Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_092485910.1 BM299_RS14600 aminotransferase class IV
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_900115975.1:WP_092485910.1 Length = 278 Score = 149 bits (376), Expect = 7e-41 Identities = 90/280 (32%), Positives = 149/280 (53%), Gaps = 8/280 (2%) Query: 5 WIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLE 64 + LNGE V + +++ D G+LYG +FE + V G L+ H+ RL SA + + Sbjct: 4 YYMLNGEPVSPERLQINALDRGFLYGYSLFETMLVREGKPVFLQAHVERLLLSAADLGIV 63 Query: 65 IPYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSLFP 124 +P + D + I + +R + + +G +RL + G PD+ +VV+ + + Sbjct: 64 LPVTGDGLAAICRDALRCSGVGSGVLRLTATAG-------PDNGNAGSVVLAVREGVPYR 116 Query: 125 QEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVA 184 + YEKGI V+ + RN L K+ NYL N+L R +A+ G E + LN +G VA Sbjct: 117 PQQYEKGIAVLELDFPRNEKSPLVRH-KTANYLENLLGRRKARSMGCDEGIFLNTRGRVA 175 Query: 185 EGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVADEV 244 EG+ N+FIV ++ TPP AG L GI R +++ + G +E+ TR ++ A E Sbjct: 176 EGTASNIFIVINGEIWTPPVEAGLLPGIIRRLVIDYSSQTGLCCQEKNITRDELACAGEC 235 Query: 245 FLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLV 284 F+T + V+ VT ++G +G G GP T ++ + + KL+ Sbjct: 236 FVTNSLMGVMPVTELNGLPVGTGVPGPVTLKVADLYNKLI 275 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: 211 Number of extensions: 5 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: 278 Length adjustment: 26 Effective length of query: 272 Effective length of database: 252 Effective search space: 68544 Effective search space used: 68544 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