Align Ribose import permease protein RbsC (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__WCS417:GFF2365 Length = 325 Score = 276 bits (707), Expect = 4e-79 Identities = 150/303 (49%), Positives = 203/303 (66%), Gaps = 9/303 (2%) Query: 18 MEQKSLIALLVLIAIVSTLSPNFF-TINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSV 76 +++ L + +L+ +V S +F T N +IL+QTS+N I+AVGMT VILT GIDLSV Sbjct: 22 LDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSV 81 Query: 77 GSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLL 136 GS+LA G +A + L AV+A + GA +G V G +VA + F+ATL M+ + Sbjct: 82 GSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSI 141 Query: 137 LRGVTMVYTNGSPVNTGFTENADLFGWFGIGR--PLGVPTPVWIMGIVFLAAWYMLHHTR 194 RG+T + +GSP+ T+ D + GIG+ P+GVP + I +V L W +L +T Sbjct: 142 ARGMTFILNDGSPI----TDLPDAYLALGIGKIGPIGVP--IIIFAVVALIFWMVLRYTT 195 Query: 195 LGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYE 254 GRY+YA+GGNE + R SGI V K+ VY + GLLA LAG++ AR +SA P AG YE Sbjct: 196 YGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYE 255 Query: 255 LDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAV 314 LDAIAAVV+GGTSL+GG G IVGTL GAL++G +NNGLNLLGVSSYYQ + K ++I+ AV Sbjct: 256 LDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAV 315 Query: 315 LVD 317 L+D Sbjct: 316 LID 318 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: 278 Number of extensions: 12 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: 325 Length adjustment: 28 Effective length of query: 293 Effective length of database: 297 Effective search space: 87021 Effective search space used: 87021 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