Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate Pf6N2E2_3578 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3578 Length = 426 Score = 412 bits (1059), Expect = e-119 Identities = 221/413 (53%), Positives = 288/413 (69%), Gaps = 9/413 (2%) Query: 8 ALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAI-LATIAVCSLLMFLRVLFSTQISA 66 A+ + L+ V P++G+ L NL+ + + I +L +FL+ +I Sbjct: 17 AILAGLISLIVFGPIVGVVLDGYSFNLQPARVGWLVAIVMIGRFALSLFLQTPKGLKILQ 76 Query: 67 MWKSS-PGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLILIYVM 125 ++S+ G+ V+P + L RWI+ ALIV A+V+PFF ++ + + L LIYV+ Sbjct: 77 GFESTGSGVHVLPPDYKSRL------RWIIPALIVIAIVFPFFANKYVLTVVILGLIYVL 130 Query: 126 LGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLLG 185 LGLGLNIVVGLAGLLDLGYV FYA+GAY AL Y GL FW LP+A + AA G +LG Sbjct: 131 LGLGLNIVVGLAGLLDLGYVAFYAIGAYGLALGYQYLGLGFWTVLPLAAIAAAMAGCILG 190 Query: 186 FPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGL 245 FPVLR+ GDYLAIVTLGFGEIIRL L N TGGPNG+ + PTF GL F R+A +G Sbjct: 191 FPVLRMHGDYLAIVTLGFGEIIRLVLNNWLSFTGGPNGMP-VPSPTFLGLEFGRRAKDGG 249 Query: 246 QTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRAL 305 FHE+FG++YN K +F+Y+V + L L+V +RL RMP+GRAWEALREDEIACR++ Sbjct: 250 VPFHEFFGIDYNPNIKFLFIYIVLFITVLLVLYVKHRLTRMPVGRAWEALREDEIACRSM 309 Query: 306 GLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLG 365 GLN ++KLSAFT+GA+ AG AG FFA+ QG V P SFTF ESA+ILAIVVLGGMGS +G Sbjct: 310 GLNHVLVKLSAFTIGASTAGLAGVFFASYQGFVNPSSFTFFESALILAIVVLGGMGSTVG 369 Query: 366 VILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK 418 V++AA V+ + PE++R FSEYR+L+FG LMVLMMIWRP+GL+ + R + RK Sbjct: 370 VVIAAFVLTVAPELLRSFSEYRVLLFGVLMVLMMIWRPRGLIRISRTGVTPRK 422 Lambda K H 0.331 0.145 0.439 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: 648 Number of extensions: 35 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: 418 Length of database: 426 Length adjustment: 32 Effective length of query: 386 Effective length of database: 394 Effective search space: 152084 Effective search space used: 152084 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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