Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_085771339.1 B1812_RS09265 branched-chain amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_002117405.1:WP_085771339.1 Length = 297 Score = 112 bits (279), Expect = 1e-29 Identities = 91/287 (31%), Positives = 140/287 (48%), Gaps = 17/287 (5%) Query: 5 YMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIP 64 + +G + N+ + + HG G VF+G RA+ G L +H+ R+ SA + L+ Sbjct: 17 FFEGAWREGNQPILGVRSHGAWLGSVVFDGARAFEGVTPDLDKHLARVNWSAANMSLDPV 76 Query: 65 ITKEEFMEIILETLRKNNLRDA--YIRPI--VTRGIGD-LGLDPRKCQNPSIIVITKPWG 119 +T E + E++ E L + DA YIRP+ +G G + DP N + + P Sbjct: 77 VTLERWRELVAEGLSRF-APDAQLYIRPMYWAEQGYGGGVRFDPAST-NWCLSIYEAPMP 134 Query: 120 KLYGDLYEKGLTAITVA-VRRNSFDALPPNIK-SLNYLNNILAKIEANAKGGDEAIFLDR 177 G A+T++ RR + + P N K S +Y N A IEA +G D + LD Sbjct: 135 APRGG-------AVTLSPFRRPTLEMAPVNAKASCHYANGARALIEAAGRGFDNCLMLDA 187 Query: 178 NGYVSEGSGDNIFVVKNGAITTP-PTINNLRGITREAVIEIINRLGIPFKETNIGLYDLY 236 G V+E + N F+ K+G + TP P L G+TR+ VI ++ G+ ET + D Sbjct: 188 LGNVAEFANSNAFMAKDGVVFTPAPNGTFLDGVTRQRVIGLLRAAGVTVVETLLSYRDFA 247 Query: 237 TADEVFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTES 283 TADE+F TG ++AP+ ID R + G + R L F+ ES Sbjct: 248 TADEIFSTGNFQKVAPMTRIDERALQAGPLYQTARALYWRFAHDPES 294 Lambda K H 0.319 0.142 0.409 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: 203 Number of extensions: 9 Number of successful extensions: 3 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: 290 Length of database: 297 Length adjustment: 26 Effective length of query: 264 Effective length of database: 271 Effective search space: 71544 Effective search space used: 71544 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: 48 (23.1 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