Align High-affinity branched-chain amino acid ABC transporter permease LivM (characterized, see rationale)
to candidate WP_012336125.1 M446_RS31395 ABC transporter
Query= uniprot:A0A159ZYE0 (418 letters) >NCBI__GCF_000019365.1:WP_012336125.1 Length = 608 Score = 162 bits (410), Expect = 3e-44 Identities = 97/288 (33%), Positives = 161/288 (55%), Gaps = 31/288 (10%) Query: 123 YVMLGLGLNIVVGLAGLLDLGYVGFYAVGAYSYALLSHYFGLSFWICLPIAGMMAA-TFG 181 Y + +GL +V+GL G ++L F+ +GAY+ L + G+SFW+CL AGM+AA G Sbjct: 57 YAIAVIGLTVVLGLCGQINLAQAAFFGLGAYAVGLGTVDLGVSFWLCL-AAGMLAALVAG 115 Query: 182 FLLGFPVLRLRGDYLAIVTLGFGEIIRLFLRNLTDITGGPNGISNIEKPTFFGLTFERKA 241 LG LRL G YLA+VT+ F +I+ L L N +T GP+G+ I++P F Sbjct: 116 AFLGASTLRLGGHYLAMVTISFQQILTLVLVNWIPVTHGPDGVPRIQRPALF-------- 167 Query: 242 AEGLQTFHEYFGLEYNSINKVIFLYLVALLLALAALFVINRLLRMPIGRAWEALREDEIA 301 ++G Y GL +A+L +A +++ + R +GRA A+R++E+A Sbjct: 168 SDG----QAYLGL------------CLAVLAVVA--WLVWHMPRTRLGRAMRAVRDNELA 209 Query: 302 CRALGLNPTVIKLSAFTLGAAFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMG 361 G++ K+ AF +GA AG G FA V+P+ F+F ES + L + +LGG+G Sbjct: 210 AGVTGIDVYRTKVMAFAIGALLAGLGGGLFAGSFTYVSPDQFSFAESIVFLTMALLGGVG 269 Query: 362 SQLGVILAAIVMILLPEMMR---EFSEYRMLMFGALMVLMMIWRPQGL 406 S G ++ ++IL+PE +R E + ++G ++L++++ P+G+ Sbjct: 270 SPAGAVIGTGLLILIPEWLRFLKEIPGLYLAIYGLAVILIVVFMPEGI 317 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: 611 Number of extensions: 34 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: 608 Length adjustment: 34 Effective length of query: 384 Effective length of database: 574 Effective search space: 220416 Effective search space used: 220416 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