Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate WP_085773086.1 B1812_RS19650 branched-chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >NCBI__GCF_002117405.1:WP_085773086.1 Length = 294 Score = 172 bits (436), Expect = 9e-48 Identities = 100/258 (38%), Positives = 140/258 (54%), Gaps = 8/258 (3%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 IWFNG + W +AK+HV+SH LHY ++VFEG R Y G +F+ REH +R SA++ Sbjct: 13 IWFNGALTPWREAKLHVLSHGLHYASAVFEGERAY----GGKIFKSREHSERFRRSAQLL 68 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYST-DVIIAAFPW 127 F + S+ EL A V++ N + Y+RP+ + G M V A ST IA + W Sbjct: 69 DFEIPYSVAELEAAKDAVVKANGMQDCYVRPIAWRGSEMMAV--AAQNSTIHTAIAVWDW 126 Query: 128 GAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALD 187 + E +GI ++ + R P T P+ AKA G Y+ + A R GY + + D Sbjct: 127 PSMFDVETKMKGIRLDIAEYRRPDPRTEPSLAKAAGLYMICTISKHRAERRGYADALMYD 186 Query: 188 VNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESL 247 G ++E G N+F VKDG L T P L GITR +I+LAK G+ V E+ + E L Sbjct: 187 WLGRVAECTGANVFFVKDGALHT-PIADCFLDGITRQTVIELAKRRGVAVFERRIMPEEL 245 Query: 248 YLADEVFMSGTAAEITPV 265 E F+ GT AE+TPV Sbjct: 246 TGFSECFICGTGAEVTPV 263 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: 240 Number of extensions: 12 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: 294 Length adjustment: 27 Effective length of query: 282 Effective length of database: 267 Effective search space: 75294 Effective search space used: 75294 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