Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_011801055.1 PNAP_RS08275 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::acidovorax_3H11:Ac3H11_1849 (381 letters) >NCBI__GCF_000015505.1:WP_011801055.1 Length = 300 Score = 139 bits (351), Expect = 8e-38 Identities = 103/281 (36%), Positives = 145/281 (51%), Gaps = 23/281 (8%) Query: 11 PMNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTLVAKHRSKDVV 70 P+ A+ A Q A NP+GL G EF+E+ + +P L V E +GF +A+HRS++V+ Sbjct: 4 PLQASAADREAIQEAA--NPLGLDGIEFIEYATAKPQALGQVLEMMGFRPIARHRSREVM 61 Query: 71 LYRQNGINFILNREPHSQAAYFGAEHG--PSACGLAFRVKDAHKAYNRALELGAQPIEIP 128 LYRQ G+N I+N H GA+ P +A RV+DA AY ALE GA + Sbjct: 62 LYRQGGMNVIVN--AHIPVMPNGAQPADKPMLAAVALRVRDAAAAYAHALEKGAWAVPPR 119 Query: 129 TGPMELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRR-PAGHGLNLIDHLTH 187 