Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_011841465.1 RSPH17029_RS10785 sugar kinase
Query= reanno::Dino:3609413 (308 letters) >NCBI__GCF_000015985.1:WP_011841465.1 Length = 302 Score = 116 bits (290), Expect = 7e-31 Identities = 105/307 (34%), Positives = 141/307 (45%), Gaps = 27/307 (8%) Query: 2 ILCAGEALIDMLPRALPDGTAGFAPVAGGAVFNTAVALGRL---GADVGLVTGLSRDLFG 58 I+ GE +++M P GFA G NTA L R A+V +T + D Sbjct: 10 IISVGECMVEMAPTGEGTFAMGFA----GDTLNTAWYLRRALPPEAEVDYLTAVGTDAIS 65 Query: 59 EVLMTALAAADVD-SDMAVLSDRPTTLAFVTLTDGHAQYAFYDENTAGRMLA--PADMPD 115 + ++ L A + S +A + DR L + LT+G +A++ +A R+LA PA + Sbjct: 66 DRMLGFLRDAGLGTSRVARVPDRTVGLYLIELTNGERSFAYWRGQSAARLLARDPAVLAA 125 Query: 116 PGPEVGTLFFGGISLAV-EPC--AAAYEALCLKAAAGRVVMLDPNIRPGFIKDETTFRAR 172 ++ GI+LA+ EP + AL AAG V DPN+RP D T A Sbjct: 126 GFAGASMIYLSGITLAILEPADRSQLLAALSAARAAGSAVAFDPNLRPRLWPDAATMCAA 185 Query: 173 IDRMLAVTDIVKVSDEDLAWLMGPGDLAESAAALRARGPAVVCVTRGGAGVEAHTATGIT 232 I DIV S ED A G D A +AA A G ++V V G + T G Sbjct: 186 IMEAARHADIVLPSHEDEAAFFGDEDAAATAARYAAAGASLVVVKDGAGPMVTLTPEGQQ 245 Query: 233 HVAAEAV-EVVDTVGAGDTFNAGFLAGLAEAGALDKDRLRALDAPVLTSALRLGAQAAAI 291 A E V EVVDT AGD+FNAGFLA AGA L A+R GA+ AA Sbjct: 246 SHAPETVSEVVDTTAAGDSFNAGFLAAHI-AGA------------PLAEAVRAGARLAAR 292 Query: 292 TVSRAGA 298 + + GA Sbjct: 293 VIGQRGA 299 Lambda K H 0.320 0.136 0.398 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: 203 Number of extensions: 13 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: 308 Length of database: 302 Length adjustment: 27 Effective length of query: 281 Effective length of database: 275 Effective search space: 77275 Effective search space used: 77275 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 Apr 10 2024. 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