Align ABC transporter permease (characterized, see rationale)
to candidate WP_072909157.1 BUB13_RS12790 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_900142125.1:WP_072909157.1 Length = 286 Score = 178 bits (452), Expect = 1e-49 Identities = 103/299 (34%), Positives = 167/299 (55%), Gaps = 18/299 (6%) Query: 5 LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGA 64 LQ +GL G++YALIALG+ +V + ++NF + + +G + +S + + +P Sbjct: 6 LQFSFSGLTSGAIYALIALGFCVVNNTMGIVNFVQVDFVSLGGMLMFSALFAL--GLPMV 63 Query: 65 PGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124 PG LLLA +VA ++E+ RP RS L + +G+SI+L+ + ++W Sbjct: 64 PG---LLLAVAGVGLVA----MIVERFGLRPARSDNHLVLIFLTVGLSIILRGIIKLVWG 116 Query: 125 PNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENP 184 N P + P P I GA + P + IL +T VA+A L++ T LG +MRA A N Sbjct: 117 KNRMALPPLTPDEPINILGATVLPQALWILLLTVVAIALLMWFFYRTPLGLSMRAVASNT 176 Query: 185 RVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGI 244 A+++G+ + ++ I L +AG++ + T + +G L GLK F AA+ GG Sbjct: 177 TAAAVVGIPAGRIRLTSYAIAGALGGLAGVL-VTPITTLNYDVGVLLGLKGFAAAILGGF 235 Query: 245 GNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGE 303 G+ GA++GG+ LGL+E++ +GY L S Y D+ AF VL+++L +RP GLLG+ Sbjct: 236 GSFPGAILGGVGLGLLESLSAGY--------LSSAYKDVVAFAVLLLVLFVRPKGLLGK 286 Lambda K H 0.327 0.142 0.419 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: 227 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: 286 Length adjustment: 26 Effective length of query: 283 Effective length of database: 260 Effective search space: 73580 Effective search space used: 73580 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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