Align Ribose import permease protein RbsC (characterized)
to candidate SM_b20854 SM_b20854 sugar uptake ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Smeli:SM_b20854 Length = 331 Score = 222 bits (566), Expect = 9e-63 Identities = 127/299 (42%), Positives = 185/299 (61%), Gaps = 8/299 (2%) Query: 22 SLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNA-IMAVGMTLVILTSGIDLSVGSLL 80 +L LVL+A+ + S +F T NL N+L+Q + A IMAVGM VILT GIDLSVGS++ Sbjct: 28 TLAIFLVLVAVATWWSDSFLTRGNLLNVLRQVASTAGIMAVGMLFVILTRGIDLSVGSVM 87 Query: 81 ALTGAVAA---SIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLL 137 AL + +++G A + + L GAA G VTG +A R+ +F+ +L MM + Sbjct: 88 ALGSVLTGYFCAMLGYGTGATIFLV--LLCGAACGLVTGGFIAYLRLPSFVMSLAMMAVA 145 Query: 138 RGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLGR 197 RG++++ + G P+ ++ F FG G LG+P PV +M +++A +L+ TR GR Sbjct: 146 RGLSLIISEGRPIP--LSDAGAAFSSFGSGFVLGIPQPVILMFAIYIAGGVVLNFTRFGR 203 Query: 198 YIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDA 257 I A+G NE A RLSGI V + + VY + GLLA LAGII +R G G EL+ Sbjct: 204 VITAIGSNEEAVRLSGIAVPRYIVAVYVISGLLAGLAGIIAASRTGVGSAQVGIGAELNV 263 Query: 258 IAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLV 316 IAAVV+GG SL GGKG ++ TL+GAL++G + N +NL GV Y+Q + +I++A+L+ Sbjct: 264 IAAVVIGGASLMGGKGGVINTLLGALVMGIITNIMNLAGVPGYHQQVYMGAIIVVAMLL 322 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: 272 Number of extensions: 14 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: 331 Length adjustment: 28 Effective length of query: 293 Effective length of database: 303 Effective search space: 88779 Effective search space used: 88779 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