Align Ribose import permease protein RbsC (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 190 bits (482), Expect = 5e-53 Identities = 105/301 (34%), Positives = 174/301 (57%), Gaps = 2/301 (0%) Query: 17 LMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSV 76 L +Q LIA + I + +P F T++N N+++ +++ +MA+G+T V+++ +DLSV Sbjct: 13 LAKQGILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSV 72 Query: 77 GSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLL 136 GS+++ + V + ++ +A+ A A+ +GA+ G +V ++ + I TL M+ Sbjct: 73 GSMMSFSTIVVLDLHD-KLGPTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSA 131 Query: 137 LRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLG 196 + G+T+ Y+ G ++ E F FG G LG+ TP+ I + +L T G Sbjct: 132 IHGLTLTYSGGKNMDIADKEGT-WFAIFGQGNILGIQTPILIFIALAALLGIILAKTPFG 190 Query: 197 RYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELD 256 R +YA+GGN A SGI ++ + Y + L + AG+I+ +R +Q T G G EL+ Sbjct: 191 RKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVGQGLELE 250 Query: 257 AIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLV 316 +AAV+LGG SL GG G I T+IG LILGF+ NGL L+G+ Q +V ++I+LAV + Sbjct: 251 VLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILAVWL 310 Query: 317 D 317 D Sbjct: 311 D 311 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: 235 Number of extensions: 7 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: 324 Length adjustment: 28 Effective length of query: 293 Effective length of database: 296 Effective search space: 86728 Effective search space used: 86728 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