Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_028322231.1 H567_RS0116450 hypothetical protein
Query= curated2:O29329 (290 letters) >NCBI__GCF_000422285.1:WP_028322231.1 Length = 285 Score = 112 bits (279), Expect = 1e-29 Identities = 89/263 (33%), Positives = 127/263 (48%), Gaps = 9/263 (3%) Query: 4 VYMDGEFVPENEAKVSIFDHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEI 63 ++++G FVPE+ + D GFLYGDG+FE +RA NGR L +H+DRL A+ + L + Sbjct: 12 IWLNGRFVPEDRPAIHPLDRGFLYGDGLFETLRAQNGRPLYLSQHLDRLRQGAEELRLNL 71 Query: 64 PITKEEFMEIILETLRKNNL--RDAYIRPIVTRGIGD-LGLDPRKCQNPSIIVITKPWGK 120 P + II L+ N L A ++ IVTRG LGL P C+ P+II+ + + Sbjct: 72 P-GDLHWDGIIARLLQVNGLCKSAARVKIIVTRGQEPRLGL-PTACR-PTIILSAERYHP 128 Query: 121 LYGDLYEKGLTAITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGY 180 Y +G + NS+ KSLNYL + A+ A G EA+ LD G Sbjct: 129 PTARDYLEGW---RLHCHLNSYAPPLARYKSLNYLFYLCARQAALDAGCHEAVVLDPEGR 185 Query: 181 VSEGSGDNIFVVKNGAITTPPTINNLRGITREAVIEIINRLGIPFKETNIGLYDLYTADE 240 V E + ++ G TP + + L GIT + V ++ G P DL Sbjct: 186 VCETAAGSLLCRSGGTWWTPESPHQLTGITLQQVRRLLGLSGTPVDTRAARPADLRNVGT 245 Query: 241 VFVTGTAAEIAPIVVIDGRKIGD 263 V+V + P V IDGR I D Sbjct: 246 VWVLNALIGVMPAVQIDGRIIPD 268 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: 197 Number of extensions: 9 Number of successful extensions: 2 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: 285 Length adjustment: 26 Effective length of query: 264 Effective length of database: 259 Effective search space: 68376 Effective search space used: 68376 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