Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_025274501.1 HALAL_RS0113470 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000527155.1:WP_025274501.1 Length = 366 Score = 132 bits (333), Expect = 9e-36 Identities = 109/325 (33%), Positives = 152/325 (46%), Gaps = 29/325 (8%) Query: 6 ADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPV-VFRHREHMQRLHDS 64 AD W + + + + + LHY +FEG++ Y G V +FR + QR + S Sbjct: 47 ADRGWHSARVEPFGPLTLSPATAVLHYAQEIFEGLKAYHRSDGTVGLFRPEANAQRFNGS 106 Query: 65 AKIYRFP------VSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYST 118 A+ P SI EL+ RD + +S Y+RP + + +GV P Y Sbjct: 107 ARRLAMPELPEKWFLASIRELISVDRDWVPTEGESSLYVRPFMIATESFLGVRPSQEYLY 166 Query: 119 DVIIAAFPWGAYLGAEALEQGIDAMVSS-WNRAAPNTIPTAAKAGGNYLSSLLVGSEARR 177 VI + P GAY + + + VS + RAAP AAK GGNY +SL S+A Sbjct: 167 GVITS--PAGAYF--KTGPKPVTLWVSEDYTRAAPGGTG-AAKCGGNYAASLAPHSQAIE 221 Query: 178 HGYQEGIALDV--NGYISEGAGENLFEV--KDGVLFTPPFTSSALPGITRDAIIKLAKEL 233 G + + LD + YI E G NLF V + V++TP T S LPGITRDAII L E Sbjct: 222 KGCDQVVFLDAVEHKYIDELGGMNLFFVYGDEKVIYTPRLTGSILPGITRDAIITLLSEE 281 Query: 234 GIEVREQVLSRESLYLAD-------EVFMSGTAAEITPVRSV----DGIQVGEGRCGPVT 282 G +V E S E + AD E F GTAA ITPV + + E + G +T Sbjct: 282 GWDVHETDYSLEK-WRADAQSGRLTETFACGTAAVITPVGMIREQGGEFSINESKTGELT 340 Query: 283 KRIQQAFFGLFTGETEDKWGWLDQV 307 +R++ + G ED W + Sbjct: 341 RRLRSRILDIQHGRAEDTHNWTQTI 365 Lambda K H 0.319 0.136 0.413 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: 301 Number of extensions: 18 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: 309 Length of database: 366 Length adjustment: 28 Effective length of query: 281 Effective length of database: 338 Effective search space: 94978 Effective search space used: 94978 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: 49 (23.5 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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