Align Ribose import permease protein RbsC (characterized)
to candidate CCNA_00904 CCNA_00904 inositol ABC transport system, permease protein IatP
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Caulo:CCNA_00904 Length = 332 Score = 236 bits (603), Expect = 4e-67 Identities = 136/314 (43%), Positives = 192/314 (61%), Gaps = 9/314 (2%) Query: 10 RYFTKAWLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILT 69 R+ A+ + ++++ LL+L+A+ + F T N NIL + S+ I+AVGMT VIL Sbjct: 16 RFDLLAFARKHRTILFLLLLVAVFGAANERFLTARNALNILSEVSIYGIIAVGMTFVILI 75 Query: 70 SGIDLSVGSLLALTGAVAASIVGIEVNA-----LVAVAAALALGAAIGAVTGVIVAKGRV 124 GID++VGSLLA AA +V V L+A+ + +G A G V G V V Sbjct: 76 GGIDVAVGSLLAFASIAAAYVVTAVVGDGPATWLIALLVSTLIGLAGGYVQGKAVTWLHV 135 Query: 125 QAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFL 184 AFI TL M + RG T++ +G P++ GF D + W+G G L +P PV I +V Sbjct: 136 PAFIVTLGGMTVWRGATLLLNDGGPIS-GFN---DAYRWWGSGEILFLPVPVVIFALVAA 191 Query: 185 AAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSS 244 A L +TR GR +YA+GGN A RLSG+NV+ I VY++ G LA L+G + ARL S Sbjct: 192 AGHVALRYTRYGRQVYAVGGNAEAARLSGVNVDFITTSVYAIIGALAGLSGFLLSARLGS 251 Query: 245 AQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMI 304 A+ AGTGYEL IA+VV+GG SL GG G + GT++GAL++G L+NGL +L V+SY Q + Sbjct: 252 AEAVAGTGYELRVIASVVIGGASLTGGSGGVGGTVLGALLIGVLSNGLVMLHVTSYVQQV 311 Query: 305 VKAVVILLAVLVDN 318 V ++I+ AV D+ Sbjct: 312 VIGLIIVAAVAFDH 325 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: 15 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: 332 Length adjustment: 28 Effective length of query: 293 Effective length of database: 304 Effective search space: 89072 Effective search space used: 89072 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