Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AO356_05330 AO356_05330 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05330 Length = 418 Score = 268 bits (685), Expect = 2e-76 Identities = 156/351 (44%), Positives = 218/351 (62%), Gaps = 47/351 (13%) Query: 8 WIIGAVALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAV 66 WI+ + L+V+ L+ FG+ V IA L L+YV+L LGLNIVVG AGLLDLGYV FYAV Sbjct: 93 WIV--LGLIVVALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAV 150 Query: 67 GAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGD 126 GAY +AL++ + S WI +P+A ++AA FG +LG P L+LRGD Sbjct: 151 GAYSYALLS----------------HYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGD 194 Query: 127 YLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL--------EV 178 YLAIVTLGFGEIIR+FL NL ++T GP G+ I+ FGL ++ E Sbjct: 195 YLAIVTLGFGEIIRLFLRNL---TDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEY 251 Query: 179 FGFDINSVTLYYYLFLV---LVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRN 235 FG + NS+ +L+LV L + ++ + RL IGRAW A+REDEIA +A+G+N Sbjct: 252 FGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTV 311 Query: 236 MKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAV 295 +KL AF +GA+F G +G+ F A QG V+PESF+ +ES +I+A+VVLGG+G GVIL A+ Sbjct: 312 IKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAI 371 Query: 296 LLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346 ++ LPE++R + + R L+ M+++M+ RP+GL P Sbjct: 372 VMILLPEMMR--------------EFSEYRMLMFGALMVLMMIWRPQGLLP 408 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: 417 Number of extensions: 19 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: 358 Length of database: 418 Length adjustment: 30 Effective length of query: 328 Effective length of database: 388 Effective search space: 127264 Effective search space used: 127264 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 Apr 09 2024. 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