 1373345191 131 SGPRPVGAILTDWGGQEIKTI 151
Cdd:cd02240   106 DDGTFADVSLPWWLAMTPEEV 126

Arabidopsis thaliana DRT102 and related proteins, cupin domain; This family includes bacterial and eukaryotic proteins homologous to DNA-damage-repair/toleration protein DRT102 found in Arabidopsis thaliana. DRT102 may be involved in DNA repair from UV damage. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1373345191  56 LRIPPNSWSPIHHNSEqDAIINVVSGT------GTLVVKEGfkgelrhHELHPGDFAFVPAWTEHQARNDsDQDLVWVIT 129
Cdd:cd06989    23 LKFPAGYKIPPHTHPD-DERVTVISGTfylgmgDKFDEAKA-------KALPAGSFFTLPAGTPHFAWAK-DEETVVQVT 93

                  ....
gi 1373345191 130 QSGP 133
Cdd:cd06989    94 GEGP 97

cysteine dioxygenase, cupin domain; This family contains cysteine dioxygenase (CDO; EC 1.13.11.20), which catalyzes the conversion of cysteine to cysteine sulfinic acid, the first step in the biosynthesis of essential oxidized cysteine metabolites such as sulfate, hypotaurine, and taurine. CDO also plays an important role in the regulation of intracellular cysteine levels in mammals; CDO expression is altered in cancer cells, and abnormal or deficient CDO activity has been linked to Parkinson's disease, Alzheimer's disease, and rheumatoid arthritis. CDO is an iron-dependent thiol dioxygenase that uses molecular oxygen to oxidize the sulfhydryl group of cysteine to generate cysteine sulfinic acid. The CDO active site contains an amino acid-derived cofactor. These enzymes are found in prokaryotes as well as eukaryotes and belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1373345191  55 VLRIPPNSWSPIHHNSEQDAIINVVSGTGTLVV----KEGFKGELRHHELHPGDFAFVPAWTE-HQARNDSDQDLV 125
Cdd:cd10548    16 LLCWPPGQGSPIHDHGGSWCVVKVLEGELTETRyrrpDDGSLSGEETLEETPGDVTYINPDGGiHRVENPSDEPAV 91