Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate GFF1300 PS417_06605 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__WCS417:GFF1300 Length = 417 Score = 726 bits (1873), Expect = 0.0 Identities = 364/418 (87%), Positives = 396/418 (94%), Gaps = 1/418 (0%) Query: 1 MTRHLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLF 60 M+R+LKSA FSALLVWAVA+PVLGLKL+IVGINLEVHGT P L IA+CS+LMFLRVLF Sbjct: 1 MSRYLKSAFFSALLVWAVAFPVLGLKLSIVGINLEVHGTGPVTLTIIALCSVLMFLRVLF 60 Query: 61 STQISAMWKSSPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLI 120 + Q+ A++KS+ G P++ K S FLTLP TQR+I++ALI+ AL+WPFFGSRGAVDIATLI Sbjct: 61 TQQVGALFKSNRG-PLVSPKVSQFLTLPRTQRYIIIALIIAALIWPFFGSRGAVDIATLI 119 Query: 121 LIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATF 180 LIYV+LGLGLNIVVGLAGLLDLGYVGFYAVGAY+YALLSHY G SFWICLP+AGM AATF Sbjct: 120 LIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYTYALLSHYLGWSFWICLPLAGMAAATF 179 Query: 181 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERK 240 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGIS+I KPTFFGL+F+R Sbjct: 180 GFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISSIPKPTFFGLSFDRT 239 Query: 241 AAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI 300 AAEG+QTFHEYFG++YN ++KV+FLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI Sbjct: 240 AAEGMQTFHEYFGIDYNPVSKVVFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEI 299 Query: 301 ACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 360 ACRALGLNPT+IKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM Sbjct: 300 ACRALGLNPTIIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGM 359 Query: 361 GSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELRK 418 GSQLGVILAAIVMILLPEMMREFSEYRMLMFGA+MVLMMIWRPQGLLPMQRPHMELRK Sbjct: 360 GSQLGVILAAIVMILLPEMMREFSEYRMLMFGAMMVLMMIWRPQGLLPMQRPHMELRK 417 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: 711 Number of extensions: 27 Number of successful extensions: 2 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: 417 Length adjustment: 32 Effective length of query: 386 Effective length of database: 385 Effective search space: 148610 Effective search space used: 148610 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