Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_084274637.1 B8779_RS00495 branched-chain amino acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_900176045.1:WP_084274637.1 Length = 304 Score = 263 bits (671), Expect = 5e-75 Identities = 141/296 (47%), Positives = 196/296 (66%), Gaps = 9/296 (3%) Query: 4 KKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHD 63 +KA YIW NGE V W+DAKVHV++H LHYG VFEG R Y + KG +FR R+H +RL + Sbjct: 2 EKAKYIWMNGEFVPWDDAKVHVLTHTLHYGNGVFEGTRAYKTAKGLAIFRLRDHTKRLLN 61 Query: 64 SAKIYRFPVSQSIDELMEACRDVIRKNNLT-SAYIRPLIFVGDVGMG---VNPPAGYSTD 119 SAKI V +++EL A +++R+N+ + YIRPLI++G MG VN P + Sbjct: 62 SAKITAIKVPYTLEELENAQIELLRQNSFDGNVYIRPLIYLGYGVMGLYHVNAP----VE 117 Query: 120 VIIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHG 179 V IAA+ WGAYLG E LE+GI VSS+ R + + AKA NYL+S + EA G Sbjct: 118 VAIAAWKWGAYLGDEGLEKGIRVKVSSFARNSVKSTMGKAKAVANYLNSQMAKYEAIIAG 177 Query: 180 YQEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVRE 239 Y+E + LD G+++EG+GE LF V+DGVL +PP ++L IT+D I+K+A E GI V Sbjct: 178 YEEALLLDEEGFVAEGSGECLFIVRDGVLISPP-NDNSLESITQDTILKIAHEKGIPVER 236 Query: 240 QVLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTG 295 + ++R+ +Y+ADE F +GTAAE+TP+R VDG +G G G +TK +Q A+F + G Sbjct: 237 RRVTRDEVYIADEAFFTGTAAEVTPIREVDGRIIGSGSRGEMTKELQTAYFDIVYG 292 Lambda K H 0.319 0.136 0.413 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: 284 Number of extensions: 14 Number of successful extensions: 4 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: 309 Length of database: 304 Length adjustment: 27 Effective length of query: 282 Effective length of database: 277 Effective search space: 78114 Effective search space used: 78114 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