Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate HSERO_RS07545 HSERO_RS07545 2-dehydro-3-deoxygluconokinase
Query= SwissProt::Q6XZ79 (323 letters) >FitnessBrowser__HerbieS:HSERO_RS07545 Length = 313 Score = 115 bits (287), Expect = 2e-30 Identities = 94/313 (30%), Positives = 145/313 (46%), Gaps = 14/313 (4%) Query: 8 VVSFGEMLIDFVPTVAGVSLAEAPAFLKAPGGAPANVAIAVSRLGGGAAFVGKLGDDEFG 67 VV++GE L V G E + + GA NVAI ++RLG + ++G+D FG Sbjct: 7 VVTWGEALALLVADEVG-PFEEVEKYTRRLAGAETNVAIGLARLGLKVGWASRVGNDAFG 65 Query: 68 RMLAAILRDNGVDDGGVVFDSGARTALAFVTLRADG-EREFMFYRNPSADMLLTADELNV 126 R + + GV+ V+ D RTA+ G + +YR SA L+ D+ + Sbjct: 66 RFIRQRVAQEGVEVSRVITDMEFRTAIQLKAKAVGGADPAIEYYRKGSAASHLSVDDFDA 125 Query: 127 ELIKRAAVFHYGSIS--LIAEPCRTAHLRAMEIAKEAGALLSYDPNLREALWPSREEART 184 A H I+ L A AH +AM+ + G +S+DPNLR LWPS+E Sbjct: 126 GYFGAARHLHATGIAPALSATTMAFAH-QAMDFMRGQGKTISFDPNLRPMLWPSQEVMAQ 184 Query: 185 QILSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYARDF 244 Q+ ++ +AD V E + LTG D + L R +KL+++ LG +G + Sbjct: 185 QLNALAFKADWVLPGLSEGKILTGHDDAREIAGFYLER-GVKLVVIKLGAEGAYWRNGQG 243 Query: 245 HGAVPSFKVQQ-VDTTGAGDAFVGALLQRIVKDPSSLQDEKKLVESIKFANACGAITTTK 303 G V V++ VDT GAGD F ++ S + + + +++ N GA Sbjct: 244 EGRVAGVPVKEVVDTVGAGDGFAVGVI-------SGMLEGLPVPQAVMRGNRIGAFAIQV 296 Query: 304 KGAIPSLPTEAEV 316 G + LPT AE+ Sbjct: 297 VGDMEGLPTRAEL 309 Lambda K H 0.319 0.136 0.388 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: 222 Number of extensions: 13 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: 323 Length of database: 313 Length adjustment: 27 Effective length of query: 296 Effective length of database: 286 Effective search space: 84656 Effective search space used: 84656 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