Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate Ga0059261_2226 Ga0059261_2226 Aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__Korea:Ga0059261_2226 Length = 399 Score = 187 bits (474), Expect = 6e-52 Identities = 128/372 (34%), Positives = 198/372 (53%), Gaps = 22/372 (5%) Query: 23 LVAQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKA 82 L Q DVI L G+PDF TP VK AA +AI + +T YT G EL+ A+ + Sbjct: 25 LKRQGIDVIGLGAGEPDFDTPDFVKEAAIEAIRKGITKYTNVDGTPELKAAIVGKFARDN 84 Query: 83 DFNYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT 142 Y AE++I + +G + AF + GDEV++P P + Y ++ G KPV + Sbjct: 85 GLTY-AENQISVNSGGKHTLFNAFCATIDAGDEVVIPAPYWVSYPDVVEFAGGKPVFIAA 143 Query: 143 TSHG-FKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGR-NVFVLSD 200 + +K+ +E A+T TK VVL PSNPTG S ELK++ +L+ NV + +D Sbjct: 144 GAEANYKIKPEQLEAAITARTKWVVLNSPSNPTGAAYSAAELKALGEVLERHPNVLIYAD 203 Query: 201 EIYSELTYDRPHYS----IATYLRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKV 256 ++Y + YD ++ + L ++T+ NG+SK+++MTGWRIG+ P+ + K + K+ Sbjct: 204 DMYEHILYDGFEFATIAQVCPSLYERTLTANGVSKAYAMTGWRIGYAGGPQWLIKAMGKL 263 Query: 257 HQYNVSCASSISQKAALEAVTNGFDDALIMR-EQYKKRLDYVYDRLVSM-GLDVVKPSGA 314 + S S+SQ A++ A+ NG L R ++KR D V L + G++ +P GA Sbjct: 264 QSQSTSNPCSVSQAASVAAL-NGDQSFLKDRAAAFQKRRDLVVSMLGQINGMNCPRPEGA 322 Query: 315 FYIFPSIKS-FGMTS-------FDFSMA--LLEDAGVALVPGSSFSTYGEGYVRLSFACS 364 FY++P G T+ D +M LL+DA VA V G +F +R+S+A S Sbjct: 323 FYVYPEFSQLIGKTTPKGLVIDTDETMVGYLLDDAKVAAVHGGAFGF--SPALRISYATS 380 Query: 365 MDTLREGLDRLE 376 D L E R++ Sbjct: 381 EDVLAEACGRIQ 392 Lambda K H 0.319 0.135 0.388 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 353 Number of extensions: 17 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 393 Length of database: 399 Length adjustment: 31 Effective length of query: 362 Effective length of database: 368 Effective search space: 133216 Effective search space used: 133216 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory