Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_020177274.1 A3OQ_RS0120255 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000385335.1:WP_020177274.1 Length = 450 Score = 341 bits (875), Expect = 2e-98 Identities = 184/312 (58%), Positives = 221/312 (70%), Gaps = 17/312 (5%) Query: 120 ILIYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAAT 179 ILIYVMLG GLNIVVGLAGLLDLGYV FYAVGAY+YALL+ G SFW+CLPI G +AA Sbjct: 129 ILIYVMLGWGLNIVVGLAGLLDLGYVAFYAVGAYAYALLATDLGWSFWLCLPICGAIAAL 188 Query: 180 FGFLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFER 239 FG LGFPVLRLRGDYLAIVTL FGEI R+ N T +T G G+S I K TF G+ F Sbjct: 189 FGIALGFPVLRLRGDYLAIVTLAFGEITRVVAVNWTALTNGDAGVSLIPKITFLGIPF-- 246 Query: 240 KAAEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDE 299 +G F +FGL + I + IFLY + L LAL F+ RL R+P+GR WEALREDE Sbjct: 247 --TKGEAGFAAHFGLPFFPIERTIFLYYLILALALLTNFLTTRLRRLPLGRVWEALREDE 304 Query: 300 IACRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGG 359 IACR+LG++ KLSAF +GA AG AG+FFA RQG V+P SF FIESA IL+IVVLGG Sbjct: 305 IACRSLGIDTVKAKLSAFAIGALIAGIAGAFFAVRQGFVSPSSFGFIESATILSIVVLGG 364 Query: 360 MGSQLGVILAAIVMILLPEMMREF-------------SEYRMLMFGALMVLMMIWRPQGL 406 GSQLG++LAAI++I E +RE ++YRML+ G MV MM WRP+GL Sbjct: 365 AGSQLGIVLAAILIIGGSEFLRELDVLQEFFGYTFDPTQYRMLLVGLAMVAMMNWRPRGL 424 Query: 407 LPMQRPHMELRK 418 + ++RP + L+K Sbjct: 425 VSVRRPSIFLKK 436 Score = 27.7 bits (60), Expect = 7e-04 Identities = 25/105 (23%), Positives = 43/105 (40%), Gaps = 23/105 (21%) Query: 71 SPGLPVIPAKASNFLTLPTTQRWIVLALIVGALVWPFFGSR---------GAVDIATLIL 121 S G+ + AK S F + ++ + FF R G ++ AT++ Sbjct: 309 SLGIDTVKAKLSAF----------AIGALIAGIAGAFFAVRQGFVSPSSFGFIESATILS 358 Query: 122 IYVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSF 166 I V+ G G + + LA +L +G F +L +FG +F Sbjct: 359 IVVLGGAGSQLGIVLAAILIIGGSEFLR----ELDVLQEFFGYTF 399 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: 654 Number of extensions: 34 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 418 Length of database: 450 Length adjustment: 32 Effective length of query: 386 Effective length of database: 418 Effective search space: 161348 Effective search space used: 161348 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: 51 (24.3 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