Align Putative PTS system sugar phosphotransferase component IIA (characterized, see rationale)
to candidate PfGW456L13_4832 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= uniprot:Q9KZP2 (149 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4832 Length = 838 Score = 84.0 bits (206), Expect = 5e-21 Identities = 48/121 (39%), Positives = 73/121 (60%), Gaps = 4/121 (3%) Query: 3 TVSSPLAGRAIGLAAVPDPVFSGAMVGPGTAIDPVREPSEAVAPVDGVIVSLHP--HAFV 60 T+S+PL+G + LA VPD VF+ +G G AIDP+ + A P GV+V + HA Sbjct: 9 TLSAPLSGPVLTLAKVPDAVFASGAMGDGIAIDPLNDTLHA--PCAGVVVHVARTGHAVT 66 Query: 61 VVDESGHGVLTHLGIDTVQLNGEGFELLVNKGDTVVRGQGVVRWDPAAVEAAGKSPICPI 120 + ++G +L HLG+DTV+L G+GF +LV +G V GQ ++R+D V KS + + Sbjct: 67 LRADNGAELLLHLGLDTVELQGQGFSMLVKEGARVSNGQPLLRYDLDKVAQQCKSLVSLL 126 Query: 121 V 121 + Sbjct: 127 I 127 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: 316 Number of extensions: 27 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: 838 Length adjustment: 28 Effective length of query: 121 Effective length of database: 810 Effective search space: 98010 Effective search space used: 98010 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