Align 1-phosphofructokinase; EC 2.7.1.56; Fructose 1-phosphate kinase (uncharacterized)
to candidate GFF1892 Psest_1933 hexose kinase, 1-phosphofructokinase family
Query= curated2:O51575 (307 letters) >FitnessBrowser__psRCH2:GFF1892 Length = 312 Score = 127 bits (320), Expect = 3e-34 Identities = 95/305 (31%), Positives = 162/305 (53%), Gaps = 11/305 (3%) Query: 1 MIYTLTLNPSVDYKI-VLKEFQEESLNYALNNNFFAGGKGINVSTVLKNLGKPSTALGFL 59 +I TLTLNP++D + + E L +L + GG GINV+ V+K LG + A+ Sbjct: 3 LIATLTLNPAMDLSVSTARVISTEKLRCSLPRHD-PGGGGINVARVVKTLGGKAVAVYPA 61 Query: 60 GGFTGDYIRFSLDSRGIKNDFIKIKYDTR--LNIKMIANGRETEINANSPDISENEFELL 117 GG GD ++ SLD G+ + + I DTR + +A+G + P +S E + Sbjct: 62 GGPFGDLLQRSLDELGLVHRPVPIAGDTRESFTVDELASGLQYRFVLPGPTLSAQELQQC 121 Query: 118 KNKLKNL-ANNSTLVMSGSVPAALGEDAYNE-IANSISNDVKLIIDTSGKPLRKILRL-N 174 + L L + +V+SGS P ++E +A + +L++D SG+PLR R Sbjct: 122 LDSLAALRPAPAYVVLSGSFPPGADLGFFDELLALARRIGARLVVDLSGEPLRHAARQGG 181 Query: 175 PFLIKPNIYELEDLFNAKFDSTKELIKIGKNLVESG-VQNIIISMGSDGAIFIGGKNVAF 233 +L+KP++ EL L + E + ++L+ G + I++S+G+DGA++ G V Sbjct: 182 VYLMKPSLDELGTLMGRTVSAEAEQEQALRSLIRQGCAEVIVLSLGADGALYAYGDQVG- 240 Query: 234 RAFVPKINFVSTIGAGDSVIAGFVYAFDNGSTLEDSFKFGVAAGTATALK--GNLCEFQD 291 R P++ S +GAGDS++ V A +G ++ ++ G+AAG AT ++ LC +D Sbjct: 241 RLRTPEVPVASAVGAGDSMLGAIVLAMADGRSIPEAVCQGIAAGAATVMRPGTELCHRED 300 Query: 292 VKKML 296 V+++L Sbjct: 301 VQRLL 305 Lambda K H 0.317 0.137 0.381 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: 184 Number of extensions: 15 Number of successful extensions: 5 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: 307 Length of database: 312 Length adjustment: 27 Effective length of query: 280 Effective length of database: 285 Effective search space: 79800 Effective search space used: 79800 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 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