Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_013420533.1 RVAN_RS14870 ABC transporter
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_000166055.1:WP_013420533.1 Length = 661 Score = 177 bits (449), Expect = 1e-48 Identities = 106/320 (33%), Positives = 173/320 (54%), Gaps = 12/320 (3%) Query: 161 AFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHY 220 AFPF + + + ++ Y +L GL+IVVG G + LG+ + +GAY A++ H+ Sbjct: 19 AFPFLAGQNSYYIHLVQMMAIYAILILGLDIVVGYTGQVSLGHAGLFGIGAYGAAVIFHH 78 Query: 221 FGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQFTGGP 280 +G W L + + + G +L P LR+ G Y A+VTL FG II+I++ W T GP Sbjct: 79 YGLGVWPGLLVGVIVTGIFGAVLAVPALRVIGPYLAMVTLAFGTIIQIVINEWTGLTNGP 138 Query: 281 NGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALVVNLFT 340 G++ +P P AD+ R+ +GT GL+ + R+ F YYL ++L LV L Sbjct: 139 LGVT-LPPPRVVDFADW-RSFWQGT------LGLKAAEFQRLEF-YYLCVLLMLVAILVV 189 Query: 341 MRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISP 400 RV + GRA+EALR+ IAC +G++ K+ AF ++A G AG+ F+ + ++SP Sbjct: 190 NRVVRSQYGRAFEALRDSPIACDCMGVSVYRYKVYAFVVSAALAGLAGALFSWSERYVSP 249 Query: 401 ESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFGMGMVLIML 460 ++ F S + L V+LGG S+ G ++ AF+++ LP ++ R++A GM+ Sbjct: 250 NTYNFELSILFLLAVILGGRKSRAGPLIGAFIIVYLPNVLSDIELVRIMA---GMIAAAA 306 Query: 461 WRPRGLLAHRDPTILLHGRP 480 ++A R L+ P Sbjct: 307 LVALAIIALRSREKLVRALP 326 Lambda K H 0.329 0.144 0.438 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: 750 Number of extensions: 39 Number of successful extensions: 3 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: 505 Length of database: 661 Length adjustment: 36 Effective length of query: 469 Effective length of database: 625 Effective search space: 293125 Effective search space used: 293125 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 53 (25.0 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