auxin-binding protein 1, cupin domain; Auxin-binding protein 1 (ABP1) is a soluble glycoprotein receptor that binds the plant hormone auxin, indole-3-acetic acid (IAA). ABP1 belongs to the ancient and functionally diverse germin/seed storage 7S protein superfamily. It is an important mediator of auxin action in plants and is essential for cell cycle control. Cellular auxin responses typically depend on auxin concentrations that mainly result from intercellular auxin transport and auxin biosynthesis, as well as metabolism. The functional inactivation of ABP1 results in cell cycle arrest, showing that ABP1 plays a critical role in cell cycle regulation, acting at both the G1/S and G2/M checkpoints. ABP1 is ubiquitous among green plants, found mainly within the endoplasmic reticulum (ER) and in smaller quantities at the cell surface associated with the plasma membrane. In Arabidopsis thaliana, ABP1 null mutations result in embryonic lethality while decreased ABP1 expression leads to severe retardation of leaf growth.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985665896  42 PIVRNISDLPQDNYGRPGLSHMTVAGSVLHGMKEVEIWLQTFAPGSETPIHRHSCEEVFVVLKGSGTLYLAETHGNFPGK 121
Cdd:cd02220     1 PLVRNISELPQDSYGRPGLSHMTVAGAVHHGMKEVEVWLQTFAPGSGTPIHRHSCEEVFVVLKGSGTLYLASSSLKYPGK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1985665896 122 PIEFPIFANSTIHIPINDAHQVKNTG-HEDLQVLVIISRPPIKIFIYEDWFMPHTAARLKFPYYWDEQCVQ 191
Cdd:cd02220    81 PQEFPIFPNSTFHIPVNDVHQVWNTGeHEDLQVLVIISRPPVKVFIYDDWSMPHTAAKLKFPYVWDEQCYQ 151

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        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985665896   82 TFAPGSETPIHRHS-CEEVFVVLKGSGTLYLAETHGNfpgKPIEFPIFANSTIHIPINDAHQVKNTGHEDLQVLVI-ISR 159
Cdd:smart00835  36 NLEPGGMLPPHYHPrATELLYVVRGEGRVGVVDPNGN---KVYDARLREGDVFVVPQGHPHFQVNSGDENLEFVAFnTND 112

                   ....*..
gi 1985665896  160 PPIKIFI 166
Cdd:smart00835 113 PNRRFFL 119

auxin-binding protein 1, cupin domain; Auxin-binding protein 1 (ABP1) is a soluble glycoprotein receptor that binds the plant hormone auxin, indole-3-acetic acid (IAA). ABP1 belongs to the ancient and functionally diverse germin/seed storage 7S protein superfamily. It is an important mediator of auxin action in plants and is essential for cell cycle control. Cellular auxin responses typically depend on auxin concentrations that mainly result from intercellular auxin transport and auxin biosynthesis, as well as metabolism. The functional inactivation of ABP1 results in cell cycle arrest, showing that ABP1 plays a critical role in cell cycle regulation, acting at both the G1/S and G2/M checkpoints. ABP1 is ubiquitous among green plants, found mainly within the endoplasmic reticulum (ER) and in smaller quantities at the cell surface associated with the plasma membrane. In Arabidopsis thaliana, ABP1 null mutations result in embryonic lethality while decreased ABP1 expression leads to severe retardation of leaf growth.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985665896  42 PIVRNISDLPQDNYGRPGLSHMTVAGSVLHGMKEVEIWLQTFAPGSETPIHRHSCEEVFVVLKGSGTLYLAETHGNFPGK 121
Cdd:cd02220     1 PLVRNISELPQDSYGRPGLSHMTVAGAVHHGMKEVEVWLQTFAPGSGTPIHRHSCEEVFVVLKGSGTLYLASSSLKYPGK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1985665896 122 PIEFPIFANSTIHIPINDAHQVKNTG-HEDLQVLVIISRPPIKIFIYEDWFMPHTAARLKFPYYWDEQCVQ 191
Cdd:cd02220    81 PQEFPIFPNSTFHIPVNDVHQVWNTGeHEDLQVLVIISRPPVKVFIYDDWSMPHTAAKLKFPYVWDEQCYQ 151

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985665896  46 NISDLPQDNYGrpglsHMTVAGSVLHGMKeveIWLQTFAPGSETPIHRHS-CEEVFVVLKGSGTLYLAEThgnfpgkpiE 124
Cdd:COG0662     5 NIEELKAIGWG-----SYEVLGEGGERLS---VKRITVPPGAELSLHVHPhRDEFFYVLEGTGEVTIGDE---------E 67

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1985665896 125 FPIFANSTIHIPINDAHQVKNTGHEDLQVLVIISRPPI 162
Cdd:COG0662    68 VELKAGDSVYIPAGVPHRLRNPGDEPLELLEVQAPAYL 105

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 1985665896  84 APGSETPIHRHSC-EEVFVVLKGSGTLYLAEthgnfpgkpIEFPIFANSTIHIPINDAHQVKNTGHEDLQVLVIISrPP 161
Cdd:cd02214    27 PPGESTLPHRLKGsEEVYYILEGEGTMEIDG---------EPREVGPGDAVLIPPGAVQRIENTGEEDLVFLCICS-PA 95

