Cupriavidus pinatubonensis reut_a1446 and related proteins, cupin domain; This family includes bacterial and some eukaryotic proteins homologous to reut_a1446, a Cupriavidus pinatubonensis protein of unknown function that may be related to mannose-6-phosphate isomerase. 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 504058623   1 MHNLFQDLPAKLAGEQFDELLATPHVRIERIVSHGHTSPAEGWYDQSEDEWVLVLTGSGTLAFADGRRQRLEPGDHLYIP 80
Cdd:cd06981    1 MGNLFDNLPDDLPEELFETLLENGGVRIERIVSTGQASPPGFWYDQDEDEWVLLLQGEAELEFEDGEEVELKPGDYLLIP 80

                         90       100
                 ....*....|....*....|..
gi 504058623  81 AHQKHRVCHTAPDEFTIWLAVF 102
Cdd:cd06981   81 AHCRHRVAWTSPEPPTIWLAVH 102

Cupriavidus pinatubonensis reut_a1446 and related proteins, cupin domain; This family includes bacterial and some eukaryotic proteins homologous to reut_a1446, a Cupriavidus pinatubonensis protein of unknown function that may be related to mannose-6-phosphate isomerase. 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 504058623   1 MHNLFQDLPAKLAGEQFDELLATPHVRIERIVSHGHTSPAEGWYDQSEDEWVLVLTGSGTLAFADGRRQRLEPGDHLYIP 80
Cdd:cd06981    1 MGNLFDNLPDDLPEELFETLLENGGVRIERIVSTGQASPPGFWYDQDEDEWVLLLQGEAELEFEDGEEVELKPGDYLLIP 80

                         90       100
                 ....*....|....*....|..
gi 504058623  81 AHQKHRVCHTAPDEFTIWLAVF 102
Cdd:cd06981   81 AHCRHRVAWTSPEPPTIWLAVH 102

Uncharacterized conserved protein, cupin superfamily [Function unknown];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 504058623  35 GHTSPaEGWYDQSEDEWVLVLTGSGTLAFaDGRRQRLEPGDHLYIPAHQKHRVCHTApDEFTIWLAVFVPPA 106
Cdd:COG3837   38 GASSS-PYHAHSAEEEFVYVLEGELTLRI-GGEEYVLEPGDSVGFPAGVPHRLRNRG-DEPARYLVVGTRAP 106

Cupriavidus pinatubonensis reut_a1446 and related proteins, cupin domain; This family includes bacterial and some eukaryotic proteins homologous to reut_a1446, a Cupriavidus pinatubonensis protein of unknown function that may be related to mannose-6-phosphate isomerase. 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 504058623   1 MHNLFQDLPAKLAGEQFDELLATPHVRIERIVSHGHTSPAEGWYDQSEDEWVLVLTGSGTLAFADGRRQRLEPGDHLYIP 80
Cdd:cd06981    1 MGNLFDNLPDDLPEELFETLLENGGVRIERIVSTGQASPPGFWYDQDEDEWVLLLQGEAELEFEDGEEVELKPGDYLLIP 80

                         90       100
                 ....*....|....*....|..
gi 504058623  81 AHQKHRVCHTAPDEFTIWLAVF 102
Cdd:cd06981   81 AHCRHRVAWTSPEPPTIWLAVH 102

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 504058623  28 IERIVSHGHTSPAEGWYDQsEDEWVLVLTGSGTLAFADGRRQRLEPGDHLYIPAHQKHRVcHTAPDEFTIWLAVF 102
Cdd:cd02208    1 ISVVTLPPGTSSPPHWHPE-QDEIFYVLSGEGELTLDDGETVELKAGDIVLIPPGVPHSF-VNTSDEPAVFLVVS 73

