Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_068465118.1 APY04_RS16460 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_001541235.1:WP_068465118.1 Length = 297 Score = 195 bits (496), Expect = 1e-54 Identities = 105/260 (40%), Positives = 153/260 (58%), Gaps = 6/260 (2%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IW +G+MV W +A +HV++HALHYG+ VFEG+R Y G +F+ EH QRL DSAK Sbjct: 14 IWLDGKMVPWREANIHVLTHALHYGSGVFEGLRAY----GGEIFKLSEHSQRLIDSAKTL 69 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 F + + E+ + CRDV+ NNL+ YIRP+ + G +GV A + +AA+ WG Sbjct: 70 DFDIPYTAAEIDQICRDVVAANNLSDCYIRPIAWRGSEQIGVAAQAT-KIHLSVAAWEWG 128 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 +Y E +GI ++ + R P T P+ +KA G Y+ + A G+ + + LD Sbjct: 129 SYFPMEQRLKGIKITMAKYRRPDPATAPSTSKAAGLYMICTIEKHRAENAGFADALMLDW 188 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 G ++E G N+F VKDGV+ TP L GITR +I LAK+ G +V E+ + + L Sbjct: 189 RGRVAECTGANIFFVKDGVIHTPE-ADCFLNGITRRTVIDLAKKRGYQVIERAIMPDELK 247 Query: 249 LADEVFMSGTAAEITPVRSV 268 EVF++GTAAE+TPV + Sbjct: 248 DFSEVFVTGTAAEVTPVSQI 267 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: 243 Number of extensions: 15 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: 297 Length adjustment: 27 Effective length of query: 282 Effective length of database: 270 Effective search space: 76140 Effective search space used: 76140 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