Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_044410272.1 NA59_RS07265 cytochrome c550
Query= curated2:Q58414 (288 letters) >NCBI__GCF_000934765.1:WP_044410272.1 Length = 292 Score = 167 bits (423), Expect = 3e-46 Identities = 95/282 (33%), Positives = 166/282 (58%), Gaps = 12/282 (4%) Query: 3 IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDI 62 +YLNG+F+ A++S D G L+ DGV+E I Y +F + H RL +S ++ I Sbjct: 6 VYLNGEFMPMASARISPMDRGFLFADGVYEVIPVYQQTLFEWQAHYQRLENSLAAVGIIN 65 Query: 63 PLTKEEMIDVVLETLRVNNLRDAYIRLVVTRGVGDLGLD--PRKCGKPTIFCIAIPMPPL 120 P + + ++ + + + +D +I L ++RGV + D P+K PT+F P+ PL Sbjct: 66 PFDNQAWLSILNKLIASHPWQDQFIYLQISRGV-QIPRDHLPQKDLTPTVFAYTNPLKPL 124 Query: 121 LG---EDGIRAITVS-VRRLPVDVLNPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGF 176 E+GI+ IT+ +R D+ K++ L +V+AK+QA AGVD+ L++ +G Sbjct: 125 AASILENGIKVITLEDIRWQRCDI-----KAIALLPNVMAKLQAQAAGVDDVILINQQGN 179 Query: 177 VVEGTGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTAD 236 V EG+ N+ +VK GV+ TPP+ Q IL GITR V+ KLA++ I +E + +L TAD Sbjct: 180 VTEGSASNMLMVKEGVIITPPLSQHILPGITRQVIEKLAQQHHISFIEREINQAELETAD 239 Query: 237 ELFITGTAAEIVPVFEIDGRVINNKQVGEITKKLKEKFKDIR 278 EL++ + E +P+ +++G+ + + + G++ +KL+ ++D + Sbjct: 240 ELWLASSTKEALPICQLNGQPVGDGKPGQVWQKLRAHYQDYK 281 Lambda K H 0.321 0.143 0.411 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: 232 Number of extensions: 15 Number of successful extensions: 4 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: 288 Length of database: 292 Length adjustment: 26 Effective length of query: 262 Effective length of database: 266 Effective search space: 69692 Effective search space used: 69692 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: 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