Align ABC transporter permease (characterized, see rationale)
to candidate BWI76_RS05990 BWI76_RS05990 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >FitnessBrowser__Koxy:BWI76_RS05990 Length = 299 Score = 211 bits (538), Expect = 1e-59 Identities = 118/311 (37%), Positives = 184/311 (59%), Gaps = 22/311 (7%) Query: 3 ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTS---WSCIGMMQG 59 I LQQ++NG+ LG MYALIA+GYTMVYG+++LINFAH +V+M+GA T+ +S IG+ G Sbjct: 5 IFLQQVVNGMSLGGMYALIAIGYTMVYGVLRLINFAHADVMMVGAFTTLFLFSSIGLPFG 64 Query: 60 AMPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLA 119 +A + + +I++VAYRPLR + +++ LITAIG+S L+ L Sbjct: 65 ------------VAVFLTLALCGLFGMLIDRVAYRPLRQASKISMLITAIGVSFFLENLF 112 Query: 120 MIIWKPNYKPYPTM-LPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMR 178 +++ + + + ++ G IT ++ +T + L ++++L+ T G A+R Sbjct: 113 NVLFGGSSRFFSAPDFFNNTRAFGDVIITNVAWIVPLITVLLLLAILWLLYRTRYGMAIR 172 Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238 A A + LMG+ + +IS F +G+ LAA+ G+ Y+ +Y T MG L GLKAF A Sbjct: 173 AVAFDVNTVRLMGIDANRIISLVFALGSSLAALGGVFYSISYPTIDPLMGVLIGLKAFAA 232 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 AV GGIG++ GAV+GG +LG E + L G Y D FAF+ LI++L RP Sbjct: 233 AVLGGIGSVTGAVLGGFILGFTEVVAVALFPELGG------YKDAFAFMFLILVLLFRPV 286 Query: 299 GLLGERVADRA 309 G++G+ +R+ Sbjct: 287 GIMGDERLERS 297 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: 243 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: 299 Length adjustment: 27 Effective length of query: 282 Effective length of database: 272 Effective search space: 76704 Effective search space used: 76704 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 17 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