Align Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale)
to candidate CCNA_00457 CCNA_00457 phosphoenolpyruvate-protein phosphotransferase/phosphocarrier protein HPr/PTS system, glucose-specific IIA subunit
Query= uniprot:Q9KZP2 (149 letters) >FitnessBrowser__Caulo:CCNA_00457 Length = 852 Score = 89.0 bits (219), Expect = 2e-22 Identities = 56/146 (38%), Positives = 79/146 (54%), Gaps = 6/146 (4%) Query: 4 VSSPLAGRAIGLAAVPDPVFSGAMVGPGTAIDPVREPSEAVAPVDGVIVSLHP--HAFVV 61 +++PL G L PD VF+ M+G G AIDP+ S AP DG +VS+H HA + Sbjct: 8 LTAPLQGWVSALEEAPDAVFAERMLGDGLAIDPLG--STLHAPCDGSVVSVHRARHAVTL 65 Query: 62 VDESGHGVLTHLGIDTVQLNGEGFELLVNKGDTVVRGQGVVRWDPAAVEAAGKSPICPIV 121 +G +L H+G++TV LNGEGFE+ V +G TV G ++ D + +S I P+V Sbjct: 66 RATNGAEILMHVGLETVALNGEGFEVFVEEGQTVKAGDRLIGLDLDLLAQRARSLITPVV 125 Query: 122 ALEATAEALADLREDGDVKAGESLFL 147 EA +R D D + G FL Sbjct: 126 I--TNGEAFQIVRRDQDRQIGVGQFL 149 Lambda K H 0.316 0.136 0.402 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: 365 Number of extensions: 24 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: 852 Length adjustment: 29 Effective length of query: 120 Effective length of database: 823 Effective search space: 98760 Effective search space used: 98760 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: 49 (23.5 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