Align PTS system fructose-specific EIIB component; EIIB-Fru; Fructose-specific phosphotransferase enzyme IIB component; EC 2.7.1.202 (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= SwissProt::D4GYE1 (158 letters) >FitnessBrowser__Keio:14863 Length = 658 Score = 79.0 bits (193), Expect = 1e-19 Identities = 42/107 (39%), Positives = 68/107 (63%), Gaps = 1/107 (0%) Query: 3 LVAVTSCPTGIAHSQMAAENLLQAGERLGHDIDVEVQGAMGTQDELASDAIAEADAVIIT 62 +V VT+CP GIAH+ MAAE L +AG +LG ++ VE QGA G + L +D + A A I Sbjct: 186 IVCVTACPAGIAHTYMAAEYLEKAGRKLGVNVYVEKQGANGIEGRLTADQLNSATACIFA 245 Query: 63 SDTSVSR-DRFDGKLVLKGTVKDGVNNAEAVVQKAVELAEAGKTGSV 108 ++ ++ +RF+G L V + + +AEA++Q+A+ L + +T +V Sbjct: 246 AEVAIKESERFNGIPALSVPVAEPIRHAEALIQQALTLKRSDETRTV 292 Lambda K H 0.309 0.128 0.345 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: 151 Number of extensions: 3 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: 158 Length of database: 658 Length adjustment: 27 Effective length of query: 131 Effective length of database: 631 Effective search space: 82661 Effective search space used: 82661 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 (21.7 bits) S2: 48 (23.1 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