Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_011973904.1 MAEO_RS06065 branched-chain-amino-acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000017185.1:WP_011973904.1 Length = 286 Score = 200 bits (509), Expect = 3e-56 Identities = 115/281 (40%), Positives = 162/281 (57%), Gaps = 9/281 (3%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 I+ NGE V E AK+ V H L YG VFEGIR YD V+F+ +EH+ RL DSA Sbjct: 3 IYLNGEFVEKEQAKISVYDHGLLYGDGVFEGIRVYDG----VIFKLKEHIDRLFDSATSL 58 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 + + S DE+ + D IR N L +AYIR +I G +G++P + A P Sbjct: 59 QMDIQTSKDEISKIVIDTIRINELNNAYIRLVITRGVGDLGLDPRKCPKPTIFCIAEPMN 118 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 LG E GI + SS R + + A K+ NYL+S+L +A G E LD Sbjct: 119 PLLG----EDGIKVITSSIRRLPVDVLNPAVKSL-NYLNSILAKIQANYAGCDEAFLLDS 173 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 GY++EG G+N+F +K+G + TPP +SS L GITRDA++ LAKE G E+ E+ L+ LY Sbjct: 174 EGYVAEGTGDNIFVIKNGKIKTPPVSSSVLKGITRDAVVDLAKEQGYEIIEEKLTLHDLY 233 Query: 249 LADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAF 289 +ADE+F++GTAAE+ V +DG + G +TK++ + F Sbjct: 234 VADELFITGTAAELAHVVEIDGRVINNREMGVITKKLSEEF 274 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: 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: 309 Length of database: 286 Length adjustment: 26 Effective length of query: 283 Effective length of database: 260 Effective search space: 73580 Effective search space used: 73580 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