Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate PP_0226 PP_0226 sulfur compound ABC transporter - permease subunit
Query= reanno::pseudo5_N2C3_1:AO356_09910 (229 letters) >FitnessBrowser__Putida:PP_0226 Length = 222 Score = 128 bits (321), Expect = 1e-34 Identities = 75/214 (35%), Positives = 122/214 (57%), Gaps = 9/214 (4%) Query: 5 VIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFRGTP 64 +++ P L +GA T+ L + GL+L L + R S++ + L Y+ FFRGTP Sbjct: 8 LVVDSAPFLLKGAGYTVLLSVGGMFFGLVLGFALALMRLSKILPLNWLARVYVSFFRGTP 67 Query: 65 LLVQLFLVYYGLAQFDAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAIPKG 124 LLVQLF++Y+G+ Q DP + + ++L+ AAYI EILR AI +I +G Sbjct: 68 LLVQLFVIYFGMPQIGIEL---------DPIPASLIGLSLNMAAYICEILRAAISSIDRG 118 Query: 125 EIEAARALGMSRPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGMART 184 + EAA ++GM+R +A+ +LP+A R LP N I ++K +ALA+T+ + EL A+ Sbjct: 119 QWEAAASIGMTRVQAMRRAILPQALRTALPPLGNSFISLVKDTALAATIQVPELFRQAQL 178 Query: 185 IIARTYLPVEIFFAAGMFYLLMSFLLVQGFKQLE 218 I ART+ ++ A + Y ++ +L ++E Sbjct: 179 ITARTFEVFTMYVAVAVIYWVLCSILAHFQNRME 212 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: 129 Number of extensions: 4 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: 222 Length adjustment: 22 Effective length of query: 207 Effective length of database: 200 Effective search space: 41400 Effective search space used: 41400 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