Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate CA265_RS15785 CA265_RS15785 branched-chain-amino-acid transaminase
Query= CharProtDB::CH_024500 (309 letters) >FitnessBrowser__Pedo557:CA265_RS15785 Length = 296 Score = 176 bits (446), Expect = 6e-49 Identities = 100/263 (38%), Positives = 148/263 (56%), Gaps = 8/263 (3%) Query: 9 IWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIY 68 I+ +G+ + ++ + +LHYG + FEGIR Y +H G +F+ H RL S ++ Sbjct: 10 IYLDGQFEKAVNSSTDLYGQSLHYGYAAFEGIRAYKTHNGNRIFKAAAHFDRLERSCQLA 69 Query: 69 RFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDVIIAAFPWG 128 P EL+ A +++ N L AYIRPL+F M +N P+G S ++I A+ W Sbjct: 70 NIPFPWDKQELIAATYKLLQLNKLKDAYIRPLVFCHP-NMKLNEPSGVS--ILICAWEWD 126 Query: 129 AYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDV 188 AY G + L+ VS + R P +IP AK GNY++S+L + A GY E + LD+ Sbjct: 127 AYSGNKLLK----LTVSDYERPNPKSIPMEAKLSGNYVNSILATTAANIKGYDEALLLDM 182 Query: 189 NGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQVLSRESLY 248 +G+++E +G N+F KDG LFTP + LPGITR + +L L IE E+ L+ E L Sbjct: 183 HGFVAEASGANIFLEKDGKLFTPSL-GNILPGITRATVKELCTVLDIECIEKKLTIEDLK 241 Query: 249 LADEVFMSGTAAEITPVRSVDGI 271 AD F+ GTA EI + S+D I Sbjct: 242 NADSAFLCGTATEIAGIASIDDI 264 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: 197 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: 296 Length adjustment: 27 Effective length of query: 282 Effective length of database: 269 Effective search space: 75858 Effective search space used: 75858 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