Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_110206118.1 DNK54_RS06375 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_003194585.1:WP_110206118.1 Length = 376 Score = 149 bits (377), Expect = 1e-40 Identities = 100/311 (32%), Positives = 163/311 (52%), Gaps = 15/311 (4%) Query: 140 IQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFA 199 IQ I+++ A GL ++ G+ G L LG+ AF AVG ++ A L+ FGL +WV+LPL+G+ + Sbjct: 55 IQAQIFIVGAVGLMLLSGVTGQLSLGHAAFLAVGGFAAANLALDFGLPWWVVLPLAGLIS 114 Query: 200 ALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLF---- 255 AL GV++ RL+G YLAIVTL +I+ VL+ WTD++ G G +++P F Sbjct: 115 ALVGVLIAPFAFRLKGLYLAIVTLGLVFVIQHVLLRWTDISGGHRG-TAVPMFNGFVDDP 173 Query: 256 --GIPFDATAGGFAK----LFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRA 309 P + GF + + + + +F L+ L A +R R +GRA Sbjct: 174 ENMTPMEKAEAGFGREPWEIGGVFMGRDVQMYVVFLLVTVAACLFARNVLRTR---MGRA 230 Query: 310 WEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPE-SFVFLESAV 368 A+ +IA LGI K AF + +AG AG+ + +Q +++ + F S Sbjct: 231 MAAVGSGDIAASVLGIRVKWVKTAAFGLSSFYAGVAGAMWGWKQTYLTVDPPFDLHLSME 290 Query: 369 ILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVV 428 +A++ +GG+G++ G + AI+ G L E++ L + + +FG ++V Sbjct: 291 FVAMIFIGGLGTVMGAVLGAILFASGRPLAAELAELPFLRDSSLQEGDIVLFVFGATVIV 350 Query: 429 VMLFKPRGFVG 439 MLF+PRG G Sbjct: 351 FMLFEPRGLRG 361 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: 510 Number of extensions: 34 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: 376 Length adjustment: 31 Effective length of query: 432 Effective length of database: 345 Effective search space: 149040 Effective search space used: 149040 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 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