Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_1938 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1938 Length = 358 Score = 160 bits (405), Expect = 6e-44 Identities = 103/335 (30%), Positives = 172/335 (51%), Gaps = 31/335 (9%) Query: 106 HFLKIALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLG 165 H +L+ L L VA + LT+V LIY ++ GL ++ G GL LG Sbjct: 21 HVFWYSLLGLTLVAAPWVAPEYWLAQLTFV-------LIYSIVGLGLMLLAGFTGLFSLG 73 Query: 166 YVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAF 225 + AF VGAY+ A+L+ G F + L + +A GV++G P LR++G YL + TL+F Sbjct: 74 HAAFLGVGAYTQAVLTG-MGWPFALSLACAAGLSAAVGVVVGLPALRVKGIYLGMATLSF 132 Query: 226 GEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFY 285 G I+ V W VT G G +P +FG F++T ++ Sbjct: 133 GFIVEEVFARWESVTGGNSGKHLVPPQ-MFGYSFESTES------------------FYF 173 Query: 286 LILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFA 345 L L + +++ + L R P GRA+ A+R+ EI+ +S+GI+ K +F+ A AG Sbjct: 174 LCLVIAVVSTLAILNLLRSPTGRAFVAIRDSEISAQSMGIHLARYKTLSFSLSAALAGVG 233 Query: 346 GSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLR-EMSFL 404 G+ +A + F+SP+ F L+S +L ++V+GG+GS+ G + AI ++ +++ +L Sbjct: 234 GALYAHKLQFISPDQFNILQSIDLLLMIVIGGLGSVHGAFLGAIFLISMPQMISLSKDWL 293 Query: 405 KLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVG 439 G P L + +++G ++ +LF+P G G Sbjct: 294 PAAIGQ--APGL-QAVVYGAVLIAFVLFEPMGLYG 325 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: 440 Number of extensions: 28 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: 463 Length of database: 358 Length adjustment: 31 Effective length of query: 432 Effective length of database: 327 Effective search space: 141264 Effective search space used: 141264 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