Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_018233679.1 THITHI_RS0113690 D-amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000378965.1:WP_018233679.1 Length = 284 Score = 172 bits (436), Expect = 8e-48 Identities = 100/275 (36%), Positives = 160/275 (58%), Gaps = 6/275 (2%) Query: 2 LYVYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDL 61 + VY++G ++PE+EA+VS+ D GFL+GDGV+E + AY GR+FRL++H+DRL S A+ + Sbjct: 1 MIVYLNGHYLPESEARVSVLDRGFLFGDGVYEVVPAYGGRLFRLEQHLDRLDRSLAAVRI 60 Query: 62 EIPITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKL 121 P+ + + ++ E L +N D + VTRG + +P++ + P Sbjct: 61 MPPLDRAGWTRMLTELLARNPGGDRSVYLQVTRGAARRDHAFPEDASPTVFAMVNPLQPG 120 Query: 122 YGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181 L E G+ A+T+ R + +IK++ L NILA+ +A G EAI L R G Sbjct: 121 DPALLETGVAAVTMPDTRWA----RCDIKAITLLANILARQQAVEAGATEAI-LVRAGRA 175 Query: 182 SEGSGDNIFVVKNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTADE 240 EG+ N+FVV +G I TPP + L GITR+ V+E+ +P ET + DL A+E Sbjct: 176 IEGAASNLFVVGDGVIVTPPKDQSLLPGITRDLVVELAEAHNVPLMETPVTEADLRAAEE 235 Query: 241 VFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLME 275 +++T + EI P+ +D R +GDG+PG + ++M+ Sbjct: 236 IWLTSSTKEILPVTRLDDRPVGDGRPGPVWARMMK 270 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: 236 Number of extensions: 12 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: 284 Length adjustment: 26 Effective length of query: 264 Effective length of database: 258 Effective search space: 68112 Effective search space used: 68112 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: 47 (22.7 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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