Align ABC transporter permease (characterized, see rationale)
to candidate WP_043743902.1 AMB_RS08455 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000009985.1:WP_043743902.1 Length = 291 Score = 192 bits (488), Expect = 8e-54 Identities = 108/304 (35%), Positives = 167/304 (54%), Gaps = 19/304 (6%) Query: 5 LQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPGA 64 LQ + +GL G++YAL LG+ ++Y +INFA GE +MIG + + + + G Sbjct: 6 LQYLFSGLTSGAIYALAGLGFAIIYNASHVINFAQGEFIMIGGMATATMVAA------GV 59 Query: 65 PGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIWK 124 P + LA +A + + +EK A P R++ + +I IG SI ++ A +IW Sbjct: 60 P----IYLAIPLAMAASMLVGVAMEKFAIEPARNADVVTIIIITIGASIFMRGAAQLIWD 115 Query: 125 PNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAENP 184 + P +P + GA + P + + G++AVA+A L Y N T G+AM T+ N Sbjct: 116 KEFHSLPAFSGETPIAVMGATLMPQSLWVFGISAVAIALLWYFFNRTMFGKAMLGTSHNR 175 Query: 185 RVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGGI 244 A L+GV V+ A+F + A+L A+ GI+ T + G + GLK F+AAV GG+ Sbjct: 176 LAAQLVGVAVKRVLLASFALSALLGAVGGIVVTPITFT-NYEAGIMLGLKGFSAAVLGGL 234 Query: 245 GNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGER 304 GN GA++GG+++G+ EA+ SGY L S Y D AFI+++ +L PSGL G+R Sbjct: 235 GNGTGAIIGGLIVGIAEAMASGY--------LSSAYKDAIAFIIILFVLFFMPSGLFGKR 286 Query: 305 VADR 308 DR Sbjct: 287 GTDR 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: 202 Number of extensions: 16 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: 291 Length adjustment: 27 Effective length of query: 282 Effective length of database: 264 Effective search space: 74448 Effective search space used: 74448 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