Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_028313408.1 G491_RS0102105 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000429905.1:WP_028313408.1 Length = 330 Score = 176 bits (445), Expect = 1e-48 Identities = 98/289 (33%), Positives = 156/289 (53%), Gaps = 22/289 (7%) Query: 118 TLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMA 177 T I I+ +L +GLN+++G AG + LG+ FY +GAY+ L+ + G S W LP A + Sbjct: 43 TFIGIFTLLAVGLNMLMGYAGQISLGHAAFYGIGAYTTGALTVHLGWSPWASLPCALAAS 102 Query: 178 ATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTF 237 +++G P L+L G YL + TLGFG I+ + R ITGGPNG+ I + +G+ Sbjct: 103 GIIAYIVGKPTLKLSGYYLGMGTLGFGMIMHVLFREWGGITGGPNGLVGIPSLSLWGI-- 160 Query: 238 ERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALRE 297 L T Y + + + L F+ +RL+ +GRA A+ Sbjct: 161 ------DLSTGRNYLWVVWGCV--------------LITFFICDRLVNSRVGRALRAIHF 200 Query: 298 DEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVL 357 E A A+G++ KL F A A AG +A ++P SF F+ S ++A+VV+ Sbjct: 201 SEQAASAVGVDTAKAKLQVFVFSAMVAALAGFLYAHLVMFISPGSFGFLVSVKLVAMVVI 260 Query: 358 GGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGL 406 GGM S G +L + ++ +LPE + FS+Y M+++G +++ +MI+ PQGL Sbjct: 261 GGMASIWGALLGSTLLTMLPEWLHRFSDYEMVIYGGILMGVMIFLPQGL 309 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: 396 Number of extensions: 29 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: 330 Length adjustment: 30 Effective length of query: 388 Effective length of database: 300 Effective search space: 116400 Effective search space used: 116400 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