Align PTS system, fructose-specific, IIA 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 BWI76_RS27580 BWI76_RS27580 PTS fructose transporter subunit IIA
Query= TCDB::Q3JZE3 (149 letters) >FitnessBrowser__Koxy:BWI76_RS27580 Length = 156 Score = 110 bits (275), Expect = 1e-29 Identities = 59/149 (39%), Positives = 88/149 (59%), Gaps = 1/149 (0%) Query: 1 MEARDAIKRKLIKTNMNVTTKDEAFSELVSLLKNEGFVSDEGGFIKDIYLRESEGQTGIG 60 M+ + K + +M+ T K EA EL LL+ +G +S FI+D++ RESEG TG Sbjct: 1 MDITRILNTKRVLLDMHATNKAEAIEELTDLLQKDGAISCRETFIQDVWQRESEGSTGFE 60 Query: 61 NYIAIPHGKSSHVTEPAVVIGINSSEIPWETLDDNGVKVIVLFAVGNDSIAAQEHLKILS 120 N+IAIPHGKSS V + IG +I WETLD + V+ I+LFAV + H+++LS Sbjct: 61 NHIAIPHGKSSAVVNTTLAIGRTRQDIAWETLDGSQVRCIILFAVRLED-QNTTHIRLLS 119 Query: 121 LFARKLGNDQIVEKLINAKNEDDVIEAFS 149 A L +D I+E+L+ + +I+ F+ Sbjct: 120 QVAGALADDDIIEQLLKETSPQRIIDLFN 148 Lambda K H 0.314 0.134 0.365 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: 69 Number of extensions: 5 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: 149 Length of database: 156 Length adjustment: 17 Effective length of query: 132 Effective length of database: 139 Effective search space: 18348 Effective search space used: 18348 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 43 (21.2 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