Align Ribose import permease protein RbsC (characterized)
to candidate 18114 b4086 D-allose transporter subunit (NCBI)
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Keio:18114 Length = 326 Score = 217 bits (553), Expect = 3e-61 Identities = 123/294 (41%), Positives = 185/294 (62%), Gaps = 6/294 (2%) Query: 26 LLVLIAIVSTLSPNFF-TINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLALTG 84 L +++AI +LSP +F T NN+ I Q+SV ++ +G IL +GIDLSVG++LAL+G Sbjct: 32 LAIIVAIFGSLSPEYFLTTNNITQIFVQSSVTVLIGMGEFFAILVAGIDLSVGAILALSG 91 Query: 85 AVAASIVGIEVNA-LVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVTMV 143 V A ++ V+ L A+ + +G A+GA+ G +V + FI TL + RG+T+V Sbjct: 92 MVTAKLMLAGVDPFLAAMIGGVLVGGALGAINGCLVNWTGLHPFIITLGTNAIFRGITLV 151 Query: 144 YTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGRYIYALG 203 ++ + V GF+ + F F +G+P PV IV L W++ RLGR IYALG Sbjct: 152 ISDANSVY-GFSFD---FVNFFAASVIGIPVPVIFSLIVALILWFLTTRMRLGRNIYALG 207 Query: 204 GNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVL 263 GN+ + SGI+V ++V+ + G+ A LAG++ ARL +A+P AG G+E AIA+ ++ Sbjct: 208 GNKNSAFYSGIDVKFHILVVFIISGVCAGLAGVVSTARLGAAEPLAGMGFETYAIASAII 267 Query: 264 GGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVD 317 GGTS GGKGRI +IG LI+G +NNGLN+L V +YYQ++V +I+ AV +D Sbjct: 268 GGTSFFGGKGRIFSVVIGGLIIGTINNGLNILQVQTYYQLVVMGGLIIAAVALD 321 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: 261 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 321 Length of database: 326 Length adjustment: 28 Effective length of query: 293 Effective length of database: 298 Effective search space: 87314 Effective search space used: 87314 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: 48 (23.1 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