Align 1-phosphofructokinase; Fructose 1-phosphate kinase; EC 2.7.1.56 (characterized)
to candidate N515DRAFT_0916 N515DRAFT_0916 Sugar or nucleoside kinase, ribokinase family
Query= SwissProt::D4GYE6 (305 letters) >FitnessBrowser__Dyella79:N515DRAFT_0916 Length = 312 Score = 62.8 bits (151), Expect = 1e-14 Identities = 76/266 (28%), Positives = 110/266 (41%), Gaps = 20/266 (7%) Query: 30 DDAVFTAGGKGINVAKYASALDADVTASGFLGGH-FGKFVRDRLDADGIASDFVTVDADT 88 DD + T G + A + L V G LG +G + D L GI + +A Sbjct: 37 DDFLMTPGSSSMICAMGLARLGNAVAFHGRLGADAWGSYCLDALRDAGIDVASLQPEAAL 96 Query: 89 RLNTTV-LAADGEYKLNHNGPQIRAADVDELVETAQANEPDTLLVGGSLPPGMSLSDVDR 147 R TV L+ + L I A +++ + A + L + +D+ + Sbjct: 97 RTGITVSLSTPRDRSLVTFSGAIAALRAEDVSDALLAGAGHLHVSSFYLQKALR-ADIRQ 155 Query: 148 L---ARAGDWKIAVDMG-------GEYLAELDADYYVCKPNRSELAAATGRTVETEADAV 197 L AR +++D G G+ L + D V PN EL A TG + V Sbjct: 156 LFARARKAGLTLSLDPGFDPEQRWGDDLRGVLEDVDVFLPNEEELRALTGE------NHV 209 Query: 198 EAAEELHARGFEYVLASLGADGALLVTDDEVLSAPALDVEVVDTVGAGDAVMSGFLAARE 257 A G ++A G G ++ D ++L APAL VE VD+ GAGD+ +GFL A Sbjct: 210 RKALAALDNGRTLIVAKRGRQGCAVLHDGKLLVAPALAVEAVDSTGAGDSFDAGFLHAWL 269 Query: 258 HGLSDADALRMGVLTAS-RVVGVAGT 282 GL D LR G S G+ GT Sbjct: 270 RGLPLRDCLRWGNACGSLSTRGIGGT 295 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: 214 Number of extensions: 10 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: 305 Length of database: 312 Length adjustment: 27 Effective length of query: 278 Effective length of database: 285 Effective search space: 79230 Effective search space used: 79230 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 Apr 09 2024. 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