Align PTS system fructose-specific EIIA component; EIIA-Fru; Fructose-specific phosphotransferase enzyme IIA component; lev-PTS; p16 (characterized)
to candidate WP_092346502.1 BLU87_RS08010 PTS system fructose subfamily IIA component
Query= SwissProt::P26379 (146 letters) >NCBI__GCF_900107645.1:WP_092346502.1 Length = 135 Score = 74.3 bits (181), Expect = 7e-19 Identities = 46/136 (33%), Positives = 72/136 (52%), Gaps = 2/136 (1%) Query: 1 MISVIISGHGDFPIALKESSGMIFGEENNLIAVPFFKGEGIQTLQEKYHQALKDIPEEHE 60 MI +++ H L ++ +I G ++ AV + I +EK QALK + + Sbjct: 1 MIGIVLVSHAGIADELLHAAELILGPVRSIAAVSISRDMSIDVAKEKLQQALKAVNNNQD 60 Query: 61 -VLFLVDIFGGTPYNAAASFIAEDQRMDMAAGVNLPILLEVLSLREHLALKDLLNNLKAM 119 V+ L D+FGGTP N +A F+ +D +++ GVNLP+LL+ +S RE L L LK Sbjct: 61 GVIILTDLFGGTPTNLSAEFL-QDGDIEILTGVNLPMLLKGISSREDHDLNGLATLLKDY 119 Query: 120 SQQSFQVCSEHLEKVK 135 +Q + SE L V+ Sbjct: 120 AQNAIMRPSELLRSVR 135 Lambda K H 0.318 0.135 0.375 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: 48 Number of extensions: 3 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: 146 Length of database: 135 Length adjustment: 15 Effective length of query: 131 Effective length of database: 120 Effective search space: 15720 Effective search space used: 15720 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: 41 (21.7 bits) S2: 42 (20.8 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