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 504058623  49 DEWVLVLTGSGTlAFADGRRQRLEPGDHLYIPAHQKHRVCHTaPDEFTIWLAVFVPPA 106
Cdd:cd07006   34 DQWLYVVSGSGE-AIVEGERVALKPGSLLLIEAGETHEIRNT-GDEPLKTLNFYVPPA 89

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

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504058623  42 GWYDQSEDEWVLVLTGSGTLaFADGRRQRLEPGDHLYIPAHQKHRVcHTAPDEFTIWLAVFVPPA 106
Cdd:COG1917   37 PWHSHPGEELIYVLEGEGEV-EVGGEEYELKPGDVVFIPPGVPHAF-RNLGDEPAVLLVVFSPGL 99

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
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 504058623  46 QSEDEWVLVLTGSGTLAfADGRRQRLEPGDHLYIPAHQKHRVCHTAPDEF---TIW 98
Cdd:cd06988   20 HHEYEIFIVISGKGIVV-VDGEREPVKAGDVVYIPPGTEHYVKNDGDEDFefySIW 74

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
                 ....*....|....*....|....*....|....*..
gi 504058623  51 WVlVLTGSGTLAFaDGRRQRLEPGDHLYIPAHQKHRV 87
Cdd:cd02213   65 WV-VVSGTAEVTL-DGKEKLLKEGESIYIPKGTKHRL 99

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 504058623  25 HVRIERIVSHGHTSPAEGwydqseDEWVLVLtgSGTLAF-ADGRRQRLEPGDHLYIPAHQKHRV 87
Cdd:cd02209   20 LVTLPPGGSGGEPYSHEG------EEFGYVL--EGELELtVGGETYVLEAGDSIYFDSDVPHRY 75

TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of the tetracenomycin (TCM) polyketide synthase (PKS) type II complex in Streptomyces glaucescens. TcmJ is a quinone-forming monooxygenase involved in the modification of aromatic polyketides synthesized by polyketide synthases of types II and III. Orthologs of TcmJ include the Streptomyces BenD (benastatin biosynthetic pathway), the Streptomyces olivaceus ElmJ (polyketide antibiotic elloramycin biosynthetic pathway), the Actinomadura hibisca PdmL (pradimicin biosynthetic pathway), the Streptomyces cyaneus CurC (curamycin biosynthetic pathway), the Streptomyces rishiriensis Lct30 (lactonamycin biosynthetic pathway), and the Streptomyces WhiE II (spore pigment polyketide biosynthetic pathway). 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 504058623  29 ERIVSHGHtspaegwyDQSEdEWVLVLTGSGTLaFADGRRQRLEPGDHLYIPAHQKHRVCHTAPDE 94
Cdd:cd06991   30 ERVSEHYH--------PYSE-EFLYVVRGRLVV-RVDGEPVVLEAGEALLVPRGVRHRLENAGDEP 85

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504058623  25 HVRIERIVS---HGHTSPAEGWYdqsedewvlVLTGSGTLaFADGRRQRLEPGDHLYIPAHQKHRVCHTAPDEFTIwLAV 101
Cdd:cd02214   23 HARVPPGEStlpHRLKGSEEVYY---------ILEGEGTM-EIDGEPREVGPGDAVLIPPGAVQRIENTGEEDLVF-LCI 91

                 ....
gi 504058623 102 FVPP 105
Cdd:cd02214   92 CSPA 95

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.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504058623  36 HTSPAEgwydqsedEWVLVLTGSGTLAFADGRRQRLEPGDHLYIPAHQKHRVCHTAPDEFTIwLAVFV 103
Cdd:cd02235   35 HTHPGE--------ESGYVLEGSLELEVDGQPPVTLKAGDSFFIPAGTVHNAKNVGSGPAKL-LATYI 93

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.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 504058623  50 EWVL-VLTGSGTLAFA--DGRRQR-LEPGDHLYIPA 81
Cdd:cd02244   49 DMVFyVHTGRGTITWVdeDKRESYnLERGDVYRIPA 84