Align fructokinase (EC 2.7.1.4) (characterized)
to candidate H281DRAFT_00856 H281DRAFT_00856 2-keto-3-deoxygluconate kinase
Query= BRENDA::Q42645 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_00856 Length = 311 Score = 132 bits (333), Expect = 9e-36 Identities = 96/312 (30%), Positives = 153/312 (49%), Gaps = 16/312 (5%) Query: 10 SKELVVSFGEMLIDFVPTSSGVSLAEAPGFLKAPGGAPANVAIAVSRLGGNAAFVGKLGD 69 +K +++ GE +I+F S + P +L+ GG +N IA +R G FV +G Sbjct: 7 AKPEILALGEAMIEF-----NQSAKDEPNYLQGFGGDTSNFCIAAARQGARTGFVSAVGA 61 Query: 70 DEFGHMLAGILKKNGVSADGLSFDKGARTALAFVTLKSDGEREFMFYRNPSADMLLTPDE 129 D FG +L + ++ V + D A T + FV+ DG F + R SA P + Sbjct: 62 DHFGRLLIDLWEREQVDTALVRVDPHASTGVYFVSHGPDG-HAFDYLRAGSAASRYAPRD 120 Query: 130 LNLDLIRSAKVFHYGSIRLIVE-PCRSAHLKAMEEAKKAGALLSYDPNLRLPLWPSAEEA 188 L LD I +AKV H I L + A L+A+ A+ G +S+D NLRL LWP A Sbjct: 121 LPLDAIAAAKVIHLSGISLAISLSACDAALEAITHARANGVQVSFDTNLRLKLWP-LNRA 179 Query: 189 REQIMSIWDKAEVIKVSDNELEFLTGNSTIDDATAMSLWHPNLKLLLVTLGDQGCRYYTK 248 R ++ + ++ S +++ LTG + D+ L H +++ + LG +G T Sbjct: 180 RAVMLEAIRQTDICLPSWDDVTELTGLTGRDEIVDFLLSH-GPRVVALKLGKEGSYIATP 238 Query: 249 NFKGSLDGFKVNAVDTTGAGDSFVGALLNKIVDDHSIIEDESRLKEVLKFANACGAITTT 308 + + + G VNAVD TGAGD F GA + ++V+ E ++AN A++T Sbjct: 239 DERRVVPGHVVNAVDATGAGDCFGGAFIARLVEGDDPF-------EAARYANVAAALSTQ 291 Query: 309 KKGAIPALPTVA 320 GA+ +P+ A Sbjct: 292 GYGAVAPIPSRA 303 Lambda K H 0.316 0.134 0.385 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: 244 Number of extensions: 17 Number of successful extensions: 4 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: 331 Length of database: 311 Length adjustment: 28 Effective length of query: 303 Effective length of database: 283 Effective search space: 85749 Effective search space used: 85749 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 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