Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_011653019.1 RL_RS18270 sugar kinase
Query= reanno::Dino:3609413 (308 letters) >NCBI__GCF_000009265.1:WP_011653019.1 Length = 306 Score = 96.3 bits (238), Expect = 8e-25 Identities = 94/306 (30%), Positives = 132/306 (43%), Gaps = 27/306 (8%) Query: 3 LCAGEALIDMLPRALPDGTAGFAPVAGGAVFNTA-VALGRLGAD--VGLVTGLSRDLFGE 59 L GE ++++ GFA G FNTA LG D V T L D + Sbjct: 6 LSIGECMVELSQAGDGLLRKGFA----GDTFNTAWYVRACLGPDWSVDYFTALGDDAMSD 61 Query: 60 VLMTALAAADVDSDMAV-LSDRPTTLAFVTLTDGHAQYAFYDENTAGRMLA--PADMPDP 116 ++ + A + + + + R L + L DG ++++ ++ A R LA P + + Sbjct: 62 EMVAFIDKAGIGTSLIRRIRGRTPGLYMINLKDGERSFSYWRDSAAARSLAADPDRLREA 121 Query: 117 GPEVGTLFFGGISLAVEPCAAAYEALC---LKAAAGRVVMLDPNIRPGFIKDETTFRARI 173 ++F GI+LA+ P A L AAG++V+ DPNIRP I Sbjct: 122 VESAEVVYFSGITLAILPHEDAETLLAEVRRAKAAGKLVVFDPNIRPRLWSSYDIMHTTI 181 Query: 174 DRMLAVTDIVKVSDEDLAWLMGPGDLAESAAALRARGPAVVCVTRGGAGVEAHTATGITH 233 + +V S +D A G + + RA G + V G GV + A T Sbjct: 182 SEGARSSMLVMPSFDDEAAHFGDDSIEATIHRYRALGAVHIVVKNGAEGVTLNFAGEQTF 241 Query: 234 VAAEAVE-VVDTVGAGDTFNAGFLAGLAEAGALDKDRLRALDAPVLTSALRLGAQAAAIT 292 V AE VE VVDT AGD+FN FLA EAG DAP +A R A+ AA Sbjct: 242 VPAEKVEKVVDTTSAGDSFNGAFLARYLEAG----------DAP---AAARFAAKVAARV 288 Query: 293 VSRAGA 298 VS GA Sbjct: 289 VSEHGA 294 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: 174 Number of extensions: 5 Number of successful extensions: 1 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: 306 Length adjustment: 27 Effective length of query: 281 Effective length of database: 279 Effective search space: 78399 Effective search space used: 78399 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 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