Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_011840341.1 RSPH17029_RS02110 D-amino-acid transaminase
Query= curated2:Q58414 (288 letters) >NCBI__GCF_000015985.1:WP_011840341.1 Length = 286 Score = 149 bits (375), Expect = 9e-41 Identities = 95/278 (34%), Positives = 148/278 (53%), Gaps = 7/278 (2%) Query: 3 IYLNGKFVDEKDAKVSVFDHGLLYGDGVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDI 62 +Y+NG+++ E++A VS+FD G L DGV+E G + H RL S L + Sbjct: 5 VYVNGEYLPEEEATVSIFDRGFLMADGVYEVTSVLGGKLIDFPGHAARLDRSLTELEMTA 64 Query: 63 PLTKEEMIDVVLETLRVNNLRDAYIRLVVTRG-VGDLGLD-PRKCGKPTIFCIAIPMPPL 120 P+ E++++V E +R N + + I L +TRG GD P KPT+ P L Sbjct: 65 PMNAEDLLEVHRELVRRNGIDEGLIYLQITRGNPGDRDFAFPPADTKPTVVLFTQAKPGL 124 Query: 121 LGEDGIRAITVSVRRLPVDVL--NPAVKSLNYLNSVLAKIQANYAGVDEAFLLDDKGFVV 178 R + + V +P D+ +K++ L +AK+ A A VD+A+ ++D G V Sbjct: 125 AANPTAR-VGIKVISIP-DIRWGRRDIKTVQLLYPSMAKMAAKKAHVDDAWFVED-GLVT 181 Query: 179 EGTGDNIFIVKNGVLKTPPVYQSILKGITRDVVIKLAKEEGIEVVEEPLTLHDLYTADEL 238 EGT +N +IVK G + T + IL GITR V++ A+E +EV E P T+ + ADE Sbjct: 182 EGTSNNAYIVKGGKIITRNLSNDILHGITRAAVVRFAREAQMEVEERPFTIEEAQGADEA 241 Query: 239 FITGTAAEIVPVFEIDGRVINNKQVGEITKKLKEKFKD 276 F T +A ++PV EIDG+ + G + +L+E + D Sbjct: 242 FFTSASAFVMPVVEIDGKAVGTGAPGPVAARLREIYLD 279 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: 240 Number of extensions: 13 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: 288 Length of database: 286 Length adjustment: 26 Effective length of query: 262 Effective length of database: 260 Effective search space: 68120 Effective search space used: 68120 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: 47 (22.7 bits)
This GapMind analysis is from Apr 10 2024. 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