Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate WP_013403236.1 CALHY_RS06830 branched-chain amino acid ABC transporter permease
Query= uniprot:G8ALI9 (505 letters) >NCBI__GCF_000166355.1:WP_013403236.1 Length = 312 Score = 182 bits (463), Expect = 1e-50 Identities = 115/323 (35%), Positives = 180/323 (55%), Gaps = 41/323 (12%) Query: 155 AVVVALAFPFTPLADRQLLDIGI-----LLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAV 209 A ++ L T L ++D I L++ I+L LN++ G+ G LG+ F A+ Sbjct: 10 AFIIVLYLTITLLMKIGIIDDYIKLNLFLIMLNIILAVSLNLINGITGQFSLGHAGFMAI 69 Query: 210 GAYSYALLAHYFG-FSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRI 268 GAY+ A+L F++ + + G A + G+++G PVLRLRGDY AI TLGFGEIIR+ Sbjct: 70 GAYTTAVLTTLEKPVPFYLTVLIGGLFAMICGLIIGLPVLRLRGDYLAIATLGFGEIIRV 129 Query: 269 ILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYL 328 I+ N + GG +GIS IP+ G++++ Y++ Sbjct: 130 IIQN-IDYLGGASGISDIPQ------------------------GIDWTG-------YFV 157 Query: 329 ILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAG 388 I VL++VV L + GRA A+RED+IA ++GIN T K+ AF I A F G AG Sbjct: 158 ITVLSVVVIL---NIINSSFGRAMIAIREDEIAAEAMGINTTLYKVLAFMIGAFFAGVAG 214 Query: 389 SFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRM 448 S ++ GFI P+ F F +S IL IVVLGG+GS G +++A ++ + ++ RM Sbjct: 215 SIYSGSFGFIQPDMFNFFKSIDILVIVVLGGLGSISGSIISAIVLTIISALLQDYPAVRM 274 Query: 449 LAFGMGMVLIMLWRPRGLLAHRD 471 + + + +++IML+RP+GL+ ++ Sbjct: 275 VLYSLILIIIMLFRPQGLMGTKE 297 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: 394 Number of extensions: 26 Number of successful extensions: 4 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: 312 Length adjustment: 31 Effective length of query: 474 Effective length of database: 281 Effective search space: 133194 Effective search space used: 133194 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 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