Align 6-phosphofructokinase (EC 2.7.1.11) (characterized)
to candidate GFF1892 Psest_1933 hexose kinase, 1-phosphofructokinase family
Query= BRENDA::P06999 (309 letters) >FitnessBrowser__psRCH2:GFF1892 Length = 312 Score = 209 bits (531), Expect = 9e-59 Identities = 119/304 (39%), Positives = 176/304 (57%), Gaps = 1/304 (0%) Query: 1 MVRIYTLTLAPSLDSATITPQIYPEGKLRCTAPVFEPGGGGINVARAIAHLGGSATAIFP 60 M I TLTL P++D + T ++ KLRC+ P +PGGGGINVAR + LGG A A++P Sbjct: 1 MPLIATLTLNPAMDLSVSTARVISTEKLRCSLPRHDPGGGGINVARVVKTLGGKAVAVYP 60 Query: 61 AGGATGEHLVSLLADENVPVATVEAKDWTRQNLHVHVEASGEQYRFVMPGAALNEDEFRQ 120 AGG G+ L L + + V TR++ V ASG QYRFV+PG L+ E +Q Sbjct: 61 AGGPFGDLLQRSLDELGLVHRPVPIAGDTRESFTVDELASGLQYRFVLPGPTLSAQELQQ 120 Query: 121 LEEQVLEIESG-AILVISGSLPPGVKLEKLTQLISAAQKQGIRCIVDSSGEALSAALAIG 179 + + + A +V+SGS PPG L +L++ A++ G R +VD SGE L A G Sbjct: 121 CLDSLAALRPAPAYVVLSGSFPPGADLGFFDELLALARRIGARLVVDLSGEPLRHAARQG 180 Query: 180 NIELVKPNQKELSALVNRELTQPDDVRKAAQEIVNSGKAKRVVVSLGPQGALGVDSENCI 239 + L+KP+ EL L+ R ++ + +A + ++ G A+ +V+SLG GAL + Sbjct: 181 GVYLMKPSLDELGTLMGRTVSAEAEQEQALRSLIRQGCAEVIVLSLGADGALYAYGDQVG 240 Query: 240 QVVPPPVKSQSTVGAGDSMVGAMTLKLAENASLEEMVRFGVAAGSAATLNQGTRLCSHDD 299 ++ P V S VGAGDSM+GA+ L +A+ S+ E V G+AAG+A + GT LC +D Sbjct: 241 RLRTPEVPVASAVGAGDSMLGAIVLAMADGRSIPEAVCQGIAAGAATVMRPGTELCHRED 300 Query: 300 TQKI 303 Q++ Sbjct: 301 VQRL 304 Lambda K H 0.314 0.131 0.363 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: 265 Number of extensions: 6 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: 309 Length of database: 312 Length adjustment: 27 Effective length of query: 282 Effective length of database: 285 Effective search space: 80370 Effective search space used: 80370 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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