Align Fructose import permease protein FrcC (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Keio:17810 Length = 321 Score = 181 bits (460), Expect = 2e-50 Identities = 104/302 (34%), Positives = 171/302 (56%), Gaps = 9/302 (2%) Query: 53 IVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVL 112 ++ +L LIA L FF+ + ILQQ ++ I+ TLVILT+GIDLSVG+++ L Sbjct: 23 LIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82 Query: 113 SSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASN 172 + + ++V L +GA G + G +VA+ ++ FI TL M ++ Sbjct: 83 TGAVAASIV-GIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLLLRGVT 141 Query: 173 FLYSANETIRAQDISANASILQFFGQNFRIG--NAVFTYGVVVMVLLVCLLWYVLNRTAW 230 +Y+ + + NA + +FG +G V+ G+V + WY+L+ T Sbjct: 142 MVYTNGSPVNT-GFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAA-----WYMLHHTRL 195 Query: 231 GRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANI 290 GRY+YA+G + A +L+G+NV ++ I +Y+L GL+ +LAG + R+ S PTAG + Sbjct: 196 GRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYEL 255 Query: 291 ESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVA 350 ++I AVV+GG SL GG+G I+G L GALI+G + GL L+G + ++ ++I++AV Sbjct: 256 DAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVL 315 Query: 351 ID 352 +D Sbjct: 316 VD 317 Lambda K H 0.327 0.141 0.420 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: 356 Number of extensions: 23 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: 360 Length of database: 321 Length adjustment: 28 Effective length of query: 332 Effective length of database: 293 Effective search space: 97276 Effective search space used: 97276 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 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