Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate GFF3114 HP15_3057 leucine/isoleucine/valine transporter permease subunit
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Marino:GFF3114 Length = 423 Score = 497 bits (1280), Expect = e-145 Identities = 249/421 (59%), Positives = 318/421 (75%), Gaps = 10/421 (2%) Query: 4 HLKSALFSALLVWAVAYPVLGLKLTIVGINLEVHGTSPAILATIAVCSLLMFLRVLFSTQ 63 + + ALF A + ++YP++G L GIN+ + G + + + ++++FL +F Q Sbjct: 5 NFRHALFCAFITLIISYPIIGFNLEAQGINVTLTGADASTIVMVLFAAVIVFLFQMFREQ 64 Query: 64 ISAMWKSSPGLPVIPAKASNFLTLPTTQR-----WIVLALIVGALVWPFFGSRGAVDIAT 118 I KS P P SN + +R W++ ++V AL WPFF SRGAVD+AT Sbjct: 65 IMGGLKSIPH----PLPQSNKEPMAENRRAKIESWVLTGIVVLALFWPFFVSRGAVDLAT 120 Query: 119 LILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAA 178 L+LIY+ML LGLN+VVGLAGLLDLGYV FYAVGAY++ALLS Y G+SFW+ LPI ++AA Sbjct: 121 LVLIYIMLALGLNVVVGLAGLLDLGYVAFYAVGAYTFALLSQYTGISFWLALPIGALLAA 180 Query: 179 TFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFE 238 FG +LGFPVLRLRGDYLAIVTLGFGEIIR+ L N T +TGGPNGI I PT FG+ F Sbjct: 181 LFGLVLGFPVLRLRGDYLAIVTLGFGEIIRILLNNWTTLTGGPNGIGGIPDPTLFGMEFG 240 Query: 239 RKAAE-GLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALRE 297 R+ E G +FHE FG+ Y+ +KVIFLYL+AL+LA+ VI R +RMP+GRAWEALRE Sbjct: 241 RRVKEEGNTSFHETFGIAYSGEHKVIFLYLIALVLAVFTALVIRRFMRMPVGRAWEALRE 300 Query: 298 DEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVL 357 DEIA R+LGL+ T +KLSAFT+GA FAGFAG+ FA++QG ++PESF F+ESAIILAIVVL Sbjct: 301 DEIAARSLGLSRTAVKLSAFTIGAFFAGFAGTVFASKQGFISPESFVFLESAIILAIVVL 360 Query: 358 GGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLPMQRPHMELR 417 GGMGSQ+GV+LAAI + +LPE+ REFSEYRML+FGA MVLMM+WRPQGL+PM+R H+EL+ Sbjct: 361 GGMGSQIGVVLAAIAVTILPELAREFSEYRMLIFGAAMVLMMVWRPQGLMPMRRIHIELK 420 Query: 418 K 418 + Sbjct: 421 R 421 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: 611 Number of extensions: 29 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: 423 Length adjustment: 32 Effective length of query: 386 Effective length of database: 391 Effective search space: 150926 Effective search space used: 150926 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