Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_089322400.1 CHB58_RS01815 hypothetical protein
Query= curated2:Q58414 (288 letters) >NCBI__GCF_900188395.1:WP_089322400.1 Length = 254 Score = 92.8 bits (229), Expect = 7e-24 Identities = 78/253 (30%), Positives = 122/253 (48%), Gaps = 24/253 (9%) Query: 29 GVFEGIRAYDGVVFMLKEHIDRLYDSAKSLCIDIPLTKEEMIDVVLETLRVN-NLRDAYI 87 G+FE +R +G + H +RL SA SL I ++ E+ VV + NL + Sbjct: 23 GIFETVRVENGKAVFISYHYERLRKSAVSLDIPFSISLEKFNSVVEKECGDGLNL----V 78 Query: 88 RLVVTRGVGDLGLDPRKCGKPTIFCIAIPMPPLLGEDGIRAITVSVRRLPVDVLNPAVKS 147 + V+ G+ + R+C P + SVRR D L+ K+ Sbjct: 79 KFVLYHD-GNFTVSTRECFVPKEVSLTFDF--------------SVRRKK-DFLSD-FKT 121 Query: 148 LNYLNSVLAKIQANYAGVDEAFLLDDKGFVVEGTGDNIFIVKNGVLKTPPVYQSILKGIT 207 L+ +S+ A ++A G DE LLD GFV E NIF +KNGV+ TP + L G Sbjct: 122 LSIYDSLYALLKAKNKGFDEVVLLDTSGFVSETAFANIFFLKNGVVFTPSLETGCLPGTR 181 Query: 208 RDVVIKLAKEEGIEVVEEPLTLHDLYTADELFITGTAAEIVPVFEIDGRVINNKQVG--E 265 R++VI++ KE G+ V+E L +A+E FIT ++V V IDG+ + + + Sbjct: 182 REIVIEILKEMGVPVIEGFFKPEFLLSAEEAFITSARYDVVRVSYIDGKKFKVEGISFTD 241 Query: 266 ITKKLKEKFKDIR 278 KK+ E+ K ++ Sbjct: 242 RVKKVIERLKFLK 254 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: 204 Number of extensions: 8 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: 288 Length of database: 254 Length adjustment: 25 Effective length of query: 263 Effective length of database: 229 Effective search space: 60227 Effective search space used: 60227 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 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