Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_011385249.1 AMB_RS14460 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000009985.1:WP_011385249.1 Length = 329 Score = 132 bits (333), Expect = 1e-35 Identities = 106/338 (31%), Positives = 165/338 (48%), Gaps = 40/338 (11%) Query: 112 LIALLLYPMVVVAIKGPQGSLTYVDNFGIQ------ILIYVMLAWGLNIVVGLAGLLDLG 165 L LLL + +A+ G L + + I+I +LA L+++VG+AGL+ LG Sbjct: 8 LSLLLLVLLAALALFPAWGPLAFSAKYAFLLQKLTGIMILAILAMSLDLLVGVAGLVSLG 67 Query: 166 YVAFYAVGAYSYALLS-SYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLA 224 + AF+ +G Y ALLS Y + WV+LP + A ++GF +R G Y +VTLA Sbjct: 68 HAAFFGLGGYMLALLSPQYEAANAWVVLPAAMGAVAAVSAVVGFLAIRTAGIYFIMVTLA 127 Query: 225 FGEIIRLVLINWTDVTKGTFG--ISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIF 282 FG++ N + + G+ G I P FGI L +L A+ Sbjct: 128 FGQM-GYYFFNDSKLAGGSDGAYIYVKPNVEAFGIT----------LVNLESKQAF---- 172 Query: 283 LFYLILALCMLTAYVTIRL-RRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMF 341 F+++L C++ Y+ +R+ P GR A+ +E R LG N + KL AFA Sbjct: 173 -FFVVLG-CLVAVYLWLRVVLASPFGRVLAAIGVNEGRVRGLGFNPMVYKLVAFALAGAL 230 Query: 342 AGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREM 401 AG AG A + GFVSP + +S +L +V+LGGMG+L G + A ++ EL Sbjct: 231 AGLAGFLAATQYGFVSPAMLGWHQSGHVLVMVILGGMGTLFGPVLGAFIL----ELAH-- 284 Query: 402 SFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVG 439 FG + E + +L G+ ++ ++L P+G G Sbjct: 285 ------FGLEAVTE-HWLLPMGVLVITIVLALPKGVAG 315 Lambda K H 0.330 0.145 0.432 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: 477 Number of extensions: 28 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: 463 Length of database: 329 Length adjustment: 30 Effective length of query: 433 Effective length of database: 299 Effective search space: 129467 Effective search space used: 129467 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 (21.8 bits) S2: 50 (23.9 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