Align ABC transporter permease (characterized, see rationale)
to candidate WP_072908983.1 BUB13_RS11885 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_900142125.1:WP_072908983.1 Length = 303 Score = 214 bits (545), Expect = 2e-60 Identities = 115/304 (37%), Positives = 181/304 (59%), Gaps = 10/304 (3%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGA 60 MD + Q ++N L GS YALIALGYT+VYG+++LINFAHG++ M+GA S+ G + G Sbjct: 1 MDFIFQNVLNALQWGSFYALIALGYTLVYGVLRLINFAHGDIFMVGAYISFFVAGFLLGP 60 Query: 61 MPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLR--SSPRLAPLITAIGMSILLQTL 118 + G + LL + ++ A + +E++AYRPLR + RL +ITA+ ++L+ Sbjct: 61 LAGLSPMMTFLLTVPLTMILTACVGVTLERIAYRPLRRKGAHRLYVVITALMCGLILEYS 120 Query: 119 AMIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMR 178 + + + +P ++ + +GG IT ++L++ L ++V T +G AMR Sbjct: 121 NLAVLGASRLKFPELVDKQIWNVGGVAITNLKVLVIVAAIAVFLFLQWVVTRTRVGMAMR 180 Query: 179 ATAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTA 238 A + + LMG+ D +I TFI+G+ A +AG+++A +Y + MG L G KAF A Sbjct: 181 AISYDKFAIPLMGIPMDNIIVITFILGSGFAGLAGLLFAMSYPVLEPFMGMLIGWKAFIA 240 Query: 239 AVFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPS 298 AV GGIG++ GA VGG LLG IE + +T + S Y D+FAF +L++IL ++P+ Sbjct: 241 AVVGGIGDIKGAFVGGFLLGAIE------VAVVT--VFPSTYRDLFAFTILLLILWMKPT 292 Query: 299 GLLG 302 GL G Sbjct: 293 GLFG 296 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: 228 Number of extensions: 9 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: 303 Length adjustment: 27 Effective length of query: 282 Effective length of database: 276 Effective search space: 77832 Effective search space used: 77832 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