Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate YP_428496.1 Rru_A3415 inner-membrane translocator
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000013085.1:YP_428496.1 Length = 295 Score = 148 bits (373), Expect = 2e-40 Identities = 102/304 (33%), Positives = 156/304 (51%), Gaps = 34/304 (11%) Query: 116 IATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGM 175 + + LIY ++ LGLN+ G GL++ G VGF+A+GAY+ ALL G + LP A Sbjct: 8 VTVIALIYSLMTLGLNLQYGFTGLINFGVVGFFAIGAYTSALLV-VAGWPILLALPCAVA 66 Query: 176 MAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGL 235 +A + + LRLR +Y AIV LGF E IRL + + +TGG G++ I Sbjct: 67 ASALVSWPVALLSLRLRIEYFAIVMLGFAETIRLVVTSEGWLTGGVQGVTGIPSLA---- 122 Query: 236 TFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEAL 295 AA GL S+ + LVAL + +++ RL+ P GR A+ Sbjct: 123 -----AALGL------------SMESTLLTALVALGAVIGVVWLSRRLVASPFGRIIRAI 165 Query: 296 REDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIV 355 R+DE A +ALG P K++ F LG+A AG AG+ +A ++P+ F + + I + Sbjct: 166 RDDEDAVQALGKAPGRFKVAVFVLGSASAGLAGALYAHYITYISPDQFMSLLTFYIWVAM 225 Query: 356 VLGGMGSQLGVILAAIVMILLPEMMR------------EFSEYRMLMFGALMVLMMIWRP 403 +LGG+G G +L V+I L E R E + R+ + G ++++M +RP Sbjct: 226 ILGGVGRVGGAVLGTAVLIGLMEGSRFLRDILPGVAEVEMASIRLGVIGLALMVLMRFRP 285 Query: 404 QGLL 407 +GLL Sbjct: 286 EGLL 289 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: 395 Number of extensions: 25 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: 295 Length adjustment: 29 Effective length of query: 389 Effective length of database: 266 Effective search space: 103474 Effective search space used: 103474 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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