Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_017549722.1 C792_RS0112120 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000330705.1:WP_017549722.1 Length = 355 Score = 144 bits (364), Expect = 2e-39 Identities = 99/316 (31%), Positives = 158/316 (50%), Gaps = 21/316 (6%) Query: 7 DYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAK 66 +Y W +V +++ ++ + A+HYG SVFEG++ Y ++FR ++ +R+++S Sbjct: 40 EYGWSGASIVPYQNLQLSPSAQAIHYGQSVFEGLKAYKQGDDILLFRPDQNFKRMNESLS 99 Query: 67 IYRFP------VSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120 P ++ EL++ RD + S YIRP +F + +GV P Y ++ Sbjct: 100 RLSMPEINEENALNALYELLKVERDWVPDGEGQSLYIRPFVFADEPFLGVRPSETYQFNI 159 Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180 I++ P G Y GA L + + R+ + A K GNY +SLL +A GY Sbjct: 160 ILS--PVGGYYGATQLNPTSIYVEDDFVRSVRGGVGFA-KVSGNYAASLLAQKKANELGY 216 Query: 181 QEGIALD--VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVR 238 ++ + LD Y+ E N+F V+DG L TP S LPGITR +II+LAK G V+ Sbjct: 217 EQVLWLDGVEQKYVEEVGSMNIFFVRDGELITPQLNGSILPGITRKSIIELAKHKGYTVK 276 Query: 239 EQVLSRESLY------LADEVFMSGTAAEITPV--RSVDGIQ--VGEGRCGPVTKRIQQA 288 E+ + + L EVF +GTAA I PV ++ GI V + + G V+ + Sbjct: 277 EEKIHIDDLVEDIHGGRVTEVFGAGTAAVIAPVGKLNIHGIDYIVNDNQVGEVSLDLFND 336 Query: 289 FFGLFTGETEDKWGWL 304 + G ED +GW+ Sbjct: 337 LTDIQYGRKEDPFGWV 352 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: 293 Number of extensions: 11 Number of successful extensions: 5 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: 355 Length adjustment: 28 Effective length of query: 281 Effective length of database: 327 Effective search space: 91887 Effective search space used: 91887 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: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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