Align Triokinase/FMN cyclase; Bifunctional ATP-dependent dihydroxyacetone kinase/FAD-AMP lyase (cyclizing); EC 2.7.1.28; EC 2.7.1.29; EC 4.6.1.15 (characterized)
to candidate AZOBR_RS23290 AZOBR_RS23290 dihydroxyacetone kinase subunit K
Query= SwissProt::F1RKQ4 (579 letters) >FitnessBrowser__azobra:AZOBR_RS23290 Length = 332 Score = 204 bits (520), Expect = 3e-57 Identities = 119/335 (35%), Positives = 188/335 (56%), Gaps = 9/335 (2%) Query: 4 KKLVNSVAGCADDALAGLVACNPSLQLLQGHRVALRSDLDSLKGRVALLSGGGSGHEPAH 63 KKL+N A D+ L GL A +PSL +R + G+V +++GGGSGH P Sbjct: 2 KKLINDPAHYVDEMLDGLCAAHPSLMRDGPAGRVIRRTEGARAGKVGIVTGGGSGHLPLF 61 Query: 64 AGFIGKGMLTGVIAGAVFTSPAVGSILAAIRAVAQAGTVGTLLIVKNYTGDRLNFGLARE 123 G++G G++ G VF P V S +AAI+A G G L + NY GDR+NF +A E Sbjct: 62 TGYVGPGLVDACSIGNVFEGPTVDSCMAAIKAAD--GGRGVLRLYGNYGGDRMNFDMAGE 119 Query: 124 QARAEGIPVEMVVVGDDSAFTV-LKKAGRRGLCGTVLIHKVAGALAEAGVGLEEITNRVS 182 EG+ + V+ DD A +++ RRG+ G V +K+AGA A+ G L E+T + Sbjct: 120 FLEEEGLELSTVLGTDDIASAAPAERSKRRGVAGIVYAYKIAGARADEGASLAEVTAAAA 179 Query: 183 VVAKAMGTLGVSLSSCSVPGS-RPTFELSADEVELGLGIHGEAGVLRIKMATADEIVAHM 241 + T+G +LSSC +PG+ P+F ++ E+E+G+GIHGE G+ R + AD + M Sbjct: 180 KAVERTRTIGCALSSCQIPGAAEPSFRIAPSEMEMGIGIHGEPGIWRDTLKPADAVADEM 239 Query: 242 LNHMTDSSNVSHVPVQSGSSVVLMVNNLGGLSYLELGIIADAAVRFLEGRGVKIARALVG 301 ++ + ++ P SG+ V ++VN+LG EL I+ L+ G+ + + LVG Sbjct: 240 VDRL-----LAERPEGSGNRVSVLVNSLGATPLEELFILYRRIAERLDKAGLAVVQPLVG 294 Query: 302 TFMSALEMPGVSLTLLLVDEPLLKLIDAETTAAAW 336 +++++EM GVSL+L +D+ L +L+ A + W Sbjct: 295 PYVTSMEMTGVSLSLCFLDDELERLLAAPASCPFW 329 Lambda K H 0.315 0.131 0.367 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: 447 Number of extensions: 20 Number of successful extensions: 6 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: 579 Length of database: 332 Length adjustment: 32 Effective length of query: 547 Effective length of database: 300 Effective search space: 164100 Effective search space used: 164100 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 (21.6 bits) S2: 51 (24.3 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