Align Probable branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42 (uncharacterized)
to candidate WP_034997597.1 DL88_RS14845 hypothetical protein
Query= curated2:O67733 (311 letters) >NCBI__GCF_000745425.1:WP_034997597.1 Length = 293 Score = 62.8 bits (151), Expect = 1e-14 Identities = 49/158 (31%), Positives = 87/158 (55%), Gaps = 8/158 (5%) Query: 143 KVSSWRRNDDNSIPSRWKVAGAYVNSALAKTEALMSGYDEAILLNSQGYVAEGSGENIFI 202 +VS RRN+ S SR K A +++ +A EA+M+G DEA+ L++ G VA + N+F+ Sbjct: 131 QVSIIRRNE-TSPASRIKALSA-LDAVMAHHEAIMAGCDEALQLDTTGNVACAATGNLFL 188 Query: 203 IKNGKAITPSPNEHILEGITRNAVITLLKKELVVEVEERPIARSELYTADEVFLTGTAAE 262 I NG+ +TP+ + IL G R+ ++ + + + E + +++ A+ VF+T + Sbjct: 189 IVNGRIVTPATTQAILPGTIRDLLLGGVSRH-GHAIAESIVPWADVEKAEAVFMTNSLRL 247 Query: 263 VTPVVEIDNRKIGNGEIGPITKQLQEFYFNAVRGKIQR 300 + PV I +R + I LQ+F +RG I++ Sbjct: 248 LAPVSRIGDRVFASA-THEIILSLQDF----LRGDIEQ 280 Lambda K H 0.318 0.136 0.389 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: 182 Number of extensions: 10 Number of successful extensions: 1 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: 311 Length of database: 293 Length adjustment: 27 Effective length of query: 284 Effective length of database: 266 Effective search space: 75544 Effective search space used: 75544 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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