Align Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale)
to candidate H281DRAFT_01977 H281DRAFT_01977 Phosphocarrier protein HPr /phosphoenolpyruvate--protein phosphotransferase /PTS system IIA component, Glc family
Query= uniprot:P50829 (168 letters) >FitnessBrowser__Burk376:H281DRAFT_01977 Length = 854 Score = 114 bits (286), Expect = 3e-30 Identities = 60/150 (40%), Positives = 88/150 (58%) Query: 19 VIYSPADGTVMDLSDVPDPVFSQKMMGEGIAVEPSSGEIVSPAEGEVIQIFHTKHAVGIR 78 V+ +P G V+ L++VPDPVFS M G+GI V+P G +V+P EG V + T HAV + Sbjct: 9 VLLAPMTGPVVPLANVPDPVFSGGMFGDGIGVDPLEGRLVAPCEGTVTHLARTGHAVTLA 68 Query: 79 TRSGIELLIHVGLETVNMNGEGFTAHIKEGDKVKVGDPLITCDLELIKEKASSTVIPIVI 138 T G E+L+H+G++TV +NG+GF I++G V GD LI D + I A S V I I Sbjct: 69 TAEGAEILLHIGIDTVELNGKGFAPMIEQGAHVHAGDVLIEFDQDQIALHAPSLVSVIAI 128 Query: 139 MNGEAVGSMVSAGEKAARKGESKLFTIKAK 168 N +A + A + GE+ L ++ + Sbjct: 129 ANSDAFEIVERAQGGMLKAGETPLLLLRPR 158 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: 343 Number of extensions: 17 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: 854 Length adjustment: 30 Effective length of query: 138 Effective length of database: 824 Effective search space: 113712 Effective search space used: 113712 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 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