Align protein-Npi-phosphohistidine-D-fructose phosphotransferase (subunit 1/2) (EC 2.7.1.202) (characterized)
to candidate WP_068336976.1 A3K86_RS18055 PTS transporter subunit EIIA
Query= BRENDA::Q8DWE6 (150 letters) >NCBI__GCF_001650345.1:WP_068336976.1 Length = 622 Score = 76.3 bits (186), Expect = 8e-19 Identities = 43/144 (29%), Positives = 84/144 (58%), Gaps = 1/144 (0%) Query: 1 MIDENLIKINLICESQDEVFHYLATLVVDNGYANNTESVVQALKLRESEGTTGMMEGFAI 60 +I+ +I ++L ++++V L L+ G + + + RE G TG EG AI Sbjct: 6 LIESEIICLDLKATNKEDVLAELTDLLDAAGKLVDKTQFLADVWKREEIGNTGFEEGIAI 65 Query: 61 PHAKDKSIVKPSIAILKLKTGVEWHSMDGQLINNVIALFIPEKEAGTTHLKVLSQIARLL 120 PHAK ++ KP++A+ ++G+++ + DG+L + L P+ + H++VL+Q++ L Sbjct: 66 PHAKSGAVAKPAVAVGISRSGIDYGAEDGELSDVFFMLASPDGQ-DHHHIEVLAQLSTKL 124 Query: 121 VNKTFKEKIKEADTILELKELLTE 144 + ++F K+K A+++ E ELLT+ Sbjct: 125 IEESFITKLKGAESVEEALELLTD 148 Lambda K H 0.315 0.133 0.358 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: 172 Number of extensions: 12 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: 150 Length of database: 622 Length adjustment: 26 Effective length of query: 124 Effective length of database: 596 Effective search space: 73904 Effective search space used: 73904 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 (21.6 bits) S2: 48 (23.1 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