Align Aromatic-amino-acid aminotransferase (EC 2.6.1.57) (characterized)
to candidate WP_041361650.1 MCA_RS14695 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1015 (396 letters) >NCBI__GCF_000008325.1:WP_041361650.1 Length = 390 Score = 239 bits (609), Expect = 1e-67 Identities = 144/392 (36%), Positives = 206/392 (52%), Gaps = 19/392 (4%) Query: 6 RLNNVETSAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIRAASNAALAEEPGAALQYGA 65 R + +S IR++ ++ +PG+ISFAGG P M A + + QYG Sbjct: 8 RTERLTSSLIRDILQITQRPGVISFAGGLPAEEMMPELDFGACA--------ADSRQYGP 59 Query: 66 TEGYNPLREQLAAFMTSKGAKDVAADNLIVTTGSQQALDLLGKTLISPGDKVIVEGPTFL 125 +EG LR+ +A ++ G + + ++VTTGSQQ +DL+GK I G V++E PT+L Sbjct: 60 SEGEPVLRDLIARGLSGLGLR-CQTEQVLVTTGSQQGIDLVGKLFIDEGTPVLLESPTYL 118 Query: 126 ATIQCFRLYGAELISAPIDGNGVKTDELEKLIAEHKPKFVYLIPTFGNPSGAMLSLERRK 185 A +QCFR+YGAE P+ G+ D L+ I H+P FVYLIP+F NPSG + R+ Sbjct: 119 AALQCFRVYGAEFHGLPLQVGGIDPDALKAAIVRHRPAFVYLIPSFQNPSGCCYADAARR 178 Query: 186 AVLEMAVKHNTLIVEDDPYGDLYFGDAPPPSLLNLSATVPGSRELLVHCGSLSKVLSPGL 245 AV + + T +VEDDPY DL + + P V+ GS SK+ +PGL Sbjct: 179 AVAAVLDETGTPLVEDDPYRDLVYTSCDRTPVCAYLERAP-----WVYLGSFSKITAPGL 233 Query: 246 RVGWMIAPAELLGKATMCKQFSDAHTSTFAQATAAQYLKAGRMPGTLANVRKVYAERAQA 305 RVG++ + L KQ SD HT QA A++L +G LA++ VYA R Sbjct: 234 RVGYLASSPGLFPWLVRLKQSSDLHTGRTGQAWLARFLSSGDFGKHLAHMNGVYAGRRDT 293 Query: 306 MGDALRKELGDAIEFVQPQGGLFVWARLTGAGGKVADGNVLAKRAIEKGVAFVPGTPFF- 364 M AL + E+ P GGLF W RL G D K A+ + VAF+PG PFF Sbjct: 294 MQAALERHFSGLAEWSAPAGGLFFWLRLVGN----IDTLAALKVALGRDVAFMPGEPFFP 349 Query: 365 CANPDHATFRLSFATADVDKIREGVARLGQAV 396 A+ + RL+F+ A +KI G+ L + + Sbjct: 350 VADQRYPALRLNFSHATPEKIERGIGLLSEVL 381 Lambda K H 0.319 0.136 0.394 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: 411 Number of extensions: 25 Number of successful extensions: 6 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: 396 Length of database: 390 Length adjustment: 31 Effective length of query: 365 Effective length of database: 359 Effective search space: 131035 Effective search space used: 131035 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 (21.7 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