Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate 8502039 DvMF_2752 inner-membrane translocator (RefSeq)
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Miya:8502039 Length = 330 Score = 222 bits (566), Expect = 1e-62 Identities = 138/345 (40%), Positives = 188/345 (54%), Gaps = 30/345 (8%) Query: 154 IAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYS 213 IAVVVA+ L D D+ + + Y +L LNI++G AGL +G+ AFYAVGAY Sbjct: 12 IAVVVAV---LPLLLDPYWTDVFVSIGLYSVLALSLNIILGQAGLFHMGHAAFYAVGAYV 68 Query: 214 YALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILI-N 272 A+ +G +P AG AA+ +++ P++ LRGDY IVT+G EI+RI LI N Sbjct: 69 TAIANTMWGVPVLWAMPFAGLAAALFAMVVARPIIHLRGDYLLIVTIGIVEIVRIALINN 128 Query: 273 WYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVL 332 + TGG NGI GI RP FG + + + YYL+ Sbjct: 129 VFGLTGGANGIFGISRPMLFGF-----------------------KIAKPVHFYYLVWAY 165 Query: 333 ALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFA 392 L R+ GRA ++EDD A G+N + KL AF + A + G G+ +A Sbjct: 166 VACSILLFRRLENSRFGRALNYIKEDDTAAEGSGVNIASYKLWAFVLGAFWAGMTGTIYA 225 Query: 393 TRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAFG 452 + ISPESF+F ES ++ AIV+LGG GS GV++ AFL+IGLPE FRE A RMLAFG Sbjct: 226 AKMTIISPESFSFWESVVLFAIVILGG-GSNRGVLLGAFLLIGLPEFFREFASARMLAFG 284 Query: 453 MGMVLIMLWRPRGLLAHRDPTILLHGRPK--GGAGGPAAGSAAAG 495 + MV++M++RP+G+L L R + G GG AA A G Sbjct: 285 LAMVVMMIFRPQGMLPPMPRFYKLPERIRCITGKGGDAAAQAGGG 329 Score = 25.4 bits (54), Expect = 0.003 Identities = 30/106 (28%), Positives = 43/106 (40%), Gaps = 20/106 (18%) Query: 32 TIPLVGLRTVDRPTGLGLETRWNEVAAAVGL---------VFLGRLGLCLIREGH----A 78 T G+ V L L+ W +V ++GL + LG+ G L GH A Sbjct: 6 TTSYAGIAVVVAVLPLLLDPYWTDVFVSIGLYSVLALSLNIILGQAG--LFHMGHAAFYA 63 Query: 79 VTVLVLAAAATAAGFFI--AMPTEALRVILIAGGAVIAIRAVLAIR 122 V V A A T G + AMP L L A++ R ++ +R Sbjct: 64 VGAYVTAIANTMWGVPVLWAMPFAGLAAALF---AMVVARPIIHLR 106 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: 444 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 505 Length of database: 330 Length adjustment: 31 Effective length of query: 474 Effective length of database: 299 Effective search space: 141726 Effective search space used: 141726 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