Align Fructose import permease protein FruG (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease
Query= SwissProt::Q8G845 (340 letters) >FitnessBrowser__WCS417:GFF2365 Length = 325 Score = 154 bits (388), Expect = 4e-42 Identities = 103/328 (31%), Positives = 174/328 (53%), Gaps = 18/328 (5%) Query: 3 TATANKVKAPKKGFKL--DRQMIPTLAAVVIFILMIIMGQALFGTYIRLGFISSLFIDHA 60 T TA AP+ +L DR +P L +++ ++M + + + I+ Sbjct: 5 TITAPVTAAPRNRLRLSLDRFGLP-LVFILLCVVMAFSSEYFMTWRNWMDILRQTSING- 62 Query: 61 YLIILAVAMTLPILTGGIDLSVGAIVAITAVVGLKLANAGVPAFLVMIIMLLIGAVFGLL 120 ILAV MT ILT GIDLSVG+I+A + +A G + + GA+ G++ Sbjct: 63 ---ILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVV 119 Query: 121 AGTLIEEFNMQPFIATLSTMFLARGLASIISTDSLTFPQGNDFSFISNVIKIIDNPKISN 180 G ++ ++ PF+ATL + +ARG+ I++ G+ + + + + KI Sbjct: 120 NGFMVANLSIPPFVATLGMLSIARGMTFILN-------DGSPITDLPDAYLALGIGKIG- 171 Query: 181 DLSFNVGVIIALVVVVFGYVFLHHTRTGRTIYAIGGSRSSAELMGLPVKRTQYIIYLTSA 240 V +II VV + ++ L +T GR +YA+GG+ SA G+ V++ + +Y+ S Sbjct: 172 --PIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSG 229 Query: 241 TLAALASIVYTANIGSAKNTVGVGWELDAVASVVIGGTIITGGFGYVLGSVLGSLVRSIL 300 LA LA +V +A SA GV +ELDA+A+VVIGGT ++GG G ++G++ G+L+ ++ Sbjct: 230 LLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVI 289 Query: 301 DPLTSDFGVPAEWTTIVIGLMILVFVVL 328 + + GV + + + GL I+VF VL Sbjct: 290 NNGLNLLGVSSYYQQVAKGL-IIVFAVL 316 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: 245 Number of extensions: 15 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 325 Length adjustment: 28 Effective length of query: 312 Effective length of database: 297 Effective search space: 92664 Effective search space used: 92664 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