Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate Dsui_0628 Dsui_0628 ABC-type branched-chain amino acid transport system, permease component
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__PS:Dsui_0628 Length = 358 Score = 257 bits (656), Expect = 5e-73 Identities = 162/343 (47%), Positives = 201/343 (58%), Gaps = 39/343 (11%) Query: 150 WLGPIAVVVALA-FPF---TPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVA 205 W G A+ + LA PF L + L + +L YIML GLNIVVG AGLLDLGY+A Sbjct: 14 WAGYAAIGIVLAVLPFLVGAGLGNAWLRILNFAML-YIMLALGLNIVVGFAGLLDLGYIA 72 Query: 206 FYAVGAYSYALLAH-YFGFSF--WVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGF 262 FYAVGAY YALLA +FG + W LPL +A +G LLG P LRLRGDY AIVTLGF Sbjct: 73 FYAVGAYLYALLASPHFGLHWPVWAILPLGAVVAGGAGALLGAPTLRLRGDYLAIVTLGF 132 Query: 263 GEIIRIILINW---YQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPL 319 GEIIRI + N T GP GIS I G+ A + G+ L Sbjct: 133 GEIIRIFMNNLNAPVNITNGPQGISSIDPFHVGGVT---------LAKPLSVLGVTVPSL 183 Query: 320 HRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAI 379 H YYL L+LALV+ T+R+ +GRAW A+RED+IA + GIN N+KL AF++ Sbjct: 184 HAY---YYLFLLLALVIIFVTIRLEDSRIGRAWVAIREDEIAAKACGINVRNIKLLAFSM 240 Query: 380 AAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEA 439 A FGG AG FA+ QGF+SPESF +ES ++L +VVLGGMG GV++ L+ LPEA Sbjct: 241 GATFGGVAGGLFASFQGFVSPESFGLMESIMVLCMVVLGGMGHIPGVILGGILLTILPEA 300 Query: 440 FRELA----------------DYRMLAFGMGMVLIMLWRPRGL 466 FR A RML FG+ ++ +ML+RP GL Sbjct: 301 FRHAAVPLQKYAFGKVVVDPESLRMLLFGLALIAVMLYRPAGL 343 Lambda K H 0.329 0.144 0.438 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: 537 Number of extensions: 35 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: 505 Length of database: 358 Length adjustment: 32 Effective length of query: 473 Effective length of database: 326 Effective search space: 154198 Effective search space used: 154198 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: 51 (24.3 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