Align ABC transporter for L-Lysine, periplasmic substrate-binding component (characterized)
to candidate GFF1142 PGA1_c11570 putative nopaline-binding periplasmic protein
Query= reanno::pseudo5_N2C3_1:AO356_09900 (251 letters) >FitnessBrowser__Phaeo:GFF1142 Length = 236 Score = 144 bits (364), Expect = 1e-39 Identities = 84/241 (34%), Positives = 133/241 (55%), Gaps = 13/241 (5%) Query: 6 KFLLAAAVSLVFSANAMAADKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMKVE 65 K L+ +L +A AD +++G E AYPP+N + GQV GF++++GD LC + +++ Sbjct: 2 KSLILGTAALALTAGIAMADTVRLGTEGAYPPYNFLNDDGQVDGFERELGDELCKRAELD 61 Query: 66 CEVVTSDWDGIIPALNAKKFDFLISSLSITEERKQAVDFTDPYYSNKLQFIAPKSAEFKT 125 CE VT+DWD IIP L + +D +I+ +SIT ERK+ V+FT Y A SA+ Sbjct: 62 CEWVTNDWDSIIPNLLSGNYDTIIAGMSITAERKEVVNFTTGYTRPSPSAYAAMSADV-- 119 Query: 126 DKDSLKGKVIGAQRATLAGTWLEDELGSDITTKLYDTQENAYLDLTSGRVDAILADKYVN 185 + V+ AQ +T+ + + T + T + + +G VDA++ADK Sbjct: 120 ---DVNSAVVAAQASTIQAAHV---ASTGATLVEFPTPDETVAAVKAGEVDAVMADK--- 170 Query: 186 YDWLKTEAGRA-YEFKGDPVVESDKIGIAVRKGDNELRNKLNAALKEIVADGTYKKINDK 244 D+L G EF D V+ D IG+A RK D+ELR K + A++ + ADG+ + +K Sbjct: 171 -DFLIPIVGETEMEFVADDVLLGDGIGMAFRKSDDELRGKFDVAIESMKADGSLNALLEK 229 Query: 245 Y 245 + Sbjct: 230 W 230 Lambda K H 0.316 0.133 0.381 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: 157 Number of extensions: 6 Number of successful extensions: 3 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: 251 Length of database: 236 Length adjustment: 23 Effective length of query: 228 Effective length of database: 213 Effective search space: 48564 Effective search space used: 48564 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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