Align branched-chain amino acid aminotransferase subunit (EC 2.6.1.6; EC 2.6.1.42) (characterized)
to candidate BWI76_RS10365 BWI76_RS10365 class IV aminotransferase
Query= metacyc::MONOMER-11904 (286 letters) >FitnessBrowser__Koxy:BWI76_RS10365 Length = 321 Score = 172 bits (437), Expect = 7e-48 Identities = 103/276 (37%), Positives = 167/276 (60%), Gaps = 7/276 (2%) Query: 1 MKIYLNGEFVEKEQAKISVYDHGLLYGDGVFEGIRVYDGVIFKLKEHIDRLFDSATSLQM 60 +++Y+NGEFV +++A +SV+D G + GDGV+EG+R+ +G + L+ H+DRLF A ++Q+ Sbjct: 22 VQVYVNGEFVHRDRATVSVFDSGYVCGDGVWEGLRLVNGKLIALQAHLDRLFAGAAAIQL 81 Query: 61 DIQTSKDEISKIVIDTIRINEL-NNAYIRLVITRGVGDL-GLDPR-KCPKPTIFCIAE-- 115 +I S +E++ I+ +T++IN + + A++RL+ITRG DPR TI C+AE Sbjct: 82 NIGHSPEELTDIMYNTLKINGMTDGAHLRLMITRGKKRTPNQDPRFILGGATIVCVAEYK 141 Query: 116 PMNPLLGEDGIKVITSSIRRLPVDVLNPAVKSLNYLNSILAKIQANYAGCDEAFLLDSEG 175 ++ G+ + TS+ R DV + + S + LN I A +QA AG DEA +LD G Sbjct: 142 VVDEQAKRRGLALFTSTYRTSAPDVFDLRLNSHSRLNLIQALLQALDAGADEALMLDPHG 201 Query: 176 YVAEGTGDNIFVIKNGKIKTPPVSSSVLKGITRDAVVDLAKEQGYEIIEEKLTLHDLYVA 235 +VA N F+I+ G++ T GITR ++ LA++QG + E TL + + A Sbjct: 202 FVASCNSTNFFIIRQGELWTSN-GLYCFNGITRRTILSLARQQGLGVQERSFTLAEAFTA 260 Query: 236 DELFITGTAAELAHVVEIDGRVINNREMGVITKKLS 271 DE F+TGT A + V +DGR + E +T+++S Sbjct: 261 DEAFVTGTLAGITPVSRLDGRRFDLNE-NPVTQRIS 295 Lambda K H 0.319 0.140 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: 206 Number of extensions: 11 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: 286 Length of database: 321 Length adjustment: 27 Effective length of query: 259 Effective length of database: 294 Effective search space: 76146 Effective search space used: 76146 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 (21.7 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