Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate Synpcc7942_1335 Synpcc7942_1335 probable branched-chain amino acid aminotransferase
Query= CharProtDB::CH_012531 (298 letters) >FitnessBrowser__SynE:Synpcc7942_1335 Length = 264 Score = 116 bits (290), Expect = 6e-31 Identities = 66/215 (30%), Positives = 118/215 (54%), Gaps = 7/215 (3%) Query: 7 FLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEIP 66 + NG+++P ++ ++V D G+ GDG+FE + V+ G V +H RL SA+ + + +P Sbjct: 4 YCNGQWIPTEDLTIAVTDRGFSLGDGLFETLLVWQGKVRLAEQHWQRLTSSAQQLRIPLP 63 Query: 67 YSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSLFPQE 126 + + +++ T+ N+L G +R+ ++RG G GL +P +V++ SL + Sbjct: 64 PNAN--IDLLQATVDHNELETGALRVTLTRGCGQRGLQSPEPLQPLLVIVP---SLSQPQ 118 Query: 127 YYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAEG 186 + + + ++T T R P+ + + K+L+YL N+L R EA+ EAL+L ++E Sbjct: 119 F--QPLRLITAQTVRRCPESILSRFKTLSYLENVLARQEAEQRQADEALLLTPSDRLSEA 176 Query: 187 SGDNVFIVKGNKLITPPSSAGALEGITRNAILEIG 221 + N+F + TPP S GAL GI R +L G Sbjct: 177 AAANIFFRLNDDWWTPPLSDGALPGIVRQRLLATG 211 Lambda K H 0.317 0.138 0.390 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: 152 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: 298 Length of database: 264 Length adjustment: 26 Effective length of query: 272 Effective length of database: 238 Effective search space: 64736 Effective search space used: 64736 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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