Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_012502762.1 CPAR_RS07765 branched-chain amino acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000020505.1:WP_012502762.1 Length = 303 Score = 320 bits (819), Expect = 3e-92 Identities = 156/296 (52%), Positives = 209/296 (70%), Gaps = 2/296 (0%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IW NGE+V W DAK+HVMSH HYG+S FEGIRCYD+ KG + EH++RL +S+KIY Sbjct: 7 IWMNGELVDWNDAKIHVMSHVAHYGSSTFEGIRCYDTAKGSAILFLDEHVRRLWESSKIY 66 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 R + S E+ +A I+ N + YIRPL++ G +GVNP S +V IA + WG Sbjct: 67 RIEIPYSETEIKDAIIATIKANGHKACYIRPLVYRGQGALGVNPHRA-SIEVAIATWEWG 125 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 +YLG + LE G+D VSSW+R APNT+P+ AKAGGNY++S L+ EA GY EG+ALD Sbjct: 126 SYLGEDVLETGVDVKVSSWHRLAPNTLPSWAKAGGNYMNSQLIKMEAISDGYAEGLALDQ 185 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 NGY++EG+GEN+F V+ VL+TP S LPG TR A++++AK+LG EVRE ++ RESLY Sbjct: 186 NGYVAEGSGENIFVVRHNVLYTPFAAQSILPGFTRHAVMEIAKKLGYEVRETLIPRESLY 245 Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWL 304 +ADE+F++GTAAEITPVRSVD VG+ + GPVT+ +Q + + ED + WL Sbjct: 246 IADEIFLTGTAAEITPVRSVDKYPVGQEKRGPVTEALQHEYLKI-VHSGEDPFNWL 300 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: 314 Number of extensions: 4 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: 309 Length of database: 303 Length adjustment: 27 Effective length of query: 282 Effective length of database: 276 Effective search space: 77832 Effective search space used: 77832 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