Align ABC transporter for L-Lysine, permease component 2 (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= reanno::pseudo5_N2C3_1:AO356_09910 (229 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 120 bits (302), Expect = 2e-32 Identities = 69/200 (34%), Positives = 116/200 (58%), Gaps = 9/200 (4%) Query: 20 TLELVAIAVIAGLLLAIPLGIARSSRLWQVRALPYAYIFFFRGTPLLVQLFLVYYGLAQF 79 TL L AIA I G + + + +AR+S + VR YI F+GTPLL+QLFLV++G Sbjct: 19 TLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQGTPLLMQLFLVFFG---- 74 Query: 80 DAVRSSALWPYLRDPFWCATVTMTLHTAAYIAEILRGAIQAIPKGEIEAARALGMSRPKA 139 + + +P+ A + +TL+ +A++ EI RG IQA+P+G+ EAA ALG+ P Sbjct: 75 -----ATVMGLDLNPWAAAALGLTLNASAFLGEIWRGCIQAVPRGQWEAASALGLRYPGL 129 Query: 140 LFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGMARTIIARTYLPVEIFFAA 199 + Y++LP+A ++ +P ++ ++K+++LA+ + ELT + + T+ P +F Sbjct: 130 MRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTELTRAGQIVNNATFQPFLVFGIV 189 Query: 200 GMFYLLMSFLLVQGFKQLER 219 + Y LM + L +LER Sbjct: 190 AVLYFLMCWPLSLLSARLER 209 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: 137 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: 216 Length adjustment: 22 Effective length of query: 207 Effective length of database: 194 Effective search space: 40158 Effective search space used: 40158 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: 45 (21.9 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