Align Ribose import permease protein RbsC (characterized)
to candidate 16645 b2546 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Keio:16645 Length = 332 Score = 220 bits (561), Expect = 3e-62 Identities = 124/314 (39%), Positives = 190/314 (60%), Gaps = 8/314 (2%) Query: 8 GRRYFTKAWLMEQKSLIALLVLIAIV----STLSPNFFTINNLFNILQQTSVNAIMAVGM 63 G+ K ++ + I LLV+IAI+ S +P F ++NN N+L+ + I A M Sbjct: 11 GKSVSLKQFVSRHINEIGLLVVIAILYLVFSLNAPGFISLNNQMNVLRDAATIGIAAWAM 70 Query: 64 TLVILTSGIDLSVGSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGR 123 TL+I++ ID+SVG ++A A ++ EV VA L LGA +G + GV+ Sbjct: 71 TLIIISGEIDVSVGPMVAFVSVCLAFLLQFEVPLAVACLLVLLLGALMGTLAGVLRGVFN 130 Query: 124 VQAFIATLVMMLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVF 183 V +F+ATL + LRG+ + TN PV E D W G G+ LGVP IM ++F Sbjct: 131 VPSFVATLGLWSALRGMGLFMTNALPVPIDENEVLD---WLG-GQFLGVPVSALIMIVLF 186 Query: 184 LAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLS 243 ++ T GR ++A+GGN A +L GINV +++I++++L GLLA++ GI+ ARL Sbjct: 187 ALFVFISRKTAFGRSVFAVGGNATAAQLCGINVRRVRILIFTLSGLLAAVTGILLAARLG 246 Query: 244 SAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQM 303 S A G E D IAAVV+GGT+L+GG+G + GTL+G L++ + NGL LLG++S++Q Sbjct: 247 SGNAGAANGLEFDVIAAVVVGGTALSGGRGSLFGTLLGVLVITLIGNGLVLLGINSFFQQ 306 Query: 304 IVKAVVILLAVLVD 317 +V+ V+I++AVL + Sbjct: 307 VVRGVIIVVAVLAN 320 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: 225 Number of extensions: 10 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: 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