Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_041097288.1 SUTH_RS04050 branched-chain amino acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_000828635.1:WP_041097288.1 Length = 306 Score = 290 bits (742), Expect = 3e-83 Identities = 141/300 (47%), Positives = 199/300 (66%), Gaps = 2/300 (0%) Query: 8 YIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKI 67 +IW++G++V W DA HV++H+LHYG +VFEG+R Y + G +FR +EH RL +SA I Sbjct: 9 FIWYDGKLVPWRDATTHVLTHSLHYGLAVFEGVRAYKTVSGTAIFRLKEHTDRLFNSAHI 68 Query: 68 YRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPW 127 YR P+ L+EA ++V+R N L S Y+RP+ F G MGV+ P G +T V IAA+PW Sbjct: 69 YRMPMPYDKATLIEAHKEVVRSNKLESCYLRPIAFYGSEKMGVS-PRGAATHVSIAAWPW 127 Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187 GAYLG E +E+GI SS++R N AK G Y +S+L EA GY E + LD Sbjct: 128 GAYLGEEGMEKGIRVKTSSYSRHHVNVNMARAKFAGTYANSILANMEATEDGYDEALLLD 187 Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESL 247 V+G+++EGAGENLF +KDGV++ P +SAL GITR+ +I LA ELG +V + L+R+ + Sbjct: 188 VDGFVAEGAGENLFVIKDGVIYEPEI-ASALMGITRNTVITLAAELGYQVIAKRLTRDDI 246 Query: 248 YLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDKWGWLDQV 307 Y+ADE F +GTAAE+TP+R +D +G G GP+T++IQ FF + G+ WL + Sbjct: 247 YIADEAFFTGTAAEVTPIRELDNRTIGAGSRGPITQKIQSLFFDVVNGKVPAHKDWLSYI 306 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: 6 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: 306 Length adjustment: 27 Effective length of query: 282 Effective length of database: 279 Effective search space: 78678 Effective search space used: 78678 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 09 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