Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_013402622.1 CALHY_RS03470 carbohydrate kinase
Query= BRENDA::O04897 (347 letters) >NCBI__GCF_000166355.1:WP_013402622.1 Length = 316 Score = 186 bits (472), Expect = 7e-52 Identities = 120/320 (37%), Positives = 173/320 (54%), Gaps = 16/320 (5%) Query: 28 VVCFGEMLIDFIPTVAGVSLAEAPAFEKAPGGAPANVAVCISKLGGSSAFIGKVGDDEFG 87 +VCFGE LIDF+ E FE GG P NVA I+K GG + I KVG+D FG Sbjct: 3 IVCFGEALIDFLNV-------EGNLFEANIGGGPTNVAGAIAKWGGKTFLISKVGNDMFG 55 Query: 88 RMLADILKQNNVDNSGMRFDHDARTALAFITLTAEGEREFVFFRNPSADMLLRESELDVD 147 RM+ + L++ VD SG++ T LAF+ + GER F F R AD+ + E++ + Sbjct: 56 RMIKNKLEEIGVDVSGLKITDQYFTTLAFVKVDERGERSFSFSRKHGADVYITPDEIEEE 115 Query: 148 LIKKATIFHYGSISLIDEPCRSTHLAAMDIAKRSGSILSYDPNLRLPLWPSEDAARSGIM 207 +IK + I H+ S+S+ R T ++IAK +G ++SYDPN R PLW S++ A IM Sbjct: 116 IIKSSKILHFSSLSMTHNTNRKTTFHILEIAKNNGLLISYDPNFREPLWESKNLAIDTIM 175 Query: 208 SVWNL--ADIIKISEDEISFLTGADDPNDDEVVLKRLFHPNLKLLLVTEGSAGCRYYTKE 265 L DI+K+S +E++ A P D ++K +KLL VT G G + Sbjct: 176 LPIKLGYVDILKVSLEEVNLY--ALYPEDFYQMIK----DKVKLLFVTMGEKGTIVFCGG 229 Query: 266 FKGRVNSIKVKAVDTTGAGDAFTGGVLKCLASDASLYQ-DEKRLREAIFFANVCAALTVT 324 K RV SI+V AVDTTG GD F +L + +L +L E ANV AL T Sbjct: 230 NKERVPSIEVTAVDTTGCGDCFMALILFEIWKIGTLKDISFGKLIEITRKANVAGALCAT 289 Query: 325 GRGGIPSLPTQDAVRQTLAE 344 +G +P++P + + + L++ Sbjct: 290 KKGALPAVPDYNEIERVLSK 309 Lambda K H 0.319 0.135 0.389 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: 257 Number of extensions: 12 Number of successful extensions: 2 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: 347 Length of database: 316 Length adjustment: 28 Effective length of query: 319 Effective length of database: 288 Effective search space: 91872 Effective search space used: 91872 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 (21.7 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