Align 4-hydroxyphenylpyruvate dioxygenase; 4HPPD; HPD; HPPDase; EC 1.13.11.27 (uncharacterized)
to candidate WP_011800961.1 PNAP_RS07790 sugar phosphate isomerase/epimerase and 4-hydroxyphenylpyruvate domain-containing protein
Query= curated2:Q9S2F4 (381 letters) >NCBI__GCF_000015505.1:WP_011800961.1 Length = 632 Score = 85.1 bits (209), Expect = 5e-21 Identities = 59/182 (32%), Positives = 90/182 (49%), Gaps = 13/182 (7%) Query: 186 DHCVGNVELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVV--ADGTLKVKFP 243 DH V V G++ WV F+ V+G + V D Y + S+ + D ++V Sbjct: 444 DHLVQAVPAGQVEPWVLFHRAVLGLAPERNVVMHD---PYGVIRSREIESTDREVRVSIT 500 Query: 244 INEPAIAKKKSQIDEYLEFYGGAGVQHIALNTNDIVATVRAMRAAGVEFLDTPDSYYDTL 303 ++E + + + + + GAGVQ IA+ D+VAT RA++A+G L P +YYD L Sbjct: 501 VSE----RDNTSVSRAVSSFRGAGVQQIAIAVTDLVATARALKASGAPLLPVPANYYDDL 556 Query: 304 GEWAGETRVPVDVLRELKILVDRDED-GYLLQIFTKPVQDRPTVFFEMIERH-GSMGFGK 361 + +REL IL DR+ D G L ++ P DR FE++ER G G+G Sbjct: 557 LARYDIDAGLLAAMRELGILYDREADGGEFLHLYLTPFDDR--FHFELVERRAGYAGYGA 614 Query: 362 GN 363 N Sbjct: 615 PN 616 Lambda K H 0.318 0.134 0.397 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: 530 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 381 Length of database: 632 Length adjustment: 34 Effective length of query: 347 Effective length of database: 598 Effective search space: 207506 Effective search space used: 207506 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 (21.7 bits) S2: 52 (24.6 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