Align Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale)
to candidate Pf1N1B4_833 PTS system, glucose-specific IIA component / Phosphotransferase system, phosphocarrier protein HPr / Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= uniprot:P50829 (168 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_833 Length = 844 Score = 99.0 bits (245), Expect = 2e-25 Identities = 45/123 (36%), Positives = 80/123 (65%) Query: 20 IYSPADGTVMDLSDVPDPVFSQKMMGEGIAVEPSSGEIVSPAEGEVIQIFHTKHAVGIRT 79 + +P G +M L VPD VFS +++G+G+ ++P+S + +P G + + + HAV I Sbjct: 9 LLAPLSGVLMPLDQVPDQVFSSRVIGDGLCIDPTSQTLCAPLTGVISNVQVSGHAVSITD 68 Query: 80 RSGIELLIHVGLETVNMNGEGFTAHIKEGDKVKVGDPLITCDLELIKEKASSTVIPIVIM 139 +G+++L+H+GL+TVN+ G+GFT ++EG +V VG LI D + I A S + ++++ Sbjct: 69 DNGVQVLMHIGLDTVNLAGKGFTRLVEEGQRVIVGQALIEFDADYIALHARSLLTLMLVV 128 Query: 140 NGE 142 +GE Sbjct: 129 SGE 131 Lambda K H 0.314 0.134 0.365 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: 283 Number of extensions: 8 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: 168 Length of database: 844 Length adjustment: 30 Effective length of query: 138 Effective length of database: 814 Effective search space: 112332 Effective search space used: 112332 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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