Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate RR42_RS34790 RR42_RS34790 ABC transporter permease
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Cup4G11:RR42_RS34790 Length = 348 Score = 158 bits (400), Expect = 3e-43 Identities = 109/357 (30%), Positives = 173/357 (48%), Gaps = 40/357 (11%) Query: 154 IAVVVALAFPF-TPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAY 212 + + +A+AFP TP + L + L Y + GLN++ G G L+L + F A+GAY Sbjct: 13 LLLALAIAFPLVTP--NSYYLTVMTLAFIYAIATLGLNLITGYTGQLNLAHGGFMAIGAY 70 Query: 213 SYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILIN 272 + +L FW L+G + M G +G LRL+G YF+I TL G II +++ Sbjct: 71 TLGILTVDHQVPFWAAFVLSGVVCMMVGYFVGVVSLRLKGHYFSIFTLCIGYIIYLLIEK 130 Query: 273 WYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVL 332 W T G G+ GIP P+ G F A+ YYL+L Sbjct: 131 WESLTHGTVGLIGIPVPASVGPLAFDNVQAQ----------------------YYLVLFF 168 Query: 333 ALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFA 392 + R+ LGR++ A+R D +LGIN K+ +F ++ + GFAG+ +A Sbjct: 169 LVAGTFLMHRIVTSLLGRSFMAVRNSDALAEALGINLMRTKVLSFVLSVGYAGFAGALYA 228 Query: 393 TRQGFISPE-SFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAF 451 + F+ P+ + T + +++A++V GG G+ +G ++ A LV + + + L DYRML F Sbjct: 229 GQVRFLGPDIARTDLTFEMVMAMLV-GGTGTLLGPLLGAVLVPWVTQTLQFLQDYRMLVF 287 Query: 452 GMGMVLIMLWRPRGLL-------------AHRDPTILLHGRPKGGAGGPAAGSAAAG 495 G +VL++++ P G++ A R T H AG P A +A AG Sbjct: 288 GPVLVLLIIFVPDGIVGSWAKRQARRAAAARRGGTSRAHPAGTPVAGNPNANAANAG 344 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: 433 Number of extensions: 24 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: 348 Length adjustment: 32 Effective length of query: 473 Effective length of database: 316 Effective search space: 149468 Effective search space used: 149468 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