Align Ribose import permease protein RbsC (characterized)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= SwissProt::P0AGI1 (321 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 171 bits (433), Expect = 2e-47 Identities = 110/309 (35%), Positives = 167/309 (54%), Gaps = 17/309 (5%) Query: 22 SLIALLVLIAIVST----LSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVG 77 SL+ L+VL+ V L FF+ L ILQQ + I+A +LVILT+GIDLSVG Sbjct: 41 SLVPLIVLVLSVIVFGLLLGSKFFSPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVG 100 Query: 78 SLLALTGAVAASIV---GIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMM 134 +++ L+ V G+ VAVA L G G + G +VA+ ++ FI TL M Sbjct: 101 AIMVLSSVVMGQFTFRYGLPPE--VAVACGLICGTICGFINGWLVARMKLPPFIVTLGMW 158 Query: 135 LLLRGVTMVYTNGSPVNTG-FTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAW-----Y 188 ++ +Y+ + + A L FG + + V+ G++F+ Y Sbjct: 159 QIVLASNFLYSANETIRSQTIAAEAPLLQLFG--EKIKIGGAVFTYGVIFMVILVVLLAY 216 Query: 189 MLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPT 248 +L HT GR++YA+G + A LSG+ V ++ I VY L GL+ + AG + R+ S PT Sbjct: 217 VLRHTAWGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIGSVSPT 276 Query: 249 AGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAV 308 +G +++I AVV+GG SL GG+G I+GT GALI+G GL LLG + + ++ + Sbjct: 277 SGQLANIESITAVVIGGISLFGGRGSILGTFFGALIVGVFTLGLRLLGADAQWTYLLIGL 336 Query: 309 VILLAVLVD 317 +I+ AV VD Sbjct: 337 LIIAAVAVD 345 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: 262 Number of extensions: 16 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: 353 Length adjustment: 28 Effective length of query: 293 Effective length of database: 325 Effective search space: 95225 Effective search space used: 95225 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: 49 (23.5 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