Align Fructose import permease protein FrcC (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 184 bits (466), Expect = 4e-51 Identities = 109/315 (34%), Positives = 172/315 (54%), Gaps = 24/315 (7%) Query: 49 AVPLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGA 108 A+ ++ LVLSL L +F + +++QV++ + TLVILTAGIDLSVG+ Sbjct: 12 ALIILCLVLSL------LSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGS 65 Query: 109 IMVLSSVIMGQF----------TFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPF 158 I+ L + GF P +VI G+G+G G+ NG + R K+PPF Sbjct: 66 ILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVPPF 125 Query: 159 IVTLGMWQIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLV 218 + TL M I L++ I F G + +G + + V+V L Sbjct: 126 VATLAMLTIARGLTMLWTGGFPINGL-----GEDFAFLGTGWFLGIPMPVWITAVIVALA 180 Query: 219 CLLWYVLNRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIG 278 LL +T +GRYVYA+G + AA+L+G+N++R+ +++Y ++G + A+ G + R+ Sbjct: 181 VLL---TKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLD 237 Query: 279 SVSPTAGQFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTY 338 S P AG +++I AVVIGG SL GG+G+IMG + G +I+GV + GL L+ P W Sbjct: 238 SAQPNAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQ 297 Query: 339 LLIGLLIIIAVAIDQ 353 ++ G +I++AV ID+ Sbjct: 298 VVKGAVILLAVVIDK 312 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: 357 Number of extensions: 16 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: 318 Length adjustment: 28 Effective length of query: 332 Effective length of database: 290 Effective search space: 96280 Effective search space used: 96280 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