Align Fructose import permease protein FrcC (characterized)
to candidate BPHYT_RS20745 BPHYT_RS20745 ribose ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__BFirm:BPHYT_RS20745 Length = 341 Score = 214 bits (545), Expect = 3e-60 Identities = 125/306 (40%), Positives = 177/306 (57%), Gaps = 8/306 (2%) Query: 56 VLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIMVLSSV 115 ++ L+ F F M ILQ A+ G++ A T VI+T GIDLSVG +M ++V Sbjct: 38 LILLLVFFSFASPAFMQMDNMLGILQATAVNGVLAIACTFVIITGGIDLSVGTLMTFTAV 97 Query: 116 IMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLASNFLY 175 I G F + P V+ +G GA+CG ++GTL A+MK+PPFI TLGM ++ + + Sbjct: 98 ICGVFLTYWHLPMWTGVLAAIGTGAICGTVSGTLTAKMKIPPFIATLGMMMLLKGLSLVV 157 Query: 176 SANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYV----LNRTAWG 231 SA++ I D Q+ IG+ + + V VL++ L V LNRTA G Sbjct: 158 SADKPIYFTDTEN----FYMISQDSLIGDLLPSLPVPNAVLILFFLAVVSSITLNRTALG 213 Query: 232 RYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANIE 291 RY +A+G + EA +L+GVNV R I+IY LSG IC +AG + R+ S P GQ +E Sbjct: 214 RYTFALGSNEEAVRLSGVNVDRWKIAIYGLSGAICGIAGLLIASRLNSAQPALGQGYELE 273 Query: 292 SITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVAI 351 +I AVVIGG SL GG G+I+G + GA I+ V + GLR+M +W ++ GL+II+AV Sbjct: 274 AIAAVVIGGTSLSGGAGTILGTIIGAFIMSVLTNGLRIMSVAQEWQIVVTGLIIILAVYG 333 Query: 352 DQWIRK 357 D RK Sbjct: 334 DILRRK 339 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: 379 Number of extensions: 26 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: 360 Length of database: 341 Length adjustment: 29 Effective length of query: 331 Effective length of database: 312 Effective search space: 103272 Effective search space used: 103272 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