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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1023195190  25 AGIYTYQVGKGVGLEgDLGATFVVLKPGTRFSPPYARESCDELIFCLAGEGLVWQDGQTYTLSPGDCGGWKSGTGISHTL 104
Cdd:cd02224     1 AGRHLRSLGDAAGLT-QLGVNLERLPPGARSSPRHWHSAEEEFVYVLSGEGTLRLDGEEVLPRPGDFVGFPAGTGVAHQL 79

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1023195190 105 INDSNGYgqegsdlLIFLVYETRPEVTEAIY 135
Cdd:cd02224    80 INRSDEP-------LVYLVVGTRLPDDVCTY 103

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1023195190 199 TDSVGQGELAAEATSLSQETSLsGRFGCNLEILAPGCRSSDPHAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPA 278
Cdd:COG3837     4 LDDLPGPEAGRRYRRLGDALGL-TRLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPA 82

                          90       100
                  ....*....|....*....|....*.
gi 1023195190 279 gtGIAHTIINDSSeedgEDLALLVVG 304
Cdd:COG3837    83 --GVPHRLRNRGD----EPARYLVVG 102

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1023195190  15 ILNADD-GKESAGIYTYQVGKGVGLEgDLGATFVVLKPGTRFSPPYARESCDELIFCLAGEGLVWQDGQTYTLSPGDCGG 93
Cdd:COG3837     1 IVNLDDlPGPEAGRRYRRLGDALGLT-RLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVG 79

                          90
                  ....*....|....*.
gi 1023195190  94 WKSGTGisHTLINDSN 109
Cdd:COG3837    80 FPAGVP--HRLRNRGD 93

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1023195190  46 FVVLKPGTRfSPPYARESCDELIFCLAGEGLVWQDGQTYTLSPGDCGGWKSGTGisHTLINDSNG 110
Cdd:pfam07883   2 LVTLPPGES-SPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVP--HRFRNTGDE 63

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1023195190 199 TDSVGQGELAAEATSLSQETSLsGRFGCNLEILAPGCRSSDPHAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPA 278
Cdd:COG3837     4 LDDLPGPEAGRRYRRLGDALGL-TRLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVGFPA 82

                          90       100
                  ....*....|....*....|....*.
gi 1023195190 279 gtGIAHTIINDSSeedgEDLALLVVG 304
Cdd:COG3837    83 --GVPHRLRNRGD----EPARYLVVG 102

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1023195190  15 ILNADD-GKESAGIYTYQVGKGVGLEgDLGATFVVLKPGTRFSPPYARESCDELIFCLAGEGLVWQDGQTYTLSPGDCGG 93
Cdd:COG3837     1 IVNLDDlPGPEAGRRYRRLGDALGLT-RLGVNLITLPPGASSSPYHAHSAEEEFVYVLEGELTLRIGGEEYVLEPGDSVG 79

                          90
                  ....*....|....*.
gi 1023195190  94 WKSGTGisHTLINDSN 109
Cdd:COG3837    80 FPAGVP--HRLRNRGD 93

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1023195190 221 SGRFGCNLEILAPGCRSSdPHAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGTgiAHTIINDSSeedgEDLAL 300
Cdd:COG0662    24 GERLSVKRITVPPGAELS-LHVHPHRDEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGV--PHRLRNPGD----EPLEL 96

                  ...
gi 1023195190 301 LVV 303
Cdd:COG0662    97 LEV 99

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1023195190 231 LAPGCRSsDPHAHSlEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGTgiAHTIINDSSEEdgedLALLVV 303
Cdd:COG1917    30 FEPGART-PWHSHP-GEELIYVLEGEGEVEVGGEEYELKPGDVVFIPPGV--PHAFRNLGDEP----AVLLVV 94

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1023195190 230 ILAPGCrSSDPHAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGTgiAHTIINDSSeedgEDLALLVV 303
Cdd:cd02214    25 RVPPGE-STLPHRLKGSEEVYYILEGEGTMEIDGEPREVGPGDAVLIPPGA--VQRIENTGE----EDLVFLCI 91

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1023195190 228 LEILAPGCRSSDPHAHSLEdELVYVISGRGLLWMNGIVYDIGPGDAIGFPAgtGIAHTIINDSSEE 293
Cdd:cd02209    20 LVTLPPGGSGGEPYSHEGE-EFGYVLEGELELTVGGETYVLEAGDSIYFDS--DVPHRYRNPGDEP 82

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1023195190 229 EILAPGCRSSDPHAHSLEDELVYVISGRGLLWMN-GIVYDIGPGDAIGFPAGTgiAHTIINDSSEE 293
Cdd:cd02208     3 VVTLPPGTSSPPHWHPEQDEIFYVLSGEGELTLDdGETVELKAGDIVLIPPGV--PHSFVNTSDEP 66

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.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1023195190 230 ILAPGCrSSDPHAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGTGiaHTIINdSSEEDGEDLALLV 302
Cdd:cd02221    25 TLPPGS-SIGYHQHEGEFEIYYILSGEGLYTDNGKEYEVKAGDVTFTRDGES--HGIEN-TGDEDLVFIALIL 93

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1023195190  47 VVLKPGTRFSPPYAREScDELIFCLAGEGLVWQDGQTYTLSPGDCGGWKSGTgiSHTLINdsngygqEGSDLLIFLVYET 126
Cdd:COG0662    32 ITVPPGAELSLHVHPHR-DEFFYVLEGTGEVTIGDEEVELKAGDSVYIPAGV--PHRLRN-------PGDEPLELLEVQA 101

