Align Fructose import permease protein FruG (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 150 bits (379), Expect = 4e-41 Identities = 98/320 (30%), Positives = 166/320 (51%), Gaps = 21/320 (6%) Query: 23 IPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTLPILTGGIDLSV 82 I +++ I++ ++ L ++ L ++ + I ++V MTL ILT GIDLSV Sbjct: 4 IAKFQSLIALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSV 63 Query: 83 GAIVAITAVVGLKLANAGVPAFLVMI---------IMLLIGAVFGL--LAGTLIEEFNMQ 131 G+I+A+ V L G+ + + ++L +G FGL G I F + Sbjct: 64 GSILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVP 123 Query: 132 PFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIA 191 PF+ATL+ + +ARGL + + G DF+F+ L + V I Sbjct: 124 PFVATLAMLTIARGLTMLWTGGFPINGLGEDFAFLGT----------GWFLGIPMPVWIT 173 Query: 192 LVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYT 251 V+V + T+ GR +YAIGG+ +A L G+ + R + +Y + LAA+ ++ T Sbjct: 174 AVIVALAVLLTKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVT 233 Query: 252 ANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPA 311 + + SA+ G+ +ELDA+A+VVIGGT ++GG G ++G+VLG ++ +L+ V Sbjct: 234 SRLDSAQPNAGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSP 293 Query: 312 EWTTIVIGLMILVFVVLQRA 331 W +V G +IL+ VV+ +A Sbjct: 294 FWQQVVKGAVILLAVVIDKA 313 Lambda K H 0.327 0.142 0.400 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: 257 Number of extensions: 13 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: 340 Length of database: 318 Length adjustment: 28 Effective length of query: 312 Effective length of database: 290 Effective search space: 90480 Effective search space used: 90480 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