Align 4-hydroxyphenylpyruvate dioxygenase; 4HPPD; HPD; HPPDase; EC 1.13.11.27 (uncharacterized)
to candidate AO356_15580 AO356_15580 4-hydroxyphenylpyruvate dioxygenase
Query= curated2:Q9I576 (357 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_15580 Length = 633 Score = 184 bits (467), Expect = 6e-51 Identities = 116/329 (35%), Positives = 164/329 (49%), Gaps = 16/329 (4%) Query: 16 DGFEFVEFTAPDAKGIEQLRQLFNMMGFTETAKHRSKEVFLFQQNDINIVLNGSPTGHVH 75 DG EF+EF D+ G + L +GF + +HRSK V L +Q DIN++LN P H Sbjct: 295 DGIEFLEFAVDDSLGAK-LSHWLERLGFVKAGQHRSKNVSLLRQGDINLILNSEPYSFAH 353 Query: 76 EFALKHGPSACAMAFRVKNAS----QAAAYAESQGAKLVGSHANFGELNIPSLEGIGGSL 131 F HGPS CA A RVKN++ +A AY LVG + EL + ++ GSL Sbjct: 354 SFFEAHGPSLCATAVRVKNSASALERAVAYKGQPYRGLVGPN----ELELAAVRAPDGSL 409 Query: 132 LYLVDRYGDRSIYDVDFEFIEGRSANDNSVGLTYIDHLTHNVKRGQMDVWSGFYERIANF 191 +YLVD+ D +Y DF G GL IDH+ + +D W FY+ + +F Sbjct: 410 IYLVDQEAD--VYGTDFNLQPGAVIG---AGLKRIDHMAMALPADSLDSWVLFYKSLLDF 464 Query: 192 REIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDTSQIEEFIREYHGEGIQHIALTT 251 + + SRA+ + C IR+P+N S + + I + Y G G+ HIA Sbjct: 465 EADDEVVLPDPYGLVKSRALRSRCSSIRLPLNISENRNTAISHALSSYRGSGVHHIAFDC 524 Query: 252 DDIYATVRKLRDNGVKFMSTPDTYYEKVDTRVAGHGEPLEQLRELNLLIDGAPGDDGILL 311 DDI+A V + ++ GV + P YY+ + R E L +L N+L D G L Sbjct: 525 DDIFAQVSRAKEAGVPLLDIPLNYYDDLAARFDFDDEFLSELAYFNVLYD-RDAQGGELF 583 Query: 312 QIFTDTVIGPIFFEIIQRK-GNQGFGEGN 339 ++T+ G FFEIIQRK G G+G N Sbjct: 584 HVYTEPFEGRFFFEIIQRKNGYAGYGAAN 612 Lambda K H 0.320 0.139 0.406 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: 578 Number of extensions: 35 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: 357 Length of database: 633 Length adjustment: 33 Effective length of query: 324 Effective length of database: 600 Effective search space: 194400 Effective search space used: 194400 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: 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