Align Leucine/isoleucine/valine ABC transporter,permease component (characterized, see rationale)
to candidate RR42_RS16970 RR42_RS16970 ABC transporter ATP-binding protein
Query= uniprot:G8ALI9 (505 letters) >FitnessBrowser__Cup4G11:RR42_RS16970 Length = 386 Score = 257 bits (657), Expect = 4e-73 Identities = 158/348 (45%), Positives = 205/348 (58%), Gaps = 49/348 (14%) Query: 156 VVVALAFPFT--PLADRQLLDIGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYS 213 +++AL PF L + + L YIML GLNIVVG AGLLDLGY+AFYAVGAY Sbjct: 30 LIIALCAPFLVQTLGGNYWVRVLDFALIYIMLALGLNIVVGFAGLLDLGYIAFYAVGAYM 89 Query: 214 YALL-----AHYFGF-----------SFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAI 257 ALL A+ F + S W LPLA +AA GVLLG P L+LRGDY AI Sbjct: 90 MALLGSPHLANQFEWIHQLFPNGLHLSMWFVLPLAVLVAATFGVLLGAPTLKLRGDYLAI 149 Query: 258 VTLGFGEIIRIILINW---YQFTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGL 314 VTLGFGEIIRI L N T GP GI+ + FG DF+++ HE+FGL Sbjct: 150 VTLGFGEIIRIFLNNLDRPLNITNGPKGITAVDPVHIFGF-DFSKS--------HEIFGL 200 Query: 315 EFSPLHRIIFLYYLILVLALVVNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKL 374 +F+P + YYL++VL + + +R++ +GRA+ A+RED+IA ++GIN N+KL Sbjct: 201 KFTP---VFMYYYLLVVLVIAIVFICLRLQNSRIGRAFVAIREDEIAAKAMGINTRNIKL 257 Query: 375 AAFAIAAMFGGFAGSFFATRQGFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVI 434 AFA+ A FGG +G+ F QGF+SPESF ES ILAIVVLGGMG GV++ L++ Sbjct: 258 LAFAMGASFGGASGAVFGAFQGFVSPESFVLWESIYILAIVVLGGMGHIPGVILGGILLV 317 Query: 435 GLPEAFRELAD----------------YRMLAFGMGMVLIMLWRPRGL 466 G E R +A+ R L FG+ +V +ML+RP GL Sbjct: 318 GFQELLRAVAEPAQNMIFGHTIVDAEVLRQLLFGLALVGVMLYRPAGL 365 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: 584 Number of extensions: 38 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: 1 Length of query: 505 Length of database: 386 Length adjustment: 32 Effective length of query: 473 Effective length of database: 354 Effective search space: 167442 Effective search space used: 167442 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