Align glucose-specific phosphotransferase enzyme IIA component; EC 2.7.1.- (characterized)
to candidate CCNA_00571 CCNA_00571 phosphoenolpyruvate-protein phosphotransferase/phosphocarrier protein HPr/PTS system, glucose-specific IIA subunit
Query= CharProtDB::CH_088352 (169 letters) >FitnessBrowser__Caulo:CCNA_00571 Length = 878 Score = 124 bits (310), Expect = 5e-33 Identities = 56/121 (46%), Positives = 84/121 (69%) Query: 23 IIAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIES 82 + APL G + +E+ PD VFAE+++GDG+AI P G+ + AP DG++ + HA ++ + Sbjct: 34 LTAPLQGWVSALEEAPDAVFAERMLGDGLAIDPLGSTLHAPCDGSVVSVHRARHAVTLRA 93 Query: 83 DSGVELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDTVIEFDLPLLEEKAKSTLTPVVIS 142 +G E+ +H G++TV L GEGF+ EEGQ VK GD +I DL LL ++A+S +TPVVI+ Sbjct: 94 TNGAEILMHVGLETVALNGEGFEVFVEEGQTVKAGDRLIGLDLDLLAQRARSLITPVVIT 153 Query: 143 N 143 N Sbjct: 154 N 154 Lambda K H 0.315 0.138 0.374 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: 300 Number of extensions: 10 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: 169 Length of database: 878 Length adjustment: 30 Effective length of query: 139 Effective length of database: 848 Effective search space: 117872 Effective search space used: 117872 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: 42 (21.9 bits) S2: 50 (23.9 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