Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_020561990.1 A3OW_RS0103225 D-amino acid aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000372865.1:WP_020561990.1 Length = 280 Score = 151 bits (382), Expect = 1e-41 Identities = 99/283 (34%), Positives = 158/283 (55%), Gaps = 13/283 (4%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 VY++G ++P NEA+VS+ D GFL+GDGV+E I +Y+G +F +H++RL S I L Sbjct: 6 VYLNGRYLPLNEARVSVLDRGFLFGDGVYEVIPSYSGHLFHFDKHMERLDRSLSGIRLGN 65 Query: 64 PITKEEFMEIILETLRKNNLRDAYIRPIVTRGIGDLG--LDPRKCQNPSIIVITKPWGKL 121 P +++EI+ L + D Y+ VTRG + P++ + P++ ++ L Sbjct: 66 PFPYAQWLEILTPLL--DPALDQYVYLQVTRGSAEKRDHAFPKQIR-PTVFAMSSAIVPL 122 Query: 122 YGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYV 181 G G+ A+T+ R +IK++ L NIL + EA K EAI + R +V Sbjct: 123 PGQ--NSGVRAMTMPDGRWQLC----HIKAITLLANILYRQEAVEKDCTEAILV-RGDHV 175 Query: 182 SEGSGDNIFVVKNGAITTPPTINNLR-GITREAVIEIINRLGIPFKETNIGLYDLYTADE 240 +EG+ N+F V +G + TPP + L GITR+ ++EI R I ++E +I L L +ADE Sbjct: 176 TEGAASNVFAVVDGVLVTPPKSHELLPGITRDVLLEIAERNHISYREDSISLETLKSADE 235 Query: 241 VFVTGTAAEIAPIVVIDGRKIGDGKPGEITRKLMEEFSKLTES 283 +++T + EI P+V +D IG GKPG + + F +S Sbjct: 236 IWLTSSTREIMPVVELDSAPIGGGKPGPVWATMNRLFQNYKQS 278 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: 214 Number of extensions: 11 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: 280 Length adjustment: 26 Effective length of query: 264 Effective length of database: 254 Effective search space: 67056 Effective search space used: 67056 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