HHsearch alignment for GI: 254780942 and conserved domain: TIGR00965
>TIGR00965 dapD 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase; InterPro: IPR005664 Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see . The lysine/diaminopimelic acid branch of the aspartate pathway produces the essential amino acid lysine via the intermediate meso-diaminopimelic acid (meso-DAP), which is also a vital cell wall component in Gram-negative bacteria . The production of dihydropicolinate from aspartate-semialdehyde controls flux into the lysine/diaminopimelic acid pathway. Three variants of this pathway exist, differing in how tetrahydropicolinate (formed by reduction of dihydropicolinate) is metabolised to meso-DAP. One variant, the most commonly found one in archaea and bacteria, uses primarily succinyl intermediates, while a second variant, found only in Bacillus, utilises primarily acetyl intermediates. In the third variant, found in some Gram-positive bacteria, a dehydrogenase converts tetrahydropicolinate directly to meso-DAP. In all variants meso-DAP is subsequently converted to lysine by a decarboxylase, or, in Gram-negative bacteria, assimilated into the cell wall. Evidence exists that a fourth, currently unknown, variant of this pathway may function in plants . 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase (also known as tetrahydrodipicolinate N-succinyltransferase or DapD) is part of the succinyl route of of lysine/DAP biosynthesis. The DapD protein is a homotrimer is a trimeric enzyme with each monomer composed of three domain: an N-terminal helical domain, a distinctive left-handed parallel beta-helix (LBH) domain, and a predominantly beta C-terminal domain , . The LBH structure is encoded by an imperfect tandem-repeated hexapeptide sequence. Each trimer contains three independent active sites, always occuring at the boundary of two subunits, and formed by residues from one N-terminal domain, one C-terminal domain and two adjacent LBH domains.; GO: 0016757 transferase activity transferring glycosyl groups, 0009089 lysine biosynthetic process via diaminopimelate.
Probab=99.05 E-value=6e-10 Score=75.04 Aligned_cols=120 Identities=23% Similarity=0.356 Sum_probs=85.3
Q ss_pred CCCCEECCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEEECCCCCCCCCCCCCCC
Q ss_conf 78410012232234420002111631343321211121002134432000002586443202310211247854487455
Q gi|254780942|r 272 PDTVIEPHVFFGCGVSIENYVQIRAFSYLEGVHIGKKTIIGPFARIRQETTIEKNVRIGNFCEVKKATIKEGSKINHLSY 351 (442)
Q Consensus 272 ~~~~I~~~~~Ig~~~~Ig~~~~I~~~~~i~~~~Ig~~~~Ig~~~~i~~~s~i~~~~~Ig~~~ei~~s~i~~g~~i~~~~~ 351 (442)
T Consensus 102 ~g~R~VPgA~vR~G~fiAkNvVlMPSyvNIGAYvDEGtMvDTWATvGSCAQIGKNvHlSGG~------------------ 163 (275)
T TIGR00965 102 AGFRKVPGAIVRRGTFIAKNVVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGV------------------ 163 (275)
T ss_pred CCCCCCCHHHEECCCEEEEEEEECCCEEECCCEEECCCEECCHHHHCCHHHHCCCEEEECCC------------------
T ss_conf 66654874360057357752377555210136751686010012230032206625751783------------------
Q ss_pred CCCCEECCCCEECCCEEECCCCCCCCCCCEECCCCEECCCCEEECCEEECCCCEECCC---------------CEECCCC
Q ss_conf 5663988998997980883445775456298788798869989378398899899778---------------3576643
Q gi|254780942|r 352 VGDSVVGKNVNIGAGTITCNYDGTHKYKTHINENAFIGSNSSLIAPITIGQGTYVASG---------------SIITQDT 416 (442)
Q Consensus 352 igd~~iG~~~~ig~g~i~~n~~g~~~~~~~ig~~~~iG~~~~i~~gv~ig~~~~i~ag---------------~~v~~dv 416 (442)
T Consensus 164 ----------GIG-GV----LEPLQA~P~IIEDNCFiGARSEi~EGVIVEEGSVISMGVfIG~STkI~~R~TGEI~~GRv 228 (275)
T TIGR00965 164 ----------GIG-GV----LEPLQAKPTIIEDNCFIGARSEIVEGVIVEEGSVISMGVFIGQSTKIVDRDTGEIIYGRV 228 (275)
T ss_pred ----------CCC-CC----CCCCCCCCEEEECCCEECCCEEEEEEEEECCCCEEEEEEEECCCCEEEECCCCEEEECCC
T ss_conf ----------316-52----463357875882476004611356207971685888406855601688536671765513
Q ss_pred CCCCEEEE
Q ss_conf 69868981
Q gi|254780942|r 417 PENSLVFA 424 (442)
Q Consensus 417 ~~~~~v~~ 424 (442)
T Consensus 229 PA~SVVVs 236 (275)
T TIGR00965 229 PAGSVVVS 236 (275)
T ss_pred CCEEEEEC
T ss_conf 56027971