Align PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized)
to candidate WP_009140205.1 HMPREF9452_RS00875 PTS glucose transporter subunit IIA
Query= SwissProt::P0A283 (169 letters) >NCBI__GCF_000225705.1:WP_009140205.1 Length = 186 Score = 99.0 bits (245), Expect = 4e-26 Identities = 48/147 (32%), Positives = 85/147 (57%), Gaps = 3/147 (2%) Query: 23 IVAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIES 82 I AP+SG +V + ++ D + + G G I P GN + AP +G I +NH+ + + Sbjct: 32 IYAPISGVLVELSEIDDDSISSGLFGRGYGIVPVGNVIYAPANGRIAATTVSNHSIGLRT 91 Query: 83 DSGIELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPVIEFDLPLLEEKAKSTLTPVVIS 142 D+GIEL +H GIDTV+++G+GF R+ E Q VK G P++ FD ++ + V+++ Sbjct: 92 DNGIELIIHVGIDTVKMEGKGFNRLVESEQEVKAGQPILVFDDDAIKAAGYDDVVTVIVT 151 Query: 143 NMDEIKELIKLSG--SVTVGETPVIRI 167 + + + +KL G + + P+++I Sbjct: 152 S-PSLLDKVKLVGQSNTLFADHPLVKI 177 Lambda K H 0.315 0.139 0.377 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: 103 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: 169 Length of database: 186 Length adjustment: 19 Effective length of query: 150 Effective length of database: 167 Effective search space: 25050 Effective search space used: 25050 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 44 (21.6 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