Align ABC transporter permease (characterized, see rationale)
to candidate WP_011841982.1 RSPH17029_RS14875 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000015985.1:WP_011841982.1 Length = 292 Score = 138 bits (348), Expect = 1e-37 Identities = 90/301 (29%), Positives = 153/301 (50%), Gaps = 16/301 (5%) Query: 4 LLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIGMMQGAMPG 63 LL ++ GLV ++ AL A G ++V+G+++++N AHGE M+GA+ +W + G Sbjct: 7 LLLAVMEGLVGAAVLALTASGLSLVFGVLRVVNVAHGEFFMLGAVAAWFVSQWVPGPPAL 66 Query: 64 APGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLAMIIW 123 A +++ ++A + A V++++AY P A +I IG+ +LQ A+ ++ Sbjct: 67 AFAVALVVCPLLVAGLAALADRLVLKRLAYEP------EATIIATIGLLYILQQAALTLY 120 Query: 124 KPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRATAEN 183 P +P P + ++ + ++ ++G LA L L+ + +G MRAT + Sbjct: 121 GPEARPVPPPF-EARLQLPWFGWSGYKLSVIGAAGAVLAGLWLLLARSRIGLVMRATQID 179 Query: 184 PRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAAVFGG 243 AS G+ D V + TF +GA LAAIA ++ A + MG P L +F V GG Sbjct: 180 RETASAFGIDVDRVYAGTFALGAALAAIAAVLIVP-IQQAHYLMGGDPLLLSFIVVVIGG 238 Query: 244 IGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSGLLGE 303 +G+L G +V +L+G + G I T L I A +++ ++L RP GL G Sbjct: 239 LGSLRGTLVAALLIG----VSDGVISTFFEPTLAK----ILATLLVALVLVFRPQGLFGA 290 Query: 304 R 304 R Sbjct: 291 R 291 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: 206 Number of extensions: 13 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: 292 Length adjustment: 27 Effective length of query: 282 Effective length of database: 265 Effective search space: 74730 Effective search space used: 74730 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 Apr 10 2024. 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