Align Fructokinase-1; ZmFRK1; EC 2.7.1.4 (characterized)
to candidate Pf6N2E2_629 2-ketogluconate kinase (EC 2.7.1.13)
Query= SwissProt::Q6XZ79 (323 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_629 Length = 324 Score = 121 bits (304), Expect = 2e-32 Identities = 95/312 (30%), Positives = 143/312 (45%), Gaps = 11/312 (3%) Query: 8 VVSFGEMLIDFVPTVAGVSLAEAPAFLKAPGGAPANVAIAVSRLGGGAAFVGKLGDDEFG 67 V+SFGE + V G LA F K GA +NVAI +SRL A++ ++G D G Sbjct: 6 VLSFGETMAMLVADQRG-DLASVDQFHKRIAGADSNVAIGLSRLDFKVAWLSRVGADSLG 64 Query: 68 RMLAAILRDNGVDDGGVVFDSGARTALAFVTLRADG-EREFMFYRNPSADMLLTADELNV 126 R + L + G+D V D T F + DG + + ++R SA L+ D + Sbjct: 65 RFVVQTLENEGLDCRHVAVDPTHPTGFQFKSRTDDGSDPQVEYFRRGSAASHLSIDSIAP 124 Query: 127 ELIKRAAVFHYGSISLIAEPCRTAHLRAMEIAKEAGALLSYDPNLREALWPSREEARTQI 186 L++ + G + ++ R M + AG LS+DPN+R +LW S T+I Sbjct: 125 SLLEARHLHATGIVPALSVTAREMSFELMSRMRAAGRSLSFDPNMRPSLWGSESTMITEI 184 Query: 187 LSIWDQADIVKVSEVELEFLTGIDSVEDDVVMKLWRPTMKLLLVTLGDQGCKYYARDFHG 246 + A V E LTG D D L + +L+++ LG G Y G Sbjct: 185 NRLAALAHWVLPGLGEGRLLTGFDDPADIAAFYLDQGA-ELVVIKLGADGAYYRTALDQG 243 Query: 247 AVPSFKVQQ-VDTTGAGDAFVGALLQRIVKDPSSLQDEKKLVESIKFANACGAITTTKKG 305 +P V Q VDT GAGD F L+ S+L + + + E+++ AN G+ +G Sbjct: 244 VIPGVPVAQVVDTVGAGDGFAVGLI-------SALLEGQAITEAVQRANWIGSRAVQSRG 296 Query: 306 AIPSLPTEAEVL 317 + LPT E+L Sbjct: 297 DMEGLPTRIELL 308 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: 264 Number of extensions: 10 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: 324 Length adjustment: 28 Effective length of query: 295 Effective length of database: 296 Effective search space: 87320 Effective search space used: 87320 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