Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_015818205.1 TERTU_RS17580 branched-chain amino acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000023025.1:WP_015818205.1 Length = 309 Score = 267 bits (683), Expect = 2e-76 Identities = 137/301 (45%), Positives = 193/301 (64%), Gaps = 3/301 (0%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDS-HKGPVVFRHREHMQRLHDSAKI 67 IWF+GE+V W DAKVHV++H LHYG VFEG+R Y + G +FR +EH RL SA I Sbjct: 10 IWFDGELVPWRDAKVHVLTHTLHYGMGVFEGVRAYHAGENGTSIFRLQEHTDRLFRSAHI 69 Query: 68 YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPW 127 + S DE+ EA R V+R+NNL AY+RP+ F+G GMG+ +I+AA+ W Sbjct: 70 MNMKMPWSKDEVNEAQRLVVRENNLNEAYLRPMAFLGSEGMGLRAD-NLKVHLIVAAWDW 128 Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187 +Y+ EA E GI VSS+ R N AKA G+Y++S+L EA G +E + LD Sbjct: 129 PSYMSPEAKEIGIKVRVSSYTRHHVNISMCKAKANGHYINSMLALKEALDCGCEEALLLD 188 Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESL 247 GY++EG+GEN+F V++GV++TP TS L GITR+ I +LA E G ++ E+ +SR+ + Sbjct: 189 AEGYVAEGSGENVFIVRNGVIYTPELTS-CLDGITRNTIFQLADECGYKIVEKRISRDEV 247 Query: 248 YLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307 Y+ADE F +GTAAE+ P+R +DG Q+G G GP+T+++Q +F GE WL V Sbjct: 248 YVADEAFFTGTAAEVLPIRELDGRQIGPGHRGPITEKLQSLYFAAVRGELPQHREWLAPV 307 Query: 308 N 308 + Sbjct: 308 S 308 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: 309 Number of extensions: 13 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: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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