Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_015945220.1 DHAF_RS22205 aminotransferase
Query= curated2:O29329 (290 letters) >NCBI__GCF_000021925.1:WP_015945220.1 Length = 271 Score = 97.1 bits (240), Expect = 4e-25 Identities = 76/251 (30%), Positives = 120/251 (47%), Gaps = 25/251 (9%) Query: 22 DHGFLYGDGVFEGIRAYNGRVFRLKEHIDRLYDSAKAIDLEIPITKEEFMEIILETLRKN 81 D L+G G+FE ++ + + H R+ A+ + + +P E+ E L +N Sbjct: 6 DRLVLFGYGIFETLKVNGLHIEVPRLHYRRMSKGAEQLGIPMPS-----YEVWREALEQN 60 Query: 82 NLRDAY----------IRPIVTRGIGDLGLDPRKCQNPSIIVITKPWGKLYGDLYEKGLT 131 R+A +R ++ G G P + ++P D Y++G+ Sbjct: 61 VQREASAARREGTAFALRVTLSGGAGQE-------VPPQWLYHSRPIPYTEKD-YQEGIP 112 Query: 132 AITVAVRRNSFDALPPNIKSLNYLNNILAKIEANAKGGDEAIFLDRNGYVSEGSGDNIFV 191 ++ RN + L IKS N + NILAK EA KG E ++L+ GY+ EG+ N+F Sbjct: 113 IAILSCPRNEYSPLV-QIKSTNTMENILAKQEAEEKGAREGLWLNTKGYLVEGTLSNLFF 171 Query: 192 VKNGAITTPP-TINNLRGITREAVIEIINRLGIPFKETNIGLYDLYTADEVFVTGTAAEI 250 V+NG + TP L G R+ V+E +LGIP+ E L L A+EVF+T I Sbjct: 172 VRNGILYTPSLPCGCLPGTRRQIVLECAQKLGIPWVEGEFSLAFLEDAEEVFLTNALMGI 231 Query: 251 APIVVIDGRKI 261 P+ +DGR+I Sbjct: 232 LPVSRVDGRRI 242 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: 190 Number of extensions: 10 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: 271 Length adjustment: 26 Effective length of query: 264 Effective length of database: 245 Effective search space: 64680 Effective search space used: 64680 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