Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate GFF4157 HP15_4097 inner-membrane translocator
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__Marino:GFF4157 Length = 347 Score = 176 bits (447), Expect = 7e-49 Identities = 118/336 (35%), Positives = 168/336 (50%), Gaps = 39/336 (11%) Query: 86 TLPTTQRWIVLALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYV 145 T T + W+ L++ LV+PF + + L+ I V+ GLNI+ G GL+ LG Sbjct: 18 TSQTQKLWLGFFLLI-LLVFPFVVDSYLLYLGCLVGIAVISTTGLNILTGFTGLISLGQA 76 Query: 146 GFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGE 205 GF VGAY+ A LS L F + L +AG+MAA G L+G P LR++G YLAI TL Sbjct: 77 GFMGVGAYTVAWLSINTALPFPVTLVLAGLMAAAVGILVGLPSLRVKGLYLAIATLAASV 136 Query: 206 IIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFL 265 + +TGG G+S +E FGLTF+ + Sbjct: 137 FLHFIFAEWESVTGGMGGLS-LEPAHLFGLTFQSD----------------------FMM 173 Query: 266 YLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAG 325 Y + + LA+ + + R IGRA+ A+R+ +I+ LG+N KL +F L + +AG Sbjct: 174 YFIIVPLAVLMVLAARNVFRTRIGRAFIAIRDRDISAEILGINLLRYKLMSFALSSFYAG 233 Query: 326 FAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMR---- 381 AG FA +VTPESF S LA V++GGMG+ LG IL A M L+PE ++ Sbjct: 234 IAGGLFAYFYRVVTPESFPLSMSIFYLAAVIVGGMGNLLGGILGAAFMTLVPEALKLLTA 293 Query: 382 -----------EFSEYRMLMFGALMVLMMIWRPQGL 406 S ++FGAL+V +I+ P GL Sbjct: 294 ALTPFYPNAPVFMSPMLEIIFGALIVGFLIFEPHGL 329 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: 459 Number of extensions: 34 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: 347 Length adjustment: 30 Effective length of query: 388 Effective length of database: 317 Effective search space: 122996 Effective search space used: 122996 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