Align Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale)
to candidate 17782 b3722 fused beta-glucoside-specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)
Query= uniprot:P50829 (168 letters) >FitnessBrowser__Keio:17782 Length = 625 Score = 119 bits (297), Expect = 1e-31 Identities = 63/171 (36%), Positives = 95/171 (55%), Gaps = 7/171 (4%) Query: 3 KKLFGMGKIQEKVTEEV-------IYSPADGTVMDLSDVPDPVFSQKMMGEGIAVEPSSG 55 K+ G QEK E + I SP G ++ L V D F+ ++G+GIA+ PS G Sbjct: 455 KRQPAQGAPQEKTPEVITPPEQGGICSPMTGEIVPLIHVADTTFASGLLGKGIAILPSVG 514 Query: 56 EIVSPAEGEVIQIFHTKHAVGIRTRSGIELLIHVGLETVNMNGEGFTAHIKEGDKVKVGD 115 E+ SP G + +F T HA+GI + G+E+LIHVG++TV ++G+ F+AH+ GDKV GD Sbjct: 515 EVRSPVAGRIASLFATLHAIGIESDDGVEILIHVGIDTVKLDGKFFSAHVNVGDKVNTGD 574 Query: 116 PLITCDLELIKEKASSTVIPIVIMNGEAVGSMVSAGEKAARKGESKLFTIK 166 LI+ D+ I+E P++I N + ++ G GE L I+ Sbjct: 575 RLISFDIPAIREAGFDLTTPVLISNSDDFTDVLPHGTAQISAGEPLLSIIR 625 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: 255 Number of extensions: 14 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: 625 Length adjustment: 27 Effective length of query: 141 Effective length of database: 598 Effective search space: 84318 Effective search space used: 84318 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: 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