Align ABC transporter permease (characterized, see rationale)
to candidate WP_029134157.1 A3GO_RS0115370 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000428045.1:WP_029134157.1 Length = 293 Score = 189 bits (481), Expect = 5e-53 Identities = 108/307 (35%), Positives = 170/307 (55%), Gaps = 17/307 (5%) Query: 2 DILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAM 61 D +LQ ++ G+ +GS YAL+ LG+ ++Y ++NF+ GE +MIGA+ S + + G Sbjct: 3 DQILQFLLTGITVGSTYALVGLGFAIIYNASDVVNFSQGEFVMIGAM---SAVALSAGDT 59 Query: 62 PGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMI 121 G P W L A +I +V L ++ A P R + + +I IG SI L+ +A++ Sbjct: 60 -GLPLWAAALAAVLITTLVGMAL----QRFAIXPARGASVVTTIIITIGASIFLRGVALL 114 Query: 122 IWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATA 181 +W + P + P IG A + P + ++G AV + Y HT LG+A+ A + Sbjct: 115 VWGKDLFALPPFSGNEPIXIGNATVLPQSLWVMGGAAVLVFGAQYFFTHTTLGKAILACS 174 Query: 182 ENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVF 241 N A L+G+ +++ + + A L A+AGI+ A A + G + GLK F+AA+ Sbjct: 175 CNKTAAHLVGINVGVMLLVAYGLSAALGAMAGILVAP-ITFASYDTGVMLGLKGFSAAIL 233 Query: 242 GGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLL 301 GG+GN GAV GG+LLGLIE +L+ GL+ S Y D FI+L+++L RPSGL Sbjct: 234 GGMGNPMGAVAGGLLLGLIE--------SLSAGLISSGYKDAIGFIILLLVLFFRPSGLF 285 Query: 302 GERVADR 308 G+ +R Sbjct: 286 GKASVER 292 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: 209 Number of extensions: 14 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: 293 Length adjustment: 27 Effective length of query: 282 Effective length of database: 266 Effective search space: 75012 Effective search space used: 75012 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