Align Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale)
to candidate WP_009141285.1 HMPREF9452_RS06255 PTS glucose transporter subunit IIA
Query= uniprot:P50829 (168 letters) >NCBI__GCF_000225705.1:WP_009141285.1 Length = 165 Score = 99.4 bits (246), Expect = 3e-26 Identities = 47/129 (36%), Positives = 74/129 (57%) Query: 19 VIYSPADGTVMDLSDVPDPVFSQKMMGEGIAVEPSSGEIVSPAEGEVIQIFHTKHAVGIR 78 V+ +P +G V+ LS+V D F+ +G+G+A+ P+ +++P ++ IF T HAV R Sbjct: 17 VLRAPLEGDVIPLSEVNDETFAAGYLGQGVAIRPTGDRVIAPTAVKIEAIFPTGHAVAFR 76 Query: 79 TRSGIELLIHVGLETVNMNGEGFTAHIKEGDKVKVGDPLITCDLELIKEKASSTVIPIVI 138 T G+++LIHVGLET N+ G F H GD V G+ LI D + I + +P++I Sbjct: 77 TVDGLDVLIHVGLETYNLEGRHFKVHAAPGDMVTAGETLIEFDRQAIVNEGYDITVPVLI 136 Query: 139 MNGEAVGSM 147 N S+ Sbjct: 137 RNAVEFASI 145 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: 70 Number of extensions: 4 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: 165 Length adjustment: 18 Effective length of query: 150 Effective length of database: 147 Effective search space: 22050 Effective search space used: 22050 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: 43 (21.2 bits)
This GapMind analysis is from Sep 24 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