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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742388219  33 APLAKRTGLTRLGIHHERLPPGRRTSYPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTGLCHTFINNTDS 112
Cdd:cd02224    6 RSLGDAAGLTQLGVNLERLPPGARSSPRHWHSAEEEFVYVLSGEGTLRLDGEEVLPRPGDFVGFPAGTGVAHQLINRSDE 85

                         90       100
                 ....*....|....*....|
gi 742388219 113 EVRLLVVGEaNKPENRIYYP 132
Cdd:cd02224   86 PLVYLVVGT-RLPDDVCTYP 104

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742388219  33 APLAKRTGLTRLGIHHERLPPGRRTSYPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTGLCHTFINNTDS 112
Cdd:cd02224    6 RSLGDAAGLTQLGVNLERLPPGARSSPRHWHSAEEEFVYVLSGEGTLRLDGEEVLPRPGDFVGFPAGTGVAHQLINRSDE 85

                         90       100
                 ....*....|....*....|
gi 742388219 113 EVRLLVVGEaNKPENRIYYP 132
Cdd:cd02224   86 PLVYLVVGT-RLPDDVCTYP 104

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 742388219   47 HHERLPPGRrTSYPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTGlcHTFINNTDSEVRLLVVG 120
Cdd:pfam07883   1 GLVTLPPGE-SSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVP--HRFRNTGDEPARLLDVY 71

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742388219  33 APLAKRTGLTRLGIHHERLPPGRRTSYPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTGLCHTFINNTDS 112
Cdd:cd02224    6 RSLGDAAGLTQLGVNLERLPPGARSSPRHWHSAEEEFVYVLSGEGTLRLDGEEVLPRPGDFVGFPAGTGVAHQLINRSDE 85

                         90       100
                 ....*....|....*....|
gi 742388219 113 EVRLLVVGEaNKPENRIYYP 132
Cdd:cd02224   86 PLVYLVVGT-RLPDDVCTYP 104

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 742388219   47 HHERLPPGRrTSYPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTGlcHTFINNTDSEVRLLVVG 120
Cdd:pfam07883   1 GLVTLPPGE-SSPPHRHPGEDEFFYVLEGEGELTVDGEEVVLKAGDSVYFPAGVP--HRFRNTGDEPARLLDVY 71

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 742388219  27 ERMSVGAPLAKRtgltRLGIHHERLPPG--RRTSYPHAEsseEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTGlcH 104
Cdd:cd02209    3 TYELLSPGLPGR----KMEPFLVTLPPGgsGGEPYSHEG---EEFGYVLEGELELTVGGETYVLEAGDSIYFDSDVP--H 73

                         90
                 ....*....|....*
gi 742388219 105 TFINNTDSEVRLLVV 119
Cdd:cd02209   74 RYRNPGDEPARVLWV 88

(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain; This family includes the N-terminal cupin domain of (S)-ureidoglycine aminohydrolase (UGlyAH), an enzyme that converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the ureide pathway. The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria where, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions by seven different enzymes. Thus, this pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. This enzyme from Arabidopsis thaliana(AtUGlyAH) has been shown to bind a Mn2+ ion, via the C-terminal cupin domain, which acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. The structure of AtUGlyAH shows a bi-cupin fold with a conserved "jelly roll-like" beta-barrel fold and an octameric functional unit. Several structural homologs of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742388219  51 LPPGRRTSYPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTGlcHTFINNTDSEVRLLVVgeankpeNRIY 130
Cdd:cd02211   32 VEPGGGSTAPEGGEGIERFLYVLEGEVELTVGGETHTLTAGGYAYLPPGTK--HSLRNAGDEPARLLWY-------KKRY 102

