Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_077278625.1 B1C78_RS07940 D-amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_002000365.1:WP_077278625.1 Length = 284 Score = 172 bits (437), Expect = 6e-48 Identities = 99/275 (36%), Positives = 158/275 (57%), Gaps = 6/275 (2%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 VY++GE++PE+EA+VS+ D GFL+GDGV+E + Y GR RL+EH+DRL S A+ +E Sbjct: 3 VYLNGEYLPESEARVSVLDRGFLFGDGVYEVVPVYGGRCLRLEEHLDRLERSLAAVRIEP 62 Query: 64 PITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYG 123 P+ + + +++ L N D + VTRG+ +P++ + Sbjct: 63 PLDRAGWRDMLTRLLEHNPGEDRSVYLQVTRGVARRDHAFPADTSPTVFAMVNALTPPDP 122 Query: 124 DLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVSE 183 + E G+ A+T+ R S +IK++ L NILA+ +A G EAI + R G +E Sbjct: 123 AVRETGVAAVTMPDTRWS----RCDIKAITLLANILARQQAVEAGATEAILM-RGGRATE 177 Query: 184 GSGDNIFVVKNGAITTPPTINN-LRGITREAVIEIINRLGIPFKETNIGLYDLYTADEVF 242 G+ N+FVV +G I TPP + L GITR+ V+E+ GIP E + DL A+E++ Sbjct: 178 GAASNLFVVGDGVIVTPPKDQSLLPGITRDLVVELAADHGIPLMEAPVTEADLRAAEEIW 237 Query: 243 VTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEF 277 +T + EI P+ +DG +GDG+PG + ++M+ + Sbjct: 238 LTSSTKEILPVTRLDGVPVGDGRPGPVWARMMKHY 272 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: 244 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: 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 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