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. 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 1985665896  82 TFAPGSETPIHRHSCEEVFVVLKGSGTLYLAEThgnfpgkpiEFPIFANSTIHIPINDAHQVKNTGHEDLQVLVII 157
Cdd:cd02222    23 EIEPGGHTPLHTHPWEHEVYVLRGKGVVVIGGE---------EYPVKPGDVVYIPPNEPHQFRNTGDEPLGFLCIV 89

Bacteroides fragilis BF4112 and related proteins, cupin domain; This family includes archaeal and bacterial proteins homologous to BF4112, a Bacteroides fragilis 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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985665896  77 EIWLQTFAPGSETP-IHRH-SCEEVFVVLKGSGTLYLAEThgnfpgkpiEFPIFANSTIHIPINDAHQVKNTGHEDLQVL 154
Cdd:cd06985    15 EISFNSLPAGAAVPfVHSHkENEEIYIILKGKGEFQVDGE---------VFPVKEGSVIRVAPDGKRSWRNTSDEPLIYI 85

                  ..
gi 1985665896 155 VI 156
Cdd:cd06985    86 CI 87

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 1985665896  72 GMKEVEIWLQTFAPGSE-TPIHRHSCEEVFV-VLKGSGTLYLA-ETHGNFPGKPIEFPifANSTIhipindAHQVKNTGH 148
Cdd:cd02224    13 GLTQLGVNLERLPPGARsSPRHWHSAEEEFVyVLSGEGTLRLDgEEVLPRPGDFVGFP--AGTGV------AHQLINRSD 84

                          90       100
                  ....*....|....*....|.
gi 1985665896 149 EDLQVLVIISRPPIKIFIYED 169
Cdd:cd02224    85 EPLVYLVVGTRLPDDVCTYPD 105

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1985665896  82 TFAPGSETPIHRHSC-EEVFVVLKGSGTLYLAEThgnfpgkpiEFPIFANSTIHIPINDAHQVKNTGHEDLQVL 154
Cdd:cd02213    46 TVNPGKRLSLQRHHHrSEHWVVVSGTAEVTLDGK---------EKLLKEGESIYIPKGTKHRLENPGKIPLEII 110

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985665896  76 VEIwlqtFAPGSETPIHRH-SCEEVFVVLKGSGTLYLAethgnfpGKpiEFPIFANSTIHIPINDAHQVKNTGHEDLQVL 154
Cdd:cd06987    32 VEI----FDPGGRTPPNTHpAAHEMFFVLAGEGRAYCD-------GQ--RVPLRPGDALVVPPGSEHVIENTGSGRLYCL 98

Chromobacterium violaceum CV2614 and related proteins, cupin domain; This family includes mostly bacterial proteins homologous to CV2614, a Chromobacterium violaceum 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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985665896  64 TVAGSVLH---GMKEVEIWLQTFAPGSETPIHRHSCEEVFVVLKGSGTLYLAEthgnfpGKPIEFPifANSTIHIPINDA 140
Cdd:cd02236     7 TWDGQPIPypeGQPEITVLRITIPPGAELPWHTHPVPNAGYVLSGELTVEYED------GKKRTFK--AGDAFVEAVNTW 78

                          90
                  ....*....|....*.
gi 1985665896 141 HQVKNTGHEDLQVLVI 156
Cdd:cd02236    79 HRGRNGGDEPVELLVF 94

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1985665896  75 EVEIWLQTFAPGSETPIHRHSCEE-VFVVLKGSG--TLYLAETHGNFPGKPIeFPIFANSTIHI-PINDAHQVKNTGHED 150
Cdd:cd10548    11 DFELLLLCWPPGQGSPIHDHGGSWcVVKVLEGELteTRYRRPDDGSLSGEET-LEETPGDVTYInPDGGIHRVENPSDEP 89

                  .
gi 1985665896 151 L 151
Cdd:cd10548    90 A 90

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1985665896  83 FAPGSETPIHRHSCEE-VFVVLKGSGTLYLAEThgnfpgkpiEFPIFANSTIHIPINDAHQVKNTGHEDLQVLVIIS 158
Cdd:cd06122    34 LEPGQSQKVHAHAGSDkVYFVLEGEGRFTVGDE---------ERELGAGEAVLAPAGVPHGVRNTGAERLVLLVFMA 101

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 1985665896  74 KEVEIWLQTFAPGSETPI-HRHSCEEVFVVLKGSGTLYLAEThgnfpgkpiEFPIFANSTIHIPINDAHQVKNTGHEDLQ 152
Cdd:cd02209    14 RKMEPFLVTLPPGGSGGEpYSHEGEEFGYVLEGELELTVGGE---------TYVLEAGDSIYFDSDVPHRYRNPGDEPAR 84

                  ....*.
gi 1985665896 153 VLVIIS 158
Cdd:cd02209    85 VLWVIT 90

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase bicupin aromatic ring-cleaving dioxygenases, C-terminal cupin domain; This model represents the C-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDO's and NDO's in its unique ability to oxidatively cleave many different salicylate, gentisate, and 1-hydroxy-2- naphthoate substrates with high catalytic efficiency. The active site of this enzyme is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.

                          10        20        30
                  ....*....|....*....|....*....|
gi 1985665896  79 WLQTFAPGSETPIHRHSCEEVFVVLKGSGT 108
Cdd:cd06992    22 FMQLLRAGFSTRPHRSTASAVYHVVEGSGR 51