Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate GFF3909 PGA1_65p00120 putative amino-acid ABC transporter, permease protein
Query= reanno::pseudo5_N2C3_1:AO356_09910 (229 letters) >FitnessBrowser__Phaeo:GFF3909 Length = 224 Score = 120 bits (302), Expect = 2e-32 Identities = 77/212 (36%), Positives = 120/212 (56%), Gaps = 10/212 (4%) Query: 10 LPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFRGTPLLVQL 69 +P L LTL + +A++ L+LA L + R R+ + L +I FFRGTPLLVQL Sbjct: 13 VPVLLSYVPLTLFMAVVAMVLALVLASLLAVERVLRIPVLDQLVVLFISFFRGTPLLVQL 72 Query: 70 FLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAIPKGEIEAA 129 FL YYGL Q +V + + A + +TLH AAY+AE +R AI + + + EAA Sbjct: 73 FLFYYGLPQVLSVLTQI------NGVSAAIMGLTLHFAAYMAESIRAAILGVDRSQWEAA 126 Query: 130 RALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGMARTIIART 189 +++GM+R + + I+LP+AARI P N I M+K ++LA T+ + E+ G + A + Sbjct: 127 QSIGMTRGQMMRRIVLPQAARIAAPTLVNYFIDMIKGTSLAFTLGVTEMMGATQKEAAGS 186 Query: 190 YLPVEIFFAAGMFYLLMSFLLVQGFKQLERWL 221 +L E F + Y ++LV+ ++R L Sbjct: 187 FLYFEAFLVVAVIY----WILVEALSLVQRRL 214 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: 125 Number of extensions: 6 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: 224 Length adjustment: 22 Effective length of query: 207 Effective length of database: 202 Effective search space: 41814 Effective search space used: 41814 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