Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Dsui_0628 Dsui_0628 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__PS:Dsui_0628 Length = 358 Score = 257 bits (657), Expect = 4e-73 Identities = 160/333 (48%), Positives = 204/333 (61%), Gaps = 21/333 (6%) Query: 113 IALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAV 172 I L + P +V A G + + NF ++Y+MLA GLNIVVG AGLLDLGY+AFYAV Sbjct: 22 IVLAVLPFLVGA--GLGNAWLRILNFA---MLYIMLALGLNIVVGFAGLLDLGYIAFYAV 76 Query: 173 GAYSYALLSS-YFGLSF--WVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEII 229 GAY YALL+S +FGL + W +LPL + A G +LG P LRLRGDYLAIVTL FGEII Sbjct: 77 GAYLYALLASPHFGLHWPVWAILPLGAVVAGGAGALLGAPTLRLRGDYLAIVTLGFGEII 136 Query: 230 RLVLINWT---DVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYL 286 R+ + N ++T G GISSI + G+ +P AYY YL Sbjct: 137 RIFMNNLNAPVNITNGPQGISSIDPFHVGGVTLAKPLSVLGVT--VPSLHAYY-----YL 189 Query: 287 ILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAG 346 L L ++ +VTIRL IGRAW A+REDEIA ++ GIN KL AF+ GA F G AG Sbjct: 190 FLLLALVIIFVTIRLEDSRIGRAWVAIREDEIAAKACGINVRNIKLLAFSMGATFGGVAG 249 Query: 347 SFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLRE--MSFL 404 FA+ QGFVSPESF +ES ++L +VVLGGMG + G+ + I++ E R + Sbjct: 250 GLFASFQGFVSPESFGLMESIMVLCMVVLGGMGHIPGVILGGILLTILPEAFRHAAVPLQ 309 Query: 405 KLIFGPDFT-PELYRMLIFGLAMVVVMLFKPRG 436 K FG PE RML+FGLA++ VML++P G Sbjct: 310 KYAFGKVVVDPESLRMLLFGLALIAVMLYRPAG 342 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: 571 Number of extensions: 31 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