Align Putative phosphotransferase enzyme IIA component YpqE (characterized, see rationale)
to candidate 6937493 Sama_1649 glucose-specific PTS system component (RefSeq)
Query= uniprot:P50829 (168 letters) >FitnessBrowser__SB2B:6937493 Length = 169 Score = 114 bits (286), Expect = 6e-31 Identities = 53/147 (36%), Positives = 87/147 (59%), Gaps = 1/147 (0%) Query: 20 IYSPADGTVMDLSDVPDPVFSQKMMGEGIAVEPSSGEIVSPAEGEVIQIFHTKHAVGIRT 79 I +P G + + VPD VF++K++G+GIA+ P I +P +G + +IF T HA I + Sbjct: 23 ILAPVSGEIYPIEKVPDVVFAEKIVGDGIAIAPEGDTIYAPIDGTIGKIFETNHAFSIES 82 Query: 80 RSGIELLIHVGLETVNMNGEGFTAHIKEGDKVKVGDPLITCDLELIKEKASSTVIPIVIM 139 G+EL +H G+ TV + G GF +EG +VK GDP++ DLE ++E A S + P+V+ Sbjct: 83 PQGLELFVHFGVGTVELRGNGFKRLAEEGQQVKAGDPILAFDLEYLREHADSLLTPVVLA 142 Query: 140 NGEAVGSMVSAGEKAARKGESKLFTIK 166 N E + + + G+ +FT++ Sbjct: 143 NMEDI-KYLEKSQGRVEAGKDVIFTVE 168 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: 100 Number of extensions: 6 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: 169 Length adjustment: 18 Effective length of query: 150 Effective length of database: 151 Effective search space: 22650 Effective search space used: 22650 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 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