Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1300 PS417_06605 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__WCS417:GFF1300 Length = 417 Score = 267 bits (682), Expect = 4e-76 Identities = 158/346 (45%), Positives = 213/346 (61%), Gaps = 45/346 (13%) Query: 13 VALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 +AL++ LI FG+ V IA L L+YVLL LGLNIVVG AGLLDLGYV FYAVGAY + Sbjct: 95 IALIIAALIWPFFGSRGAVDIATLILIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYTY 154 Query: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 AL++ + L S WI +P+A + AA FG +LG P L+LRGDYLAIV Sbjct: 155 ALLS----------------HYLGWSFWICLPLAGMAAATFGFLLGFPVLRLRGDYLAIV 198 Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL--------EVFGFDI 183 TLGFGEIIR+FL NL ++T GP G+ I FGL + E FG D Sbjct: 199 TLGFGEIIRLFLRNL---TDITGGPNGISSIPKPTFFGLSFDRTAAEGMQTFHEYFGIDY 255 Query: 184 NSVTLYYYLFLV---LVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLA 240 N V+ +L+LV L + ++ + RL IGRAW A+REDEIA +A+G+N +KL A Sbjct: 256 NPVSKVVFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTIIKLSA 315 Query: 241 FGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSAL 300 F +GA+F G +G+ F A QG V+PESF+ +ES +I+A+VVLGG+G GVIL A+++ L Sbjct: 316 FTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILL 375 Query: 301 PEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346 PE++R + + R L+ M+++M+ RP+GL P Sbjct: 376 PEMMR--------------EFSEYRMLMFGAMMVLMMIWRPQGLLP 407 Lambda K H 0.328 0.144 0.430 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: 409 Number of extensions: 20 Number of successful extensions: 5 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: 358 Length of database: 417 Length adjustment: 30 Effective length of query: 328 Effective length of database: 387 Effective search space: 126936 Effective search space used: 126936 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 (21.7 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