Align fructokinase; EC 2.7.1.4 (characterized)
to candidate Pf1N1B4_4765 2-ketogluconate kinase (EC 2.7.1.13)
Query= CharProtDB::CH_006622 (307 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4765 Length = 339 Score = 114 bits (286), Expect = 2e-30 Identities = 95/315 (30%), Positives = 148/315 (46%), Gaps = 29/315 (9%) Query: 9 GDAVVDLLPESEGRLLQCP------GGAPANVAVGVARLGGNSGFIGAVGGDPFGRYMRH 62 G+ + + E G L GA +NVA+G++RLG N ++ VG D GR++ Sbjct: 10 GETMAMFVAEQNGELADVDHFHKRIAGADSNVAIGLSRLGFNVAWLSRVGADSLGRFVID 69 Query: 63 TLQQEQVDVSHMYLDDQHRTSTVVVD-LDDQGERTFTFMVRPSADLFL-VEEDLPQFAAG 120 TL+++ +D SH+ +D H T + DD + + R SA L V+ PQ Sbjct: 70 TLEKQGLDCSHVDIDPAHPTGFQLKSRTDDGSDPAVEYFRRGSAASHLSVQSIAPQLLEA 129 Query: 121 QWLHVCSI--ALSAEPSRSTTFAAMESIRSAGGRVSFDPNIRPDLWQDQALLLACLDRAL 178 + LH I ALSA +R +F M +R+AG VSFDPN+RP LW + ++ ++R Sbjct: 130 RHLHATGIPPALSA-AAREMSFELMTRMRNAGRSVSFDPNLRPSLWTSEQQMIREINRLA 188 Query: 179 HMANVVKLSEEELVFISSSNDLAYGIASVTERYQPELLLVTRGKAGVLAAFQQKFTHFNA 238 +A+ V E ++ D A IA+ E + + G AG TH + Sbjct: 189 ALAHWVLPGLSEGRLLTGFEDPA-DIAAFYLDQGAEAVAIKLGPAGAYYR-----THLDE 242 Query: 239 RPVAS------VDTTGAGDAFVAGLLASLAANGMPTDMTALEPTLTLAQTCGALATTAKG 292 VA VDT GAGD F GL+++L N ++ + A G+ A ++G Sbjct: 243 GFVAGVPVETVVDTVGAGDGFAVGLISALLEN------HSVAQAVQRANWIGSRAVQSRG 296 Query: 293 AMTALPYQRDLNRQF 307 M LP + ++ +F Sbjct: 297 DMEGLPTRLEMFAEF 311 Lambda K H 0.320 0.133 0.392 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: 235 Number of extensions: 12 Number of successful extensions: 3 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: 339 Length adjustment: 28 Effective length of query: 279 Effective length of database: 311 Effective search space: 86769 Effective search space used: 86769 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 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