Align protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 1/2) (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= BRENDA::Q8DWE6 (150 letters) >FitnessBrowser__Keio:14863 Length = 658 Score = 80.5 bits (197), Expect = 5e-20 Identities = 43/138 (31%), Positives = 76/138 (55%), Gaps = 1/138 (0%) Query: 9 INLICESQDEVFHYLATLVVDNGYANNTESVVQALKLRESEGTTGMMEGFAIPHAKDKSI 68 +N S++E H L + G ++TE ++ + RES G T + EG A+PH K ++ Sbjct: 34 LNARFTSREEAIHALTQRLAALGKISSTEQFLEEVYRRESLGPTALGEGLAVPHGKTAAV 93 Query: 69 VKPSIAILKLKTGVEWHSMDG-QLINNVIALFIPEKEAGTTHLKVLSQIARLLVNKTFKE 127 + + A+ L ++W +DG + ++ V+ L IP EAGTTH+++L+ + L + + Sbjct: 94 KEAAFAVATLSEPLQWEGVDGPEAVDLVVLLAIPPNEAGTTHMQLLTALTTRLADDEIRA 153 Query: 128 KIKEADTILELKELLTEK 145 +I+ A T EL L +K Sbjct: 154 RIQSATTPDELLSALDDK 171 Lambda K H 0.315 0.133 0.358 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: 6 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: 658 Length adjustment: 27 Effective length of query: 123 Effective length of database: 631 Effective search space: 77613 Effective search space used: 77613 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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