Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate WP_011652702.1 RL_RS16490 PLP-dependent aminotransferase family protein
Query= metacyc::MONOMER-6727 (397 letters) >NCBI__GCF_000009265.1:WP_011652702.1 Length = 406 Score = 277 bits (709), Expect = 3e-79 Identities = 157/395 (39%), Positives = 228/395 (57%), Gaps = 12/395 (3%) Query: 4 LSWSEAFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREK 63 L+W F + R++AS IRELLKL RP I+SFAGG+P P LFP +E +A A I Sbjct: 2 LNWDTMFASRSSRMRASEIRELLKLLDRPDIISFAGGIPDPALFPDQEFKQAYADIFDGA 61 Query: 64 G-EVALQYSPTEGYAPLRAFV-----AEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSP 117 ALQYS +EGY PLR ++ A I + V I +GSQQ LD +GK+FL Sbjct: 62 AVNSALQYSVSEGYKPLREWLVGQMAALDIRCELDNVFIVSGSQQGLDYLGKLFLSPDDT 121 Query: 118 VLLEAPSYMGAIQAFRLQGPRF-LTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPT 176 L+ P+Y+GA+QAF P + P G P+ + +F YL F NPT Sbjct: 122 ALVTWPTYLGALQAFNAYEPAYDQLTPNGNRTPESYRAAASAAGGKVKFAYLSTDFSNPT 181 Query: 177 GGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELA-REAGYPG---VIY 232 G L RK++L + + + V+ED AY+ L + +P + L E G+ IY Sbjct: 182 GETVDLDGRKKVLALAEDLDIAVIEDAAYQSLRYDGDPIPPILALEIAEKGHINDTRTIY 241 Query: 233 LGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLER 292 GSFSK L+PGLRV F VA+ ++KLV KQ ADLH+ +NQM + ++ + GF ++ + Sbjct: 242 CGSFSKTLAPGLRVGFIVANAPVIRKLVLMKQAADLHSSTINQMAISDVAERGFDAQVAK 301 Query: 293 VRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALE-ENVAF 351 ++ Y + ML AL++ +P+ +T+P+GGMF+W+ LP+G+ L ++LE VAF Sbjct: 302 IKAAYSRRRDCMLAALEKYMPEGTSWTKPEGGMFIWITLPEGMDGAKLLAKSLETAKVAF 361 Query: 352 VPGGPFFANGGGENTLRLSYATLDREGIAEGVRRL 386 VPG FFA+G G NT R+S++ + + I +G+ RL Sbjct: 362 VPGKAFFADGSGANTFRVSFSCANEQMIEDGIGRL 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: 400 Number of extensions: 22 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: 406 Length adjustment: 31 Effective length of query: 366 Effective length of database: 375 Effective search space: 137250 Effective search space used: 137250 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 24 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