Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_011385249.1 AMB_RS14460 branched-chain amino acid ABC transporter permease
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_000009985.1:WP_011385249.1 Length = 329 Score = 137 bits (345), Expect = 6e-37 Identities = 106/338 (31%), Positives = 164/338 (48%), Gaps = 36/338 (10%) Query: 152 GPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGA 211 GP+A AF L GI++L +L L+++VG+AGL+ LG+ AF+ +G Sbjct: 26 GPLAFSAKYAFLLQKLT-------GIMILA--ILAMSLDLLVGVAGLVSLGHAAFFGLGG 76 Query: 212 YSYALLA-HYFGFSFWVCLPLA-GFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRII 269 Y ALL+ Y + WV LP A G +AA+S V+ GF +R G YF +VTL FG++ Sbjct: 77 YMLALLSPQYEAANAWVVLPAAMGAVAAVSAVV-GFLAIRTAGIYFIMVTLAFGQM-GYY 134 Query: 270 LINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLI 329 N + GG +G +P+ E FG+ L ++++ Sbjct: 135 FFNDSKLAGGSDGAYIYVKPNV------------------EAFGITLVNLESKQAFFFVV 176 Query: 330 LVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGS 389 L + V L+ V P GR A+ ++ LG N KL AFA+A G AG Sbjct: 177 LGCLVAVYLWLRVVLASPFGRVLAAIGVNEGRVRGLGFNPMVYKLVAFALAGALAGLAGF 236 Query: 390 FFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRML 449 AT+ GF+SP + +S +L +V+LGGMG+ G V+ AF++ + ++ +L Sbjct: 237 LAATQYGFVSPAMLGWHQSGHVLVMVILGGMGTLFGPVLGAFILELAHFGLEAVTEHWLL 296 Query: 450 AFGMGMVLIMLWRPRGLLAHRDPTILLHGRPKGGAGGP 487 G+ ++ I+L P+G+ +LL K G G P Sbjct: 297 PMGVLVITIVLALPKGVAG-----LLLQWCGKKGEGEP 329 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: 479 Number of extensions: 31 Number of successful extensions: 3 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: 505 Length of database: 329 Length adjustment: 31 Effective length of query: 474 Effective length of database: 298 Effective search space: 141252 Effective search space used: 141252 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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