                  ....*.
gi 1023195190 127 RPEVTE 132
Cdd:COG0662   102 PAYLGE 107

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

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1023195190  39 EGDLGATFVVLKPGTRFSPPYAREscDELIFCLAGEGLVWQDGQTYTLSPGDCggWKSGTGISHTLINDSNG 110
Cdd:COG1917    20 EDELEVVRVTFEPGARTPWHSHPG--EELIYVLEGEGEVEVGGEEYELKPGDV--VFIPPGVPHAFRNLGDE 87

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 1023195190  240 PHAHSLEDELVYVISGRGLLWM---NG---IVYDIGPGDAIGFPAGTgiAHTIINdSSEEDGEDLALLVVGQNKR 308
Cdd:smart00835  45 PHYHPRATELLYVVRGEGRVGVvdpNGnkvYDARLREGDVFVVPQGH--PHFQVN-SGDENLEFVAFNTNDPNRR 116

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
                  ....*....|....*....|....*....|....*....|....*
gi 1023195190  47 VVLKPGTRFSPPYAREScDELIFCLAGEGLVWQDGQTYTLSPGDC 91
Cdd:cd02209    21 VTLPPGGSGGEPYSHEG-EEFGYVLEGELELTVGGETYVLEAGDS 64

quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1023195190 240 PHAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGTgiAHT 285
Cdd:cd02215    47 PHYHKRHHETFYVLEGRLQLWLDGESRLLTPGDFASVPPGT--IHA 90

Phosphomannose isomerase type II, C-terminal cupin domain; This family includes the C-terminal cupin domain of mannose-6-phosphate isomerases (MPIs) which have been classified broadly into two groups, type I and type II, based on domain organization. This family contains type II phosphomannose isomerase (also known as PMI-GDP, phosphomannose isomerase/GDP-D-mannose pyrophosphorylase), a bifunctional enzyme with two domains that catalyze the first and third steps in the GDP-mannose pathway in which fructose 6-phosphate is converted to GDP-D-mannose. The N-terminal domain catalyzes the first and rate-limiting step, the isomerization from D-fructose-6-phosphate to D-mannose-6-phosphate, while the C-terminal cupin domain (represented in this alignment model) converts mannose 1-phosphate to GDP-D-mannose in the final step of the reaction. Although these two domains occur together in one protein in most organisms, they occur as separate proteins in certain cyanobacterial organisms. Also, although type I and type II MPIs have no overall sequence similarity, they share a conserved catalytic motif.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1023195190 233 PGCRSSdPHAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGTgiAHTIINDSSEE 293
Cdd:cd02213    49 PGKRLS-LQRHHHRSEHWVVVSGTAEVTLDGKEKLLKEGESIYIPKGT--KHRLENPGKIP 106

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1023195190 230 ILAPGCRSSDP-HAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGTgiAHTIINDSSE 292
Cdd:cd07006    16 VLAPGDTEGGPdNRHRGSDQWLYVVSGSGEAIVEGERVALKPGSLLLIEAGE--THEIRNTGDE 77

quercetinase, N- and C-terminal cupin domains; This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1023195190  39 EGDLGATFVVLKPGTRFSPPYAREScDELIFCLAGEGLVWQDGQTYTLSPGD 90
Cdd:cd02215    29 GGAFTLVTTEGPKGDAIPPHYHKRH-HETFYVLEGRLQLWLDGESRLLTPGD 79

Predicted enzyme of the cupin superfamily [General function prediction only];

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1023195190 246 EDELVYVISGRGLLWM-NGIVYDIGPGDAIGFPAGT 280
Cdd:COG3450    56 EDEFCYILEGRVTVTDdDGEPVEFGAGDSFVFPAGF 91

pectin degradation protein KdgF and related proteins, cupin domain; This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1023195190 240 PHAHSLEdELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGT 280
Cdd:cd02238    42 LHSHPHE-QIGYVLSGRFEFTIGGETRILKPGDSYYIPPNV 81

monomeric dehydratase Pac13 and related proteins, cupin domain; This family includes a small monomeric dehydratase Pac13 that mediates the formation of the 3'-deoxynucleotide of pacidamycins, which are uradyl peptide antibiotics (UPAs). Pac13 is involved in the formation of the unique 3'-deoxyuridine moiety found in these UPAs; it catalyzes the dehydration of uridine-5'-aldehyde. The similarity of the 3'-deoxy pacidamycin moiety with synthetic anti-retrovirals, offers a potential opportunity for the utilization of Pac13 in the biocatalytic generation of antiviral compounds. 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
                  ....*....|....*....|....*....|....*....|
gi 1023195190 241 HAHSLEDELVYVISGRGLLWMNGIVYDIGPGDAIGFPAGT 280
Cdd:cd20295    36 HYHKKSTEIYYVLEGEGIFELDGEAVPVKPGDLVLIPPGT 75

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1023195190  44 ATFVVLKPGTrFSPPYARESCDELIFCLAGEG-LVWQDGQTYTLSPGDCggWKSGTGISHTLINDSN 109
Cdd:cd02208     1 ISVVTLPPGT-SSPPHWHPEQDEIFYVLSGEGeLTLDDGETVELKAGDI--VLIPPGVPHSFVNTSD 64