Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate Ac3H11_1938 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:A0A159ZYE0 (418 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1938 Length = 358 Score = 164 bits (416), Expect = 3e-45 Identities = 93/300 (31%), Positives = 162/300 (54%), Gaps = 35/300 (11%) Query: 118 TLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMA 177 T +LIY ++GLGL ++ G GL LG+ F VGAY+ A+L+ G F + L A ++ Sbjct: 48 TFVLIYSIVGLGLMLLAGFTGLFSLGHAAFLGVGAYTQAVLTG-MGWPFALSLACAAGLS 106 Query: 178 ATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTF 237 A G ++G P LR++G YL + TL FG I+ +TGG +G ++ P FG +F Sbjct: 107 AAVGVVVGLPALRVKGIYLGMATLSFGFIVEEVFARWESVTGGNSG-KHLVPPQMFGYSF 165 Query: 238 ERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALRE 297 E + Y + L++A+ + I LLR P GRA+ A+R+ Sbjct: 166 ESTES----------------------FYFLCLVIAVVSTLAILNLLRSPTGRAFVAIRD 203 Query: 298 DEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVL 357 EI+ +++G++ K +F+L AA AG G+ +A + ++P+ F ++S +L ++V+ Sbjct: 204 SEISAQSMGIHLARYKTLSFSLSAALAGVGGALYAHKLQFISPDQFNILQSIDLLLMIVI 263 Query: 358 GGMGSQLGVILAAIVMILLPEMMREFSEY-----------RMLMFGALMVLMMIWRPQGL 406 GG+GS G L AI +I +P+M+ ++ + +++GA+++ +++ P GL Sbjct: 264 GGLGSVHGAFLGAIFLISMPQMISLSKDWLPAAIGQAPGLQAVVYGAVLIAFVLFEPMGL 323 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: 412 Number of extensions: 32 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: 418 Length of database: 358 Length adjustment: 30 Effective length of query: 388 Effective length of database: 328 Effective search space: 127264 Effective search space used: 127264 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