Align Ribose import permease protein RbsC (characterized)
to candidate BWI76_RS07245 BWI76_RS07245 ABC transporter
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Koxy:BWI76_RS07245 Length = 343 Score = 221 bits (563), Expect = 2e-62 Identities = 122/289 (42%), Positives = 177/289 (61%), Gaps = 21/289 (7%) Query: 44 NNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLALTGAVAASIVG----------- 92 N L I+ Q ++ I+AVG+T VI+T+GIDLS GS++AL VAAS+ Sbjct: 59 NRLILIVLQVAIIGIIAVGVTQVIITTGIDLSSGSVIALAAVVAASLAQTSDSLSPMFPS 118 Query: 93 -IEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTMVYTNGSPVN 151 + + A++ + A + +G G G +V + + FIATL MM+ RG+ YT G+P++ Sbjct: 119 LVNMPAIIPIGAGIGVGLLCGLTNGFLVTRTGIPPFIATLGMMVSARGLAQYYTQGNPIS 178 Query: 152 TGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRL 211 +D F G G PV I +V L HTR G+Y+YA+GGN + ++ Sbjct: 179 F----LSDSFTAIGQGA-----MPVIIFFVVAAVFHIALKHTRYGKYVYAIGGNMTSAKV 229 Query: 212 SGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGG 271 SGINVNK +IVY++ G L+ LAG++ AR+SS Q + G YELDAIAA V+GG+SL GG Sbjct: 230 SGINVNKYLVIVYAIAGALSGLAGVVLAARVSSGQSSMGMSYELDAIAAAVIGGSSLMGG 289 Query: 272 KGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVDNKK 320 GRI GTLIGA+ILG + +G +GV +Y Q I+K ++I+ AV +D ++ Sbjct: 290 VGRITGTLIGAMILGLIKSGFTFVGVDAYVQDIIKGIIIVAAVTIDMRR 338 Lambda K H 0.324 0.139 0.393 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: 290 Number of extensions: 11 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: 321 Length of database: 343 Length adjustment: 28 Effective length of query: 293 Effective length of database: 315 Effective search space: 92295 Effective search space used: 92295 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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