Align PTS system, fructose-specific, IIB 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 Pf1N1B4_1144 PTS system, fructose-specific IIB component (EC 2.7.1.69) / PTS system, fructose-specific IIC component (EC 2.7.1.69)
Query= TCDB::Q3JZE2 (103 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1144 Length = 579 Score = 92.8 bits (229), Expect = 5e-24 Identities = 43/95 (45%), Positives = 67/95 (70%), Gaps = 1/95 (1%) Query: 2 KIVGVAACTVGIAHTYIAQEKLENASKAAGHDVKIETQGTIGIENQLTSEEIAAADIVLL 61 ++V V AC G+AHT++A E L+ A+K G+D+++ETQG++G N L++E IA AD+VLL Sbjct: 121 RLVAVTACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAEAIADADVVLL 180 Query: 62 AVDVKIAGEERFEGKKVVKVPTEVAIKSPNKLIAK 96 A D+++A ERF GKK+ + T +A+K + K Sbjct: 181 AADIEVA-TERFAGKKIYRCGTGIALKQAEATLNK 214 Score = 40.4 bits (93), Expect = 3e-08 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 1/101 (0%) Query: 1 MKIVGVAACTVGIAHTYIAQEKLENASKAAGHDVKIETQGTIGIENQLTSEEIAAADIVL 60 MK+ V AC G+ + + L+ A++ G +E E QL++ I AA+ VL Sbjct: 1 MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVVDAAHPERQLSAATIEAAEWVL 60 Query: 61 LAVDVKIAGEERFEGKKVVKVPTEVAIKSPNKLIAKLVEVA 101 L + RF GK+V + A++ ++ + VE A Sbjct: 61 LVTSAPV-DMSRFVGKRVFQSTPAQALQDVEAVLRRGVEEA 100 Lambda K H 0.311 0.128 0.332 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: 98 Number of extensions: 5 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 103 Length of database: 579 Length adjustment: 23 Effective length of query: 80 Effective length of database: 556 Effective search space: 44480 Effective search space used: 44480 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 (21.8 bits) S2: 46 (22.3 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