Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate 8501894 DvMF_2609 inner-membrane translocator (RefSeq)
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Miya:8501894 Length = 415 Score = 315 bits (806), Expect = 3e-90 Identities = 174/345 (50%), Positives = 222/345 (64%), Gaps = 24/345 (6%) Query: 153 PIAVVVALAFPFTP-LADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGA 211 P VV+ AF P + +I I L Y+MLG GLNIVVGL+G L LGYVAFYAVGA Sbjct: 92 PALVVLLSAFLVLPWVVSTYQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGA 151 Query: 212 YSYALLAHYFGFSFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILI 271 YSYA+L FG FW LP+ G +AA+ G+LLGFPVLRLRGDY AIVTLGFGEIIR++L Sbjct: 152 YSYAILNSNFGLGFWSVLPIGGAMAALFGILLGFPVLRLRGDYLAIVTLGFGEIIRLVLE 211 Query: 272 NWYQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILV 331 NW F+ GP+GI+ I RP + G++ S ++YYLIL Sbjct: 212 NWSSFSQGPSGIANIERPG--------------------LLGMQLSVSDATTYIYYLILA 251 Query: 332 LALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFF 391 +V L R++ +GRAW+ALRED+IAC ++GI+ T KL AFA+ A + GFAG F Sbjct: 252 AVIVTILAVTRLKNSRIGRAWQALREDEIACQAMGIDITTTKLTAFALGACWAGFAGVIF 311 Query: 392 ATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELADYRMLAF 451 A + FI+P SFTF+ESA++LA+VVLGGMGS IGV V A ++I LPE R ++YRML F Sbjct: 312 AAKTTFINPASFTFLESAMVLAMVVLGGMGSVIGVSVGALVLILLPEYLRAFSEYRMLIF 371 Query: 452 GMGMVLIMLWRPRGLLAHRDPTILLHGRPKGGAGGPAAGSAAAGG 496 G MVL+M++RP+GL++ P + P G A AAGG Sbjct: 372 GATMVLMMVFRPQGLVS---PGRTKYNVPDAQGAGADAARPAAGG 413 Score = 25.4 bits (54), Expect = 0.004 Identities = 25/107 (23%), Positives = 42/107 (39%), Gaps = 15/107 (14%) Query: 106 LIAGGAVIAIRAVLAIRTGRSKLSQAERDKRMDHIAAQVQH-------------ASRWLG 152 LI ++ I AV ++ S++ +A + R D IA Q + W G Sbjct: 248 LILAAVIVTILAVTRLKN--SRIGRAWQALREDEIACQAMGIDITTTKLTAFALGACWAG 305 Query: 153 PIAVVVALAFPFTPLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLL 199 V+ A F A L+ ++L ++ G G I V + L+ Sbjct: 306 FAGVIFAAKTTFINPASFTFLESAMVLAMVVLGGMGSVIGVSVGALV 352 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: 559 Number of extensions: 24 Number of successful extensions: 3 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: 415 Length adjustment: 33 Effective length of query: 472 Effective length of database: 382 Effective search space: 180304 Effective search space used: 180304 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