Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate 8500844 DvMF_1582 inner-membrane translocator (RefSeq)
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Miya:8500844 Length = 313 Score = 131 bits (329), Expect = 4e-35 Identities = 101/324 (31%), Positives = 161/324 (49%), Gaps = 39/324 (12%) Query: 151 LGPIAVVVALA-FPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAV 209 L P+ V+ LA P L + ++ I IL + + + G N++ G G + G+ AF+ + Sbjct: 5 LVPLVVLAMLAGLPLLGL-NSYVMHILILSIMWTLAGMAWNLLGGYCGQVSFGHAAFFGM 63 Query: 210 GAYSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRII 269 GAYS L+ + G S W ++ L A+ + +G VLRLRG YF + TL GE++RI Sbjct: 64 GAYSAGLIHLHLGLSPWWGFLVSLPLVALVALAMGSVVLRLRGPYFVLATLAIGEVLRIT 123 Query: 270 LINWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLI 329 N FT G GI TRT E T YY+I Sbjct: 124 CENLTDFTKGTLGIM------------ITRTWVEKTQ------------------YYYII 153 Query: 330 LVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGS 389 L LAL+ + + G + A+RED A S+GI+ T K A ++AM G AG+ Sbjct: 154 LGLALLGFVVCRAIVHSRWGYYFVAIREDQDAAESMGIDTTRYKTIALTVSAMLTGLAGA 213 Query: 390 FFATRQGFISP-ESFTFIE-SAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFREL---- 443 F+ G+I P F+ E S +I+ +V++GG+ ++ G + A +++ L E R L Sbjct: 214 FYTNYMGYIDPGVVFSLGEISILIIMVVMVGGVATEWGPALGAGIMVILAEYIRSLPLIG 273 Query: 444 ADYRMLAFGMGMVLIMLWRPRGLL 467 Y+ + FG+ +++I+++ P GL+ Sbjct: 274 VAYQTM-FGVLLIVIIIYLPNGLV 296 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: 435 Number of extensions: 28 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: 313 Length adjustment: 31 Effective length of query: 474 Effective length of database: 282 Effective search space: 133668 Effective search space used: 133668 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