Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_011649172.1 RL_RS34945 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000009265.1:WP_011649172.1 Length = 328 Score = 162 bits (410), Expect = 1e-44 Identities = 101/316 (31%), Positives = 156/316 (49%), Gaps = 18/316 (5%) Query: 94 IVLALIVGALVWPFFGSRGAVDIATLILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAY 153 + L+V AL PF GSR + LI+++ GLN++VG GLL L F+ +GAY Sbjct: 19 LAAVLVVLALAAPFIGSRYITHSLIIALIFMLPAHGLNLLVGYTGLLSLAQAAFFGIGAY 78 Query: 154 SYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRN 213 + LL+ +G F++ L AG ++ LG P LRLR + TLGF I + +N Sbjct: 79 TAGLLAVTYGTPFYVNLIAAGAVSGALALPLGIPALRLRSTSFVMCTLGFVIIGQAIAKN 138 Query: 214 LTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLA 273 +T G G+S+I KP F E L + F YL AL++ Sbjct: 139 WVSLTRGDMGLSSIPKPYF-----------------ELGPLSFTVSGTTNFYYL-ALIIG 180 Query: 274 LAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAA 333 A F + ++R P GR A+RE+E +LG+ KL F + A FAG G +A Sbjct: 181 TLATFAVWAIVRSPAGRNMVAIRENETLAESLGVPTWHYKLIVFMISAVFAGVGGCLYAY 240 Query: 334 RQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGA 393 +V+P +F S +L IV+ GG G G + +++ + L E +R E RM+ +G Sbjct: 241 YLTVVSPLTFQMYYSTTMLIIVLGGGAGMISGTVFGSLLFVGLTEALRITPELRMIAYGV 300 Query: 394 LMVLMMIWRPQGLLPM 409 +++++ W +G P+ Sbjct: 301 CLLVLVFWFKKGCAPL 316 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: 30 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: 328 Length adjustment: 30 Effective length of query: 388 Effective length of database: 298 Effective search space: 115624 Effective search space used: 115624 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