Align 4-hydroxyphenylpyruvate dioxygenase; 4HPPD; HPD; HPPDase; EC 1.13.11.27 (uncharacterized)
to candidate YP_002824472.1 NGR_b22740 4-hydroxyphenylpyruvate dioxygenase
Query= curated2:Q9I576 (357 letters) >NCBI__GCF_000018545.1:YP_002824472.1 Length = 630 Score = 180 bits (456), Expect = 1e-49 Identities = 111/321 (34%), Positives = 164/321 (51%), Gaps = 4/321 (1%) Query: 20 FVEFTAPDAKGIEQLRQLFNMMGFTETAKHRSKEVFLFQQNDINIVLNGSPTGHVHEFAL 79 FVEF A D E L + +GF + A HRSK+V L+QQ DI I++N G Sbjct: 293 FVEFAADDDDAAE-LTAILKTLGFRKAATHRSKDVELYQQGDIRILINTDEGGFAGSSYA 351 Query: 80 KHGPSACAMAFRVKNASQAAAYAESQGAKLVGSHANFGELNIPSLEGIGGSLLYLVDRYG 139 HG SA AMA V +A +A A + A+ GE+ +P++ G+GG LLYL+D G Sbjct: 352 VHGSSAYAMALVVDDAKEAMERALALDAEPFSQPVAIGEVELPAVRGVGGGLLYLLDDKG 411 Query: 140 DRS-IYDVDFEFIEGRSANDNSVGLTYIDHLTHNVKRGQMDVWSGFYERIANFREIRYFD 198 D I+++DFE E + GL +DH+ V QM W FY I + D Sbjct: 412 DLGRIFEIDFEPFEDEGVTVENAGLRSVDHVAQTVAYEQMPTWLLFYTSIFAAEKTPMVD 471 Query: 199 IEGKLTGLFSRAMTAPCGKIRIPINESADDTSQIEEFIREYHGEGIQHIALTTDDIYATV 258 I + S+ + G +R+ +N + + + FI E G GIQH+A TD+I+AT Sbjct: 472 IIDPAGLVRSQVVENASGTLRLTLNGAENRRTLAGHFIAETFGSGIQHLAFHTDNIFATA 531 Query: 259 RKLRDNGVKFMSTPDTYYEKVDTRVAGHGEPLEQLRELNLLIDGAPGDDGILLQIFTDTV 318 LR NG + + YY+ V+ R + E+LR N+L D ++G Q+++ T Sbjct: 532 AALRRNGFRPLQISPNYYDDVEARFGLEPKLTERLRAENILYD--RDENGEYFQLYSPTY 589 Query: 319 IGPIFFEIIQRKGNQGFGEGN 339 FFEI++R+G +G+G N Sbjct: 590 GEGFFFEIVERRGYRGYGAAN 610 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: 571 Number of extensions: 26 Number of successful extensions: 3 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: 630 Length adjustment: 33 Effective length of query: 324 Effective length of database: 597 Effective search space: 193428 Effective search space used: 193428 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