Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_049904537.1 C447_RS14190 sugar kinase
Query= BRENDA::Q6VWJ5 (386 letters) >NCBI__GCF_000336675.1:WP_049904537.1 Length = 318 Score = 143 bits (360), Expect = 8e-39 Identities = 100/313 (31%), Positives = 158/313 (50%), Gaps = 12/313 (3%) Query: 65 SSLVVCFGEMLIDFVPTTSGLSLAEAPAFKKAPGGAPANVAVGISRLGGSSAFIGKVGED 124 SS VV GE ++ P+T+G + A F+K+ GA NVA+G++RLG + K+G D Sbjct: 2 SSRVVTLGETMVLVYPSTTG-PMKHAHEFEKSLAGAETNVAIGLARLGHDVGWYSKLGTD 60 Query: 125 EFGYMLAEILKENNVNSDGMRFDPGARTALAFVTLRKDGEREFMFYRNPSADMLLQEDEL 184 G L ++ V++ + F A T + F R+ GE +YR+ SA L+ D+L Sbjct: 61 PHGEYLEFFVRGEGVDTTTVEFTDEAPTGIMFKERREFGEPAVHYYRHGSAASLMSPDDL 120 Query: 185 DLELIRKAKVFHYGSIS-LITEPCKSAHIAAAKAAKDAGVILSYDPNLRLPLWPSAESAR 243 ++ + A+ H I+ ++E C+ A + AA+ A +AG+ +S+DPN+R LW S E R Sbjct: 121 PVDYLTNAEYLHLTGITPALSESCRDATLLAAERATEAGMTVSFDPNVRRKLWESDERMR 180 Query: 244 EGILSIWNTADIIKISEEEISFLTQGEDPYDDNVVRKLYHPNLKLLLVTEGPEGCRYYTK 303 E +L + + +DI+ EE + L +DP + + +V G G Sbjct: 181 ETMLDLVSLSDIVLPGIEEGAALFGTDDP--EAIAAACLDHGAGTAVVKLGAAGAVVADG 238 Query: 304 DFSGRVKGIKVD-AVDTTGAGDAFVAGILSQLASDVSLLQDEGKLRDALSFANACGALTV 362 + RV G V+ VD GAGD F AG L+ S ++ +G + +A ANA GA Sbjct: 239 STTERVSGYDVERVVDPVGAGDGFAAGFLA------SRIEGQGPV-EATETANAVGAFAT 291 Query: 363 MERGAIPALPTKE 375 G LPT++ Sbjct: 292 TVAGDTEGLPTRK 304 Lambda K H 0.317 0.134 0.382 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: 230 Number of extensions: 12 Number of successful extensions: 5 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: 386 Length of database: 318 Length adjustment: 29 Effective length of query: 357 Effective length of database: 289 Effective search space: 103173 Effective search space used: 103173 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 (21.7 bits) S2: 49 (23.5 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