Align ABC transporter permease (characterized, see rationale)
to candidate WP_011188509.1 DP_RS06410 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000025945.1:WP_011188509.1 Length = 296 Score = 150 bits (378), Expect = 5e-41 Identities = 97/307 (31%), Positives = 162/307 (52%), Gaps = 24/307 (7%) Query: 3 ILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMP 62 + +Q ++ G+ GSMYA++A+G+ ++Y +INFA GE +M+G + S S + M Sbjct: 5 LFVQYLLAGITYGSMYAIVAIGFNIIYNTTGIINFAQGEFVMLGGMLSISLLQFMP---- 60 Query: 63 GAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMII 122 L LA +A V+ + ++E + R L++ L ++ +G+SILL+ +A+ I Sbjct: 61 -------LPLAIGLAVVLTMAVGGLVEILFIRWLKNPGVLRMIVITVGLSILLREIALHI 113 Query: 123 WKPNYKPYPTMLPS--SPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 W P + S I GA ++P + ++GV + + L + +GR MRA Sbjct: 114 WGEGVYSLPYFYGNEISTVVILGARVSPQILWVIGVCLLLVVLLHLFFKTSPMGREMRAC 173 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAG-IMYASNYGTAQHTMGFLPGLKAFTAA 239 A N + A L G+ +++ +F++ A + A+AG +M Y Q+ G +K FT A Sbjct: 174 AVNKKAALLCGINARNMVTFSFMLSAGIGALAGAVMSPITY--TQYDSGAALAIKGFTVA 231 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 + GG+GNL GAV GILLG++EA + +L + D A +L++IL +RP G Sbjct: 232 ILGGLGNLFGAVAAGILLGVLEA--------FSVSVLPLAFQDAIAISLLLVILCVRPHG 283 Query: 300 LLGERVA 306 L G A Sbjct: 284 LFGSATA 290 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: 193 Number of extensions: 11 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: 296 Length adjustment: 27 Effective length of query: 282 Effective length of database: 269 Effective search space: 75858 Effective search space used: 75858 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