Align PTS system, fructose-specific, IIC component, component of D-allose/D-ribose transporting Enzyme II complex (Fru2; IIA/IIB/IIC) (Patron et al. 2017). This system is similar to Frz of E. coli (TC#4.A.2.1.9) which is involved in environmental sensing, host adaptation and virulence (characterized)
to candidate PP_0795 PP_0795 fructose PTS permease - IIBC component
Query= TCDB::Q3JZE4 (367 letters) >FitnessBrowser__Putida:PP_0795 Length = 580 Score = 214 bits (546), Expect = 4e-60 Identities = 125/353 (35%), Positives = 201/353 (56%), Gaps = 13/353 (3%) Query: 6 KKANFKGHLLTAISYLIPIVCGAGFLVAIGMAMGGRAQDALVIGNFSFWDTMATMGGKAL 65 +K HLLT +S+++P+V G L+A+ G A + + +GG+A Sbjct: 235 EKTGVYKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAYKEAG----TLPAALMQIGGEAA 290 Query: 66 GLLPVIIATG-IAFSIAGKPGIAPGFVVGLIANAISAGFIGGILGGYIAGFIALGILKNV 124 L V + G IA+SIA +PG+APG + GL+A+ + AGFIGGI+ G++AG+ A I + Sbjct: 291 FKLMVPLLAGYIAWSIADRPGLAPGMIGGLLASTLGAGFIGGIVAGFLAGYSAKAIARWA 350 Query: 125 KVPNWAKGLMPTLIVPFFAALLSSLIMIYLIGGPISAFTGWLTDFLKSLGNTSNLVMGAV 184 ++P+ + L P LI+P A+L + L+MIY++G P++A LT FL S+G T+ +++G + Sbjct: 351 RLPSSLEALKPILIIPLLASLFTGLVMIYVVGQPVAAMLEGLTHFLDSMGTTNAILLGLL 410 Query: 185 IGVLSGVDLGGPLNKTVYAFVLTLQAEGVKEPLTALQLVNTATPVGFGLAYFIAKLFKKN 244 +G + VDLGGP+NK YAF + L A P+ A P+G G+A F+A + Sbjct: 411 LGGMMCVDLGGPINKAAYAFSVGLLASSSYAPMAATMAAGMVPPIGLGIATFLA----RR 466 Query: 245 IYTNDEIETLKSAVPMGIVNIVEGVIPIVMNNLMPAILAIGVGGAVGGAVSMTMGADSAV 304 + E E K+A+ +G+ I EG IP + + I A GGA+ GA+SM G Sbjct: 467 KFAQSEREAGKAALALGLCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMYFGCKLMA 526 Query: 305 PFGG--ILMIP-TMTRPIAGICGLLSNILVTGLVYSLAKKPVDRNEVTIVSAE 354 P GG +L+IP + + + +++ LVT +VY++ KK +R E+ + A+ Sbjct: 527 PHGGLFVLLIPNAINHALLYLLAIVAGSLVTAVVYAVIKKS-ERVELAVAPAK 578 Lambda K H 0.323 0.143 0.415 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: 609 Number of extensions: 40 Number of successful extensions: 5 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: 367 Length of database: 580 Length adjustment: 33 Effective length of query: 334 Effective length of database: 547 Effective search space: 182698 Effective search space used: 182698 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 51 (24.3 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