Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate 15841 b1723 6-phosphofructokinase II; suppressor of pfkA (VIMSS)
Query= curated2:O31714 (303 letters) >FitnessBrowser__Keio:15841 Length = 309 Score = 136 bits (343), Expect = 5e-37 Identities = 89/287 (31%), Positives = 149/287 (51%), Gaps = 5/287 (1%) Query: 2 IYTVTLNPSVDYIVHVEDFTVGGLNRSSYDTKYPGGKGINVSRLLKRHHVASKALGFVGG 61 IYT+TL PS+D G R + PGG GINV+R + ++ A+ GG Sbjct: 4 IYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFPAGG 63 Query: 62 FTGEYIKTFLREENLETAFSEVKGDTRINVKL---KTGDETEINGQGPTISDEDFKAFLE 118 TGE++ + L +EN+ A E K TR N+ + +G++ G +++++F+ E Sbjct: 64 ATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQLEE 123 Query: 119 QFQSLQEGDIVVLAGSIPSSLPHDTYEKIAEACKQQNARVVLDISGEALLKATEMKPF-L 177 Q ++ G I+V++GS+P + + ++ A ++Q R ++D SGEAL A + L Sbjct: 124 QVLEIESGAILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIGNIEL 183 Query: 178 MKPNHHELGEMFGTAITSVEEAVPYGKKLVEQG-AEHVIVSMAGDGALLFTNEAVYFANV 236 +KPN EL + +T ++ +++V G A+ V+VS+ GAL +E Sbjct: 184 VKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCIQVVP 243 Query: 237 PKGKLVNSVGAGDSVVAGFLAGISKQLPLEEAFRLGVTSGSATAFSE 283 P K ++VGAGDS+V +++ LEE R GV +GSA ++ Sbjct: 244 PPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQ 290 Lambda K H 0.315 0.134 0.372 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: 210 Number of extensions: 12 Number of successful extensions: 3 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: 303 Length of database: 309 Length adjustment: 27 Effective length of query: 276 Effective length of database: 282 Effective search space: 77832 Effective search space used: 77832 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 (22.0 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