Align Branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate WP_011840668.1 RSPH17029_RS04535 branched-chain amino acid aminotransferase
Query= curated2:P0A1A6 (309 letters) >NCBI__GCF_000015985.1:WP_011840668.1 Length = 287 Score = 106 bits (265), Expect = 6e-28 Identities = 85/279 (30%), Positives = 132/279 (47%), Gaps = 17/279 (6%) Query: 17 RWEDAKVHVM---SHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLRDSAKIYRFPVS 73 RW + + VM H + G+SVF+G R +D V H R+ SA+ + Sbjct: 14 RWHEGDLAVMRAADHGIWQGSSVFDGARWFDG----VAPDLEAHCARVNRSAEALMITPT 69 Query: 74 QSIDELMEACRDVIRKNNLTSA-YIRPLVFVGDVG-MGVNPPPGYTTDVIIAAFPWGAYL 131 +E++ R+ +R A YIRP+ + D +GV P PG T + + Sbjct: 70 VGTEEMVAIAREGLRAYGRDQAVYIRPMYWALDGSDLGVAPKPGATGFALCLE-----EV 124 Query: 132 GAEALDQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDVNGY 191 A + + + R AKAG Y ++ + EAR G+ + D G Sbjct: 125 AMPAPEVTTTLTRTRFRRPVLEDNVCNAKAGCLYPNNARMLVEARSKGFGNALVADAMGN 184 Query: 192 ISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLYLAD 251 ++E A N+F V+DGV+FTP + L GITR I + G++V E VL+ E + AD Sbjct: 185 VAETATANVFMVRDGVVFTPVPNGTFLSGITRARHIANLRSDGVDVVETVLTFEDFHGAD 244 Query: 252 EVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFF 290 EVF+SG A++TPV D + GPVT+ ++Q ++ Sbjct: 245 EVFLSGNFAKVTPVTGFDETVY---QVGPVTRLVRQLYW 280 Lambda K H 0.319 0.137 0.416 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: 242 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 309 Length of database: 287 Length adjustment: 26 Effective length of query: 283 Effective length of database: 261 Effective search space: 73863 Effective search space used: 73863 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: 48 (23.1 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