Align 4-hydroxyphenylpyruvate dioxygenase; 4HPPD; HPD; HPPDase; EC 1.13.11.27 (uncharacterized)
to candidate WP_042445810.1 AZL_RS25390 sugar phosphate isomerase/epimerase and 4-hydroxyphenylpyruvate domain-containing protein
Query= curated2:Q9I576 (357 letters) >NCBI__GCF_000010725.1:WP_042445810.1 Length = 637 Score = 157 bits (398), Expect = 6e-43 Identities = 112/346 (32%), Positives = 166/346 (47%), Gaps = 12/346 (3%) Query: 17 GFEFVEFTAPDAKGIEQLRQLFNMMGFTETAKHRSKEVFLFQQNDINIVLNGSPTGHVHE 76 G EF+EF A DA ++L L +GF +HRSK+V L++Q +N+VLN E Sbjct: 289 GVEFLEF-AVDAAARDRLSALLASLGFHHAGRHRSKDVDLYRQGGVNLVLNSEEDSAASE 347 Query: 77 FALKHGPSACAMAFRVKNASQAAAYAESQGAKLVGSHANFGELNIPSLEGIGGSLLYLV- 135 HGPS CAMAF V +A++ A AE+ L GE IP+L G+L+YLV Sbjct: 348 HFQMHGPSVCAMAFTVDDAARTIARAEALRCVLWRERVGDGERRIPALRAPDGTLIYLVD 407 Query: 136 DRYGDRSIYDVDFE-FIEGRSANDNSVGLTYIDHLTHNVKRGQMDVWSGFYERIANFREI 194 D+ RSI++ DF F A L IDH+ + G+MD + FY + F Sbjct: 408 DKEARRSIWEDDFHLFPAEEPATSGEPPLLGIDHVAQALPFGRMDSFVLFYRAVFGFVPE 467 Query: 195 RYFDIEGKLTGLFSRAMTAPCGK----IRIPINESADDTSQIEEFIREYHGEGIQHIALT 250 +++ + SRA+ +P + +R+P+N S + F+ G G+ HIA Sbjct: 468 SLWELPDPYGLIRSRALVSPDAEPGRGVRLPLNISESRRTATGRFVSATAGAGVHHIAFA 527 Query: 251 TDDIYATVRKLRDNGVKFMSTPDTYYEKVDTRVAGHGEPLEQLRELNLLIDGAPGDDGIL 310 D A V + G F+ P YY+ + + LE L++ LL D D G Sbjct: 528 ASDAAALVGERLAAGAPFLPIPANYYDDLAVKHPLDDAALEALKQRELLYD--RDDQGDF 585 Query: 311 LQIFTDTVIGPIFFEIIQRKGN-QGFGEGNFKALFESIEEDQIRRG 355 L +TD+ FFE+++R+G + FG N A + Q+R G Sbjct: 586 LHAYTDSFADRFFFEMVERRGGYRQFGAVN--AAVRMAVQAQLREG 629 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: 563 Number of extensions: 30 Number of successful extensions: 4 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: 637 Length adjustment: 33 Effective length of query: 324 Effective length of database: 604 Effective search space: 195696 Effective search space used: 195696 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 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