Align Fructokinase (EC 2.7.1.4) (characterized)
to candidate SMc01531 SMc01531 2-dehydro-3-deoxygluconokinase
Query= reanno::Dino:3609413 (308 letters) >FitnessBrowser__Smeli:SMc01531 Length = 305 Score = 85.9 bits (211), Expect = 1e-21 Identities = 97/320 (30%), Positives = 134/320 (41%), Gaps = 33/320 (10%) Query: 2 ILCAGEALIDMLPRALPDGTAGFAPVAGGAVFNTAV-ALGRLGAD--VGLVTGLSRDLFG 58 +L GE +++++ G+A G FNTA A L AD V T + D Sbjct: 5 LLSIGECMVELMQAERDMLRKGYA----GDTFNTAYYARLFLPADWTVDYFTAVGTDTVS 60 Query: 59 EVLMTALAAADVDS-DMAVLSDRPTTLAFVTLTDGHAQYAFYDENTAGRMLAPADMPD-- 115 + L+ + + V + + + R L + L DG ++++ +A ++LA D PD Sbjct: 61 DELLAFIESTGVGTAHIRRIEGRTPGLYMIHLKDGERSFSYWRSTSAAKLLA--DDPDRL 118 Query: 116 --PGPEVGTLFFGGISLAVEPCAAAYEALC---LKAAAGRVVMLDPNIRPGFIKDETTFR 170 +FF GI+LA+ AA L A GR V+ DPNIRP D R Sbjct: 119 RAAIEAANVVFFSGITLAILSPDAAETLLAELRRAKAGGRQVVFDPNIRPRLWDDAARMR 178 Query: 171 ARIDRMLAVTDIVKVSDEDLAWLMGPGDLAESAAALRARGPAVVCVTRGGAGVE-AHTAT 229 A I+ +V S +D A G + + RA G V V G GV Sbjct: 179 ATIEAGGRAATMVMPSFDDEATHFGDASVEATIERYRALGAENVAVKDGKNGVTLCFAGK 238 Query: 230 GITHVAAEAVE-VVDTVGAGDTFNAGFLAGLAEAGALDKDRLRALDAPVLTSALRLGAQA 288 HV A V VVDT AGD+FN FLA LA D+P A A+ Sbjct: 239 ERVHVPASQVSAVVDTTSAGDSFNGSFLARLASG-----------DSP--ADAAAFAARI 285 Query: 289 AAITVSRAGANPPWRDELPR 308 AA + GA RD+LPR Sbjct: 286 AAAVIGHHGA-LIGRDKLPR 304 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: 198 Number of extensions: 10 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: 305 Length adjustment: 27 Effective length of query: 281 Effective length of database: 278 Effective search space: 78118 Effective search space used: 78118 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 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