Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate BPHYT_RS32640 BPHYT_RS32640 2-aminoadipate aminotransferase
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__BFirm:BPHYT_RS32640 Length = 398 Score = 251 bits (640), Expect = 3e-71 Identities = 149/386 (38%), Positives = 217/386 (56%), Gaps = 17/386 (4%) Query: 20 STIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPL 79 S IREL K +PG++SFAGG PA +LF +E +AAA + + LQY PT+G L Sbjct: 14 SPIRELFKYLAQPGMISFAGGYPASDLFDRE-GLDAAASRASQHATLCLQYGPTDGLPVL 72 Query: 80 RAFVAEWIGVR-----PEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRL 134 + +A + R P+++L TTGSQQ DL+ +V + G VL+E P+Y +QA L Sbjct: 73 KEQLAHLMARRGVSCTPQDMLATTGSQQGFDLLLRVMVAPGDVVLVEQPAYPATLQALTL 132 Query: 135 QGPRFLTVPAGEEGPDLDALEEVLK----RERPRFLYLIPSFQNPTGGLTPLPARKRLLQ 190 Q +T+P ++G D+DAL +L R P+ LY +P+F NPTG R LL+ Sbjct: 133 QEADVVTIPVDQDGLDIDALAALLDSGTLRRAPKLLYTVPTFANPTGATLSFERRTALLK 192 Query: 191 MVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPG----VIYLGSFSKVLSPGLRV 246 + ++VEDD Y +L F A LPSL L+ + PG V++ S SK+++PGLRV Sbjct: 193 LAARHRFLIVEDDPYGDLRFTGAALPSLLALSEQV--PGSRDWVVHFSSLSKIVAPGLRV 250 Query: 247 AFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYREKAQAML 305 + +AH E L++ V AKQ DL + Q + E L G ER L R+ Y K + + Sbjct: 251 GWMLAHAEILRRCVVAKQTVDLCSSPWTQAIAAEYLASGALERHLPRIVDAYAVKCRTLC 310 Query: 306 HALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGEN 365 AL+ ++ +++ + RP GGMFVW L G +A R +E NV FVPG F+ + + Sbjct: 311 DALEAQLAEQIAFHRPAGGMFVWARLKAGQNASDYLRACIERNVMFVPGVAFYKDNIDSS 370 Query: 366 TLRLSYATLDREGIAEGVRRLGRALK 391 LRLS+A I GV+R+ +AL+ Sbjct: 371 ALRLSFAAPGIADIETGVQRMKQALE 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: 413 Number of extensions: 23 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: 397 Length of database: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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