Align Fructokinase; EC 2.7.1.4 (characterized)
to candidate 3609639 Dshi_3022 PfkB domain protein (RefSeq)
Query= SwissProt::P26420 (307 letters) >FitnessBrowser__Dino:3609639 Length = 333 Score = 79.0 bits (193), Expect = 1e-19 Identities = 77/252 (30%), Positives = 105/252 (41%), Gaps = 31/252 (12%) Query: 24 LQCPGGAPANVAVGVARLGGDSGFIGRVGDDPFGRFMRHTLAQEQVDVNYMRLDAAQRTS 83 +Q PGG+ AN G+ LG FIGRV DD GRF + E TS Sbjct: 59 VQAPGGSVANTLAGLGELGLRCAFIGRVKDDTLGRFYAQGMEAEGTAFPNPPQQVEAPTS 118 Query: 84 TVVVDLDSHGERTFTFMVRPSADLFLQPEDLPP--FAAGQWLHVCSIALSAEPSRSTTFA 141 ++ + GER+ + AD L PED+P FA L + P ++ A Sbjct: 119 RSMIFVTPDGERSMNTYLGAGAD--LGPEDVPEAVFAQVGLLFLEGYLFDKVPGKAAFEA 176 Query: 142 ALEAIKRAGGYVSFDPNIRSDLWQDPQDLRDCLDRALALADAIKLSEEELAFISG----- 196 A + AGG+ DP C+DR AD +L +EL F+ G Sbjct: 177 AARYARGAGGHAGI-------TLSDP----FCVDR--HRADFQRLVADELNFVIGNEHEY 223 Query: 197 -----SDDIVSGIARLNARFQPTLLLVTQGKAGVQAALRGQVS-HFPARPVVAVDTTGAG 250 ++D+ + +AR + + L+V +RG P VV VD TGAG Sbjct: 224 MALYETEDLGAALARAASVCE---LVVCTRSGDPVVMIRGDARVEVPVTRVVPVDATGAG 280 Query: 251 DAFVAGLLAGLA 262 D F AG L GLA Sbjct: 281 DQFAAGFLYGLA 292 Lambda K H 0.321 0.137 0.406 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: 204 Number of extensions: 8 Number of successful extensions: 1 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: 333 Length adjustment: 28 Effective length of query: 279 Effective length of database: 305 Effective search space: 85095 Effective search space used: 85095 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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