Align ABC transporter permease (characterized, see rationale)
to candidate WP_013093681.1 BC1002_RS29775 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000092885.1:WP_013093681.1 Length = 299 Score = 270 bits (691), Expect = 2e-77 Identities = 144/308 (46%), Positives = 202/308 (65%), Gaps = 10/308 (3%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 M Q +I GL GS YAL+ALGYTMVYGII+LINFAHG++ M+GA W+ G+M A Sbjct: 1 MSDFFQFVIEGLTTGSFYALVALGYTMVYGIIRLINFAHGDLFMVGAFIGWT--GLMVLA 58 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAM 120 P + LL+A + A V L +IE++AY+PL +PRL+ LITA+G+S+ LQ + Sbjct: 59 SAHLPLALALLIAVVAAMTVTGALGLLIERLAYQPLLRAPRLSILITALGVSLALQNGVL 118 Query: 121 IIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRAT 180 +I+ ++ YP +L + FE+ G IT QI I+ + + +L + V+HT LG AMRA Sbjct: 119 LIYGAGFRTYPHVLSQAGFELHGVQITFAQIGIIVASLALMLALYFFVHHTFLGTAMRAL 178 Query: 181 AENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAV 240 A + A LMG+ + +I TF++G+VLAA+AG+M Y MGF+ GL+AFTAAV Sbjct: 179 AIDQDAARLMGIDVERLIQLTFLLGSVLAAVAGVMEGLYYTQINFFMGFVLGLRAFTAAV 238 Query: 241 FGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGL 300 GGIGN+ GA+ GGIL+GL+EA G+GY+ S +TD+F F VLI +L ++P+GL Sbjct: 239 LGGIGNIPGAMAGGILIGLLEAFGAGYV--------SSQWTDVFVFGVLIAVLVIKPTGL 290 Query: 301 LGERVADR 308 GERV +R Sbjct: 291 FGERVVER 298 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: 233 Number of extensions: 10 Number of successful extensions: 3 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 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