Align 1-phosphofructokinase; Fructose 1-phosphate kinase; EC 2.7.1.56 (characterized)
to candidate SMc01103 SMc01103 ribokinase
Query= SwissProt::D4GYE6 (305 letters) >FitnessBrowser__Smeli:SMc01103 Length = 299 Score = 68.6 bits (166), Expect = 2e-16 Identities = 71/245 (28%), Positives = 101/245 (41%), Gaps = 8/245 (3%) Query: 36 AGGKGINVAKYASALDADVTASGFLGGH-FGKFVRDRLDADGIASDFV-TVDADTRLNTT 93 AGGKG N A A A V +G +G F + L G D TV T Sbjct: 35 AGGKGANQALAARRAGASVRMAGAVGSDAFAEGALALLKEAGTDLDLTKTVGEPTGTAHI 94 Query: 94 VLAADGEYKLNH-NGPQIRAADVDELVETAQANEPDTLLVGGSLPPGM---SLSDVDRLA 149 ++ DGE + R + D AQ + DTL++ +P +LS+ R Sbjct: 95 IVGGDGENVIVVVASANARVSGDDAANVVAQMSAGDTLMLQLEIPSASVEKALSEAKRRG 154 Query: 150 RAGDWKIAVDMGGEYLAELDADYYVCKPNRSELAAATGRTVETEADAVEAAEELHARGFE 209 IA AD + EL A G+ A+ EA LHA + Sbjct: 155 IRSIINIAPLTPDAARLGRMADIVIANETEFELLA--GKAGIAGAEREEAMNGLHAETRQ 212 Query: 210 YVLASLGADGALLVTDDEVLSAPALDVEVVDTVGAGDAVMSGFLAAREHGLSDADALRMG 269 V+ +LGA+G + + + E+ A L +E VDTVGAGD A + GL+ ++ALR Sbjct: 213 TVIVTLGAEGVVAIHEGELHRAKGLTIEPVDTVGAGDTFCGYLAAGLDAGLAFSEALRRA 272 Query: 270 VLTAS 274 + S Sbjct: 273 AIAGS 277 Lambda K H 0.315 0.133 0.375 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: 224 Number of extensions: 11 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: 305 Length of database: 299 Length adjustment: 27 Effective length of query: 278 Effective length of database: 272 Effective search space: 75616 Effective search space used: 75616 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