Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate Ac3H11_1938 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1938 Length = 358 Score = 157 bits (398), Expect = 4e-43 Identities = 99/299 (33%), Positives = 156/299 (52%), Gaps = 36/299 (12%) Query: 179 LLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAM 238 +L Y ++G GL ++ G GL LG+ AF VGAY+ A+L G+ F + L A L+A Sbjct: 50 VLIYSIVGLGLMLLAGFTGLFSLGHAAFLGVGAYTQAVLTG-MGWPFALSLACAAGLSAA 108 Query: 239 SGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFT 298 GV++G P LR++G Y + TL FG I+ + W TGG +G +P P FG + Sbjct: 109 VGVVVGLPALRVKGIYLGMATLSFGFIVEEVFARWESVTGGNSGKHLVP-PQMFGYS--- 164 Query: 299 RTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALRED 358 E T +F Y+L LV+A+V L + + + P GRA+ A+R+ Sbjct: 165 ---FESTESF-----------------YFLCLVIAVVSTLAILNLLRSPTGRAFVAIRDS 204 Query: 359 DIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLG 418 +I+ S+GI+ K +F+++A G G+ +A + FISP+ F ++S +L ++V+G Sbjct: 205 EISAQSMGIHLARYKTLSFSLSAALAGVGGALYAHKLQFISPDQFNILQSIDLLLMIVIG 264 Query: 419 GMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFGM---------GMVLI--MLWRPRGL 466 G+GS G + A +I +P+ D+ A G G VLI +L+ P GL Sbjct: 265 GLGSVHGAFLGAIFLISMPQMISLSKDWLPAAIGQAPGLQAVVYGAVLIAFVLFEPMGL 323 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: 441 Number of extensions: 32 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: 358 Length adjustment: 32 Effective length of query: 473 Effective length of database: 326 Effective search space: 154198 Effective search space used: 154198 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: 51 (24.3 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