Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_043743277.1 AMB_RS02850 branched-chain amino acid aminotransferase
Query= BRENDA::P0AB80 (309 letters) >NCBI__GCF_000009985.1:WP_043743277.1 Length = 290 Score = 200 bits (508), Expect = 4e-56 Identities = 108/263 (41%), Positives = 156/263 (59%), Gaps = 10/263 (3%) Query: 8 YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKI 67 ++WF+G++V W DAK+HV++H LHYG+ VFEG R Y G VF+ REH QRL DS +I Sbjct: 12 FLWFDGKLVPWRDAKIHVLTHGLHYGSCVFEGERVY----GGKVFKLREHSQRLIDSGRI 67 Query: 68 YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV--IIAAF 125 F V +++E+ EA ++ NN+ Y+RP+ + G MGV A +T + +A + Sbjct: 68 LGFEVPWTVEEIDEATMATVKANNIVDGYVRPVAWRGSEMMGV---AAQTTKIRFAVATW 124 Query: 126 PWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIA 185 W +Y EA +GI +S+W R P T PTA+KA G Y+ + +A GY++ + Sbjct: 125 SWPSYWSPEARMKGIRLNISTWKRPHPETAPTASKAAGLYMICTMSKHKAEGDGYEDSLM 184 Query: 186 LDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRE 245 LD G ++E G N+F V L TP L GITR +I LAK+ GI V E+ + E Sbjct: 185 LDWRGQVAEATGANIFFVFGNELHTPT-PDCFLNGITRQTVIALAKKRGITVVERAIFPE 243 Query: 246 SLYLADEVFMSGTAAEITPVRSV 268 + A E F++GTAAE+TPVR + Sbjct: 244 EMTKASECFLTGTAAEVTPVREI 266 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: 233 Number of extensions: 11 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: 290 Length adjustment: 27 Effective length of query: 282 Effective length of database: 263 Effective search space: 74166 Effective search space used: 74166 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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