Align Fructose import permease protein FruG (characterized)
to candidate SMc02772 SMc02772 sugar ABC transporter permease
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__Smeli:SMc02772 Length = 324 Score = 165 bits (417), Expect = 2e-45 Identities = 109/315 (34%), Positives = 166/315 (52%), Gaps = 14/315 (4%) Query: 12 PKKGFKLDRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHAYLIILAVAMTL 71 PKKG + + TL +++ +L +++G A + IS+L A ILAV T Sbjct: 13 PKKGVSILFGL--TLVGLLV-VLWLLLGLAT-NAFWTPNNISNLLRQGAMTAILAVGQTF 68 Query: 72 PILTGGIDLSVGAIVAITAVVGLKLANAGVPAFLVMIIMLLIGAVFGLLAGTLIEEFNMQ 131 I+T GIDLSVGA+V T+V+ L AGVP +L +I L IG + G I + Sbjct: 69 VIITAGIDLSVGAVVGFTSVIVAWLLAAGVPLWLAIIATLAIGVLIGAFHAFGIVRMGLP 128 Query: 132 PFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISNDLSFNVGVIIA 191 PFI TL+T+ RG+ +I+ S + F+ S + P + + Sbjct: 129 PFIITLATLTSLRGIGLLITNGSTISITNDAFTTFSRA-DFLGIPSL---------FWMV 178 Query: 192 LVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSATLAALASIVYT 251 +VV + YVFLH +R GR ++A+G + +A L G+ V RT Y+ Y+ S+T AA ++ Sbjct: 179 IVVAIPAYVFLHLSRFGRYLFAVGSNSEAARLSGVNVNRTIYLAYILSSTCAAFVGLLLA 238 Query: 252 ANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSILDPLTSDFGVPA 311 + IG T GWEL A+AS VIGGT + G G V G +LG+ + + ++ + V + Sbjct: 239 SRIGIGNATQAEGWELQAIASSVIGGTSLFGAVGSVHGPLLGAFILATINNGANLLNVNS 298 Query: 312 EWTTIVIGLMILVFV 326 W I+ GL+I+V V Sbjct: 299 FWQRIITGLLIIVIV 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: 268 Number of extensions: 13 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: 340 Length of database: 324 Length adjustment: 28 Effective length of query: 312 Effective length of database: 296 Effective search space: 92352 Effective search space used: 92352 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