Align PTS system, fructose-specific, IIB subunnit, component of Fructose Enzyme II complex (IIAFru - IIBFru - IICFru) (based on homology) (characterized)
to candidate WP_017177510.1 A1QA_RS0103340 PTS transporter subunit EIIA
Query= TCDB::D2RXA4 (150 letters) >NCBI__GCF_000295095.1:WP_017177510.1 Length = 700 Score = 95.1 bits (235), Expect = 2e-24 Identities = 53/116 (45%), Positives = 74/116 (63%), Gaps = 2/116 (1%) Query: 4 VAVTSCPTGIAHSQMAAENLEQTATDRGHEIDVEVQGAMGQENELSSDAIAEADAVIIAA 63 V TSCPTGIAH+ MAAE LEQ DRG + +E QG+ G+ + L + IA ADAV+ A Sbjct: 201 VGATSCPTGIAHTFMAAEALEQAGKDRGITVRIEGQGS-GKIDALDPEVIARADAVVFAH 259 Query: 64 DTSV-NQDRFEGKPVVTAPVKDAVNDVEDLLERAIAAADGETSTADSAQSEGAADA 118 D + ++RF GKPV+ VK AVND L+++A+AAAD ++ A E + ++ Sbjct: 260 DLPIKGRERFAGKPVIDVGVKAAVNDAGSLVDKALAAADDPSAARVPAGGESSEES 315 Lambda K H 0.307 0.122 0.323 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: 185 Number of extensions: 4 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: 150 Length of database: 700 Length adjustment: 27 Effective length of query: 123 Effective length of database: 673 Effective search space: 82779 Effective search space used: 82779 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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