Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate Ac3H11_1015 Aromatic-amino-acid aminotransferase (EC 2.6.1.57)
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1015 Length = 396 Score = 298 bits (763), Expect = 2e-85 Identities = 170/396 (42%), Positives = 235/396 (59%), Gaps = 17/396 (4%) Query: 10 FGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQ 69 F ++ S IREL KL +PGI+SFAGG P +F E A+ L E+ ALQ Sbjct: 3 FADRLNNVETSAIRELFKLLGKPGIISFAGGFPDSAMFDVEGIRAASNAALAEEPGAALQ 62 Query: 70 YSPTEGYAPLRAFVAEWI------GVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAP 123 Y TEGY PLR +A ++ V + +++TTGSQQALDL+GK + G V++E P Sbjct: 63 YGATEGYNPLREQLAAFMTSKGAKDVAADNLIVTTGSQQALDLLGKTLISPGDKVIVEGP 122 Query: 124 SYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLP 183 +++ IQ FRL G ++ P G D LE+++ +P+F+YLIP+F NP+G + L Sbjct: 123 TFLATIQCFRLYGAELISAPIDGNGVKTDELEKLIAEHKPKFVYLIPTFGNPSGAMLSLE 182 Query: 184 ARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPG----VIYLGSFSKV 239 RK +L+M ++ ++VEDD Y +LYFG+A PSL L+ A PG +++ GS SKV Sbjct: 183 RRKAVLEMAVKHNTLIVEDDPYGDLYFGDAPPPSLLNLS--ATVPGSRELLVHCGSLSKV 240 Query: 240 LSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEG-FSERLERVRRVYR 298 LSPGLRV + +A E L K KQ +D HT Q + LK G L VR+VY Sbjct: 241 LSPGLRVGWMIAPAELLGKATMCKQFSDAHTSTFAQATAAQYLKAGRMPGTLANVRKVYA 300 Query: 299 EKAQAMLHALDREVPKEVRYTRPKGGMFVWMEL--PKGLSAEG--LFRRALEENVAFVPG 354 E+AQAM AL +E+ + + +P+GG+FVW L G A+G L +RA+E+ VAFVPG Sbjct: 301 ERAQAMGDALRKELGDAIEFVQPQGGLFVWARLTGAGGKVADGNVLAKRAIEKGVAFVPG 360 Query: 355 GPFFANGGGENTLRLSYATLDREGIAEGVRRLGRAL 390 PFF T RLS+AT D + I EGV RLG+A+ Sbjct: 361 TPFFCANPDHATFRLSFATADVDKIREGVARLGQAV 396 Lambda K H 0.320 0.139 0.401 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: 437 Number of extensions: 13 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: 397 Length of database: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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