Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate BPHYT_RS24010 BPHYT_RS24010 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09910 (229 letters) >FitnessBrowser__BFirm:BPHYT_RS24010 Length = 250 Score = 178 bits (452), Expect = 7e-50 Identities = 92/217 (42%), Positives = 138/217 (63%) Query: 2 NWDVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFR 61 ++D + + +L TL L ++I G LL++ + R S W AYI FR Sbjct: 4 DFDFLFDTIKQLLAAVPTTLGLFFCSLILGGLLSLVIVTMRVSPHWLPNRFARAYILVFR 63 Query: 62 GTPLLVQLFLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAI 121 G+PLL+Q+FLVYYG+ QF +R S LWP LR+P+ CA +++ L TA Y AEI+RG + A+ Sbjct: 64 GSPLLIQMFLVYYGMGQFGVIRESFLWPVLREPYMCAVLSLALCTAGYTAEIIRGGLMAV 123 Query: 122 PKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGM 181 P G+IEA ++G+S L ++ P A R LPAYS E +L++K++ALAS VT+ E+TG+ Sbjct: 124 PVGQIEAGYSIGLSGFALLRRVIGPIALRQCLPAYSTEAVLLVKSTALASLVTVWEVTGV 183 Query: 182 ARTIIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLE 218 A+ II +TY E+F A + YL ++F++V+ LE Sbjct: 184 AQQIIQQTYRTTEVFICAALIYLFLNFVIVRLLGMLE 220 Lambda K H 0.331 0.141 0.434 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: 156 Number of extensions: 5 Number of successful extensions: 2 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: 229 Length of database: 250 Length adjustment: 23 Effective length of query: 206 Effective length of database: 227 Effective search space: 46762 Effective search space used: 46762 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 46 (22.3 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