Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_026596194.1 H035_RS0102680 carbohydrate kinase
Query= BRENDA::G4T023 (295 letters) >NCBI__GCF_000421465.1:WP_026596194.1 Length = 292 Score = 246 bits (629), Expect = 3e-70 Identities = 130/293 (44%), Positives = 182/293 (62%), Gaps = 10/293 (3%) Query: 8 IFGEVLFDHFPDGSRVLGGAPFNVAWHLQAFRQEPHFISRVGQDATGDSVIAAMHKWGMD 67 ++GEVLFD F DG VLGGAPFNVAWHLQ F EP F+SR+G+D G V M +WGMD Sbjct: 1 MYGEVLFDCFEDGDCVLGGAPFNVAWHLQGFGLEPCFVSRIGRDDLGKQVRETMLRWGMD 60 Query: 68 MSGLQRDSRHPTGVVDIVIEQGEPAYTIVPEQAYDYIDEDELQDT---DRPGLLYHGTLS 124 + LQ D + PTG V + +++G+P++ I+P+QAYD ID + + D L+YHG+L Sbjct: 61 LRFLQEDPQKPTGRVQVALQEGQPSFDILPDQAYDRIDPNGVLAACAGDNFSLMYHGSLI 120 Query: 125 LRQPVSRAALDVLKDAHKGRIFMDVNLREPWWQKDQVLEWLGQADWVKLNHHELAALYPV 184 R AAL+ +K + +FMD+NLREPWW+ D+V L + W+KLN EL AL Sbjct: 121 ARTDAGWAALEHVKRDLQLPVFMDINLREPWWRMDRVKALLDHSRWLKLNDDELTALAAP 180 Query: 185 S-----GDLKADMRRFVELYRLQGLIVTSGKQGAFATDHQGVSCRVTPGEIAQVIDTVGA 239 S G A RR + + L ++VT G +G + V P ++++ DTVGA Sbjct: 181 SSLQSEGQTDA-ARRLLTAHGLDFVVVTLGAEGGLLVKEK-ERWTVPPAPVSRLADTVGA 238 Query: 240 GDAFASVMLLGLNLDWPLQITMERAQAFASAMVGQRGATVRDPVFYEPFIAAW 292 GD F++VM+LGL DW L++T++RA FA+A+ Q+GAT +P Y F+ AW Sbjct: 239 GDGFSAVMVLGLMRDWGLEVTLKRANTFAAALCAQKGATAENPSLYRRFLEAW 291 Lambda K H 0.322 0.138 0.432 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: 262 Number of extensions: 18 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: 295 Length of database: 292 Length adjustment: 26 Effective length of query: 269 Effective length of database: 266 Effective search space: 71554 Effective search space used: 71554 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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