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 GFF3783 HP15_3725 PTS system, fructose-specific IIBC component
Query= TCDB::Q3JZE2 (103 letters) >FitnessBrowser__Marino:GFF3783 Length = 587 Score = 94.7 bits (234), Expect = 1e-24 Identities = 46/100 (46%), Positives = 69/100 (69%), Gaps = 1/100 (1%) Query: 2 KIVGVAACTVGIAHTYIAQEKLENASKAAGHDVKIETQGTIGIENQLTSEEIAAADIVLL 61 +IV V AC G+AHT++A E L A+++AGH +++ETQG++G ++ LT EEIAAAD+V+L Sbjct: 128 RIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAADVVIL 187 Query: 62 AVDVKIAGEERFEGKKVVKVPTEVAIKSPNKLIAKLVEVA 101 A D+++ RF GK+V + T A+K P I +E A Sbjct: 188 ACDIEV-DPGRFSGKRVWRTSTGAALKKPADTIRDALEQA 226 Score = 52.0 bits (123), Expect = 1e-11 Identities = 27/97 (27%), Positives = 54/97 (55%), Gaps = 2/97 (2%) Query: 1 MKIVGVAACTVGIAHTYIAQEKLENASKAAGHDVKIETQGTIG-IENQLTSEEIAAADIV 59 M ++ V AC G+A ++A LE A+ G V +T+G G +N+ + I AD+V Sbjct: 1 MNLIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLV 60 Query: 60 LLAVDVKIAGEERFEGKKVVKVPTEVAIKSPNKLIAK 96 + AV + + + + GK+++++P A+ P+ ++ + Sbjct: 61 IAAVGIPV-NLDVYAGKRLLQIPVTAALPDPDAILTR 96 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: 110 Number of extensions: 5 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: 2 Length of query: 103 Length of database: 587 Length adjustment: 23 Effective length of query: 80 Effective length of database: 564 Effective search space: 45120 Effective search space used: 45120 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