Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate AO353_13350 AO353_13350 branched-chain amino acid ABC transporter permease
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__pseudo3_N2E3:AO353_13350 Length = 432 Score = 372 bits (956), Expect = e-107 Identities = 183/328 (55%), Positives = 243/328 (74%), Gaps = 4/328 (1%) Query: 140 IAAQVQHASRWLGPIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLL 199 +A + R++ P +V+A+ FP AD+ LL + IL L Y++LG GLNIVVGLAGLL Sbjct: 89 LAPDFKSRLRFIIPALIVIAIVFPV--FADKYLLTVVILGLIYVLLGLGLNIVVGLAGLL 146 Query: 200 DLGYVAFYAVGAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVT 259 DLGYVAFYA+GAY AL HY G FW LPL+ +AA++G +LGFPVLR+ GDY AIVT Sbjct: 147 DLGYVAFYAIGAYGLALGYHYLGLGFWTVLPLSALMAALAGCILGFPVLRMHGDYLAIVT 206 Query: 260 LGFGEIIRIILINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPL 319 LGFGEIIR+IL NW FTGGPNG+ +P PSFFGI +FTR +G FHE FG E++P Sbjct: 207 LGFGEIIRLILTNWLSFTGGPNGMP-VPSPSFFGI-EFTRVAKDGGIPFHEFFGTEYNPN 264 Query: 320 HRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAI 379 + +F+Y ++ ++ ++V R+ ++P+GRAWEALRED+IAC ++G+N +KL+AF + Sbjct: 265 IKFMFIYAVLFLVVMLVLYIKHRLTRMPVGRAWEALREDEIACRAMGLNHVLVKLSAFTL 324 Query: 380 AAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEA 439 A G AG FFA+ QGF++P SFTF ESA+ILAIVVLGGMGS +GVV+AAF++ PE Sbjct: 325 GASTAGLAGVFFASYQGFVNPTSFTFFESALILAIVVLGGMGSTVGVVIAAFVLTVAPEL 384 Query: 440 FRELADYRMLAFGMGMVLIMLWRPRGLL 467 R A+YR+L FG+ MVL+M+W+PRGL+ Sbjct: 385 LRGFAEYRVLLFGILMVLMMIWKPRGLI 412 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: 645 Number of extensions: 33 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: 432 Length adjustment: 33 Effective length of query: 472 Effective length of database: 399 Effective search space: 188328 Effective search space used: 188328 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