Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_015932925.1 MNOD_RS31075 ABC transporter
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000022085.1:WP_015932925.1 Length = 611 Score = 164 bits (415), Expect = 7e-45 Identities = 107/338 (31%), Positives = 175/338 (51%), Gaps = 32/338 (9%) Query: 73 GLPVIPAKASNFLTLPTTQRWIVLA-LIVGALVWPFFGSRGAVDIATLILIYVMLGLGLN 131 GL P A+ L L + +V A L+ A+ P G ++I Y + +GL Sbjct: 10 GLAAPPTPAARRLPLGSLVYALVAAGLVALAVTMPVNGY--LLNILMQAATYAIAVIGLT 67 Query: 132 IVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAATFGFLLGFPVLRL 191 +V+GL G ++L F+ +GAY+ L + G+SFWICL A G LG LRL Sbjct: 68 VVLGLCGQINLAQAAFFGLGAYAVGLGTVDLGVSFWICLAAGLAAALVAGAFLGASTLRL 127 Query: 192 RGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKAAEGLQTFHEY 251 G YLA+VT+ F +I+ L L N +T GP+G+ I++P F +G Y Sbjct: 128 GGHYLAMVTISFQQILTLVLVNWIPVTHGPDGVPRIQRPALF--------TDG----QAY 175 Query: 252 FGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIACRALGLNPTV 311 GL +A+L +A +++ + R +GRA A+R++E+A G++ Sbjct: 176 LGL------------CLAVLAVVA--WIVWHMPRTRLGRAMRAVRDNELAAGVTGIDVYR 221 Query: 312 IKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAI 371 K+ AF +GA AG G FA V+P+ F+F ES + L + +LGG+GS G ++ Sbjct: 222 TKVMAFAIGALLAGLGGGLFAGGFTYVSPDQFSFAESIVFLTMALLGGVGSPAGAVIGTG 281 Query: 372 VMILLPEMMR---EFSEYRMLMFGALMVLMMIWRPQGL 406 ++IL+PE +R E + ++G ++L++++ P+G+ Sbjct: 282 LLILIPEWLRFLKEIPGLYLAIYGLAVILIVVFMPEGI 319 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: 645 Number of extensions: 35 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: 611 Length adjustment: 34 Effective length of query: 384 Effective length of database: 577 Effective search space: 221568 Effective search space used: 221568 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