                 ....*....
gi 742388219 131 YPLNGAYAA 139
Cdd:cd02211  103 EPLEGGAAP 111

Pseudomonas aeruginosa PA3510 and related proteins, cupin domain; This family includes bacterial proteins homologous to PA3510, a Pseudomonas aeruginosa protein of unknown function with a beta-barrel fold that belongs to the cupin superfamily.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742388219  50 RLPPGRRTSyPHAESSEEEFvYVLEGFPDV-W-LNGELW--PLKPGDSVGFPAGtgLCHTFINNTDSEVRLLVVGEANKP 125
Cdd:cd02225   59 RLPPGQGGA-LHTHEVEEVF-FVLQGRLTVfWeDEGEEHerELGPRDMISVPAG--VYRGFKNIGEEDALMQVMLGTGKP 134

                         90
                 ....*....|....*.
gi 742388219 126 ENRIYYPLNGAYAATR 141
Cdd:cd02225  135 GRPTYPDDSELAKARR 150

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 742388219  46 IHHERLPPGRrTSYPHAESSEEEFVYVLEGFPDVWLN-GELWPLKPGDSVGFPAGTGlcHTFINNTDSEVRLLVV 119
Cdd:cd02208    1 ISVVTLPPGT-SSPPHWHPEQDEIFYVLSGEGELTLDdGETVELKAGDIVLIPPGVP--HSFVNTSDEPAVFLVV 72

Ureidoglycine aminohydrolase [Nucleotide transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742388219  53 PGRRTSYPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTGlcHTFINNTDSEVRLLVVgeankpeNRIYYP 132
Cdd:COG3257   68 PGGGSDRPEPDPGAETFLFVLEGEVTLTLGGETHELTPGGYAYLPPGTP--WTLRNAGDEPARFHWI-------RKRYEP 138

                         90       100
                 ....*....|....*....|..
gi 742388219 133 LNGayaatrpdrwIDHPPQFFG 154
Cdd:COG3257  139 VEG----------LEAPEAFVG 150

Streptomyces resistomycificus RemF cyclase and related proteins, cupin domain; RemF cyclase is a manganese-containing polyketide cyclase present in bacteria that is involved in the biosynthesis of resistomycin, the aromatic pentacyclic metabolite in Streptomyces resistomycificus. Structure of this enzyme shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold that forms a homodimer. It contains an unusual octahedral zinc-binding site in a large hydrophobic pocket that may represent the active site. The zinc ion, coordinated to four histidine side chains and two water molecules, could act as a Lewis acid in the aldol condensation reaction catalyzed by RemF, reminiscent of class II aldolases.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742388219  51 LPPGRRTSYPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTglCHTFINNTDSEV-RLLVV 119
Cdd:cd06979   24 VSPNAGMPPPHYHEDWEETIYGLEGSVTLTLPGKTVEVGPGDSIFIPRGE--VHGFVNRSGGPTcRLCVL 91

Microcystis aeruginosa MAE_RS03005 and related proteins, cupin domain; This family includes bacterial and some eukaryotic proteins homologous to MAE_RS03005, a Microcystis aeruginosa 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 742388219  53 PGRRTSyPHAESSEEEFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTglcHTFINNTDSEvRL 116
Cdd:cd06987   37 PGGRTP-PNTHPAAHEMFFVLAGEGRAYCDGQRVPLRPGDALVVPPGS---EHVIENTGSG-RL 95

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 742388219  53 PGRRTSY-PHAESSEeeFVYVLEGFPDVWLNGELWPLKPGDSVGFPAGTglCHTFINNTDSEVRLL 117
Cdd:cd02213   49 PGKRLSLqRHHHRSE--HWVVVSGTAEVTLDGKEKLLKEGESIYIPKGT--KHRLENPGKIPLEII 110

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 742388219  36 AKRTGLTRLGIHHERLPPGRRtSYPHAESSEEEFVYVLEGFPDVWLNGEL---WPLKPGDSVGFPAgtGLCHTFINNTDS 112
Cdd:COG4101   38 AETVGSTGLWMGLVTIPPGAR-AKAHHHGEHETAIYVLSGRAETRYGERLehrVVTEPGDFIFIPP--GVPHQEINLSDT 114

                 ....*..
gi 742388219 113 EVRLLVV 119
Cdd:COG4101  115 EPAVAVI 121