Align PTS system glucose-specific EIIA component; EIIA-Glc; EIII-Glc; Glucose-specific phosphotransferase enzyme IIA component (characterized)
to candidate 14809 b0679 fused N-acetyl glucosamine specific PTS enzyme: IIC, IIB , and IIA components (NCBI)
Query= SwissProt::P0A283 (169 letters) >FitnessBrowser__Keio:14809 Length = 648 Score = 162 bits (411), Expect = 8e-45 Identities = 76/149 (51%), Positives = 106/149 (71%), Gaps = 1/149 (0%) Query: 22 EIVAPLSGEIVNIEDVPDVVFAEKIVGDGIAIKPTGNKMVAPVDGTIGKIFETNHAFSIE 81 E+V+P++G++V ++ VPD FA K VGDG+A+KPT +V+P GTI KIF TNHAF +E Sbjct: 500 ELVSPITGDVVALDQVPDEAFASKAVGDGVAVKPTDKIVVSPAAGTIVKIFNTNHAFCLE 559 Query: 82 SDSGIELFVHFGIDTVELKGEGFKRIAEEGQRVKVGDPVIEFDLPLLEEKAKSTLTPVVI 141 ++ G E+ VH GIDTV L+G+GFKR+ EEG +V G P++E DL L A+S ++PVV Sbjct: 560 TEKGAEIVVHMGIDTVALEGKGFKRLVEEGAQVSAGQPILEMDLDYLNANARSMISPVVC 619 Query: 142 SNMDEIKEL-IKLSGSVTVGETPVIRIKK 169 SN+D+ L IK G + G+TP+ IKK Sbjct: 620 SNIDDFSGLIIKAQGHIVAGQTPLYEIKK 648 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: 263 Number of extensions: 14 Number of successful extensions: 2 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: 648 Length adjustment: 28 Effective length of query: 141 Effective length of database: 620 Effective search space: 87420 Effective search space used: 87420 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: 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