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 SMc01141 SMc01141 nitrogen regulatory IIA protein
Query= TCDB::Q3JZE3 (149 letters) >FitnessBrowser__Smeli:SMc01141 Length = 154 Score = 53.9 bits (128), Expect = 1e-12 Identities = 32/88 (36%), Positives = 46/88 (52%), Gaps = 2/88 (2%) Query: 48 IYLRESEGQTGIGNYIAIPHGKSSHVTEPAVVIGINSSEIPWETLDDNGVKVIVLFAVGN 107 I RE G TG+GN IAIPHGK S++ + + + +E LDD V ++ L Sbjct: 47 ILQRERLGSTGVGNGIAIPHGKLSNLPSIVGIFARLDAPVDFEALDDQPVDLVFLLLAPE 106 Query: 108 DSIAAQEHLKILSLFARKLGNDQIVEKL 135 A +HLK LS AR L + +V ++ Sbjct: 107 G--AGADHLKALSRIARVLRDHDMVSRI 132 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: 47 Number of extensions: 2 Number of successful extensions: 1 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: 154 Length adjustment: 17 Effective length of query: 132 Effective length of database: 137 Effective search space: 18084 Effective search space used: 18084 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: 42 (20.8 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