Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate Echvi_0157 Echvi_0157 hexose kinase, 1-phosphofructokinase family
Query= curated2:O31714 (303 letters) >FitnessBrowser__Cola:Echvi_0157 Length = 307 Score = 145 bits (366), Expect = 1e-39 Identities = 99/310 (31%), Positives = 156/310 (50%), Gaps = 13/310 (4%) Query: 1 MIYTVTLNPSVDYIVHVEDFTVGGLNRSSYDTKYPGGKGINVSRLLKRHHVASKALGFVG 60 M+ +V NPS+D +EDF +G NR S ++PGGKG++V+ L+ + + Sbjct: 1 MVLSVCPNPSIDTYAWLEDFQLGKANRISKQEEFPGGKGVHVAMALQEAGAPTVLMAAWA 60 Query: 61 GFTGEYIKTFLREENLETAFSEVKGDTR----INVKLKTGDETEINGQGPTISDEDFKAF 116 G GE+IK +E + T ++KG R + TE+ GP ++ EDF F Sbjct: 61 GHPGEWIKAACKERGMATVGVDLKGMNRKCYTFLAEATAIRNTELMEPGPEMNGEDFDRF 120 Query: 117 LEQFQ-SLQEGDIVVLAGSIPSSLPHDTYEKIAEACKQQNARVVLDISGEALLKATEMKP 175 + F+ +L++ + V++GS P P Y ++ A +V+LD SGE L A E K Sbjct: 121 VGVFKDNLRQSALTVMSGSWPKGAPKTAYRELIAAANGSGKKVILDCSGEQLTHALEEKI 180 Query: 176 FLMKPNHHELGEMFGTAITSVEEAVPYGKKLVEQGAEHVIVSMAGDGALLFTNEAVYFAN 235 F + N HE + GT +SV EA KL E+ E + ++ +G L AN Sbjct: 181 FGIHLNEHEAKQYCGT--SSVHEAF---DKLHEK-VELIALTKGKEGLFLSYQGTRLHAN 234 Query: 236 VPKGKLVNSVGAGDSVVAGFLAGISKQLPLEEAFRLGVTSGSATAFSEELGT--EEFVQQ 293 V K++++VG GD + AG G+S+ +EE R G G+A +LG + V++ Sbjct: 235 VTLEKVISTVGCGDCLTAGVALGVSRGYGVEEIARYGAAFGAANCLRPDLGMIYKADVER 294 Query: 294 LLPEVKVTRL 303 LLP+V + L Sbjct: 295 LLPQVNINEL 304 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: 236 Number of extensions: 12 Number of successful extensions: 4 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: 307 Length adjustment: 27 Effective length of query: 276 Effective length of database: 280 Effective search space: 77280 Effective search space used: 77280 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