Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_084075809.1 BUB04_RS00755 hypothetical protein
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_900129305.1:WP_084075809.1 Length = 629 Score = 157 bits (396), Expect = 1e-42 Identities = 90/290 (31%), Positives = 149/290 (51%), Gaps = 22/290 (7%) Query: 119 LILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAA 178 ++ + ++ LGLN ++G AG + LG+ FY +GAY+ A+++ G W L A AA Sbjct: 40 IMALNALVVLGLNFLIGCAGQISLGHAAFYGLGAYTSAIVTTTLGWPLWAGLAAALATAA 99 Query: 179 TFGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFE 238 GFLL P LRL G YL + TLGF I+ + L + ++TGGP+G F G+ Sbjct: 100 LLGFLLAVPTLRLEGHYLVMATLGFNIIVSICLNQMEELTGGPSG--------FPGIPAL 151 Query: 239 RKAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALRED 298 + T ++G + + F ++ AL L L IGRA A+ + Sbjct: 152 HVGPLVIDTDRSFYGFIWTA-----FFFVFALFL---------NLEESRIGRALRAIHDK 197 Query: 299 EIACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLG 358 E+ R LG+ K+ F L A FAG +A ++P++F S ++ +VV+G Sbjct: 198 ELTARTLGVPTHAYKVGVFVLSTVLAAFAGFCYAHYVTFISPKTFDIFYSVQVVTMVVVG 257 Query: 359 GMGSQLGVILAAIVMILLPEMMREFSEYRMLMFGALMVLMMIWRPQGLLP 408 GMG+ G ++ ++ LPE++ F + +L++G L++ +++ P GL P Sbjct: 258 GMGNLWGGLVGTALLTSLPELLHRFEDLHVLIYGLLLMGSLVFFPNGLAP 307 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: 601 Number of extensions: 41 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: 629 Length adjustment: 35 Effective length of query: 383 Effective length of database: 594 Effective search space: 227502 Effective search space used: 227502 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: 52 (24.6 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