Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate SMa0492 SMa0492 ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09910 (229 letters) >FitnessBrowser__Smeli:SMa0492 Length = 227 Score = 201 bits (510), Expect = 1e-56 Identities = 93/221 (42%), Positives = 149/221 (67%) Query: 1 MNWDVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFF 60 MN ++ +P++ G +T +L+ +++ G ++A+ L + R S W + Y + F Sbjct: 1 MNIGIVFDAIPRMLGGIVMTFQLLLLSLAIGTMIAVLLLLMRISGRWWLSWPAQFYTYVF 60 Query: 61 RGTPLLVQLFLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQA 120 RGTP+LVQ+F+VYYGL QF+ +R S WP LRDPF CA + ++L+T AY++EI RG + A Sbjct: 61 RGTPILVQIFIVYYGLPQFEWIRESIFWPILRDPFGCAILALSLNTGAYLSEIFRGGVLA 120 Query: 121 IPKGEIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTG 180 + +G +EA ALGMS YI P A RI LPAY NEVI ++K++ALAST+TL+++TG Sbjct: 121 VERGLLEAGAALGMSATHRFIYITTPLAIRIALPAYGNEVISLMKSTALASTITLVDMTG 180 Query: 181 MARTIIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLERWL 221 + RTI+A T+ P ++F + + Y+ +++++ + K+LE +L Sbjct: 181 IGRTIVAETFAPYQVFLSLAIVYVAITWIIQRSVKRLEVYL 221 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: 2 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: 227 Length adjustment: 23 Effective length of query: 206 Effective length of database: 204 Effective search space: 42024 Effective search space used: 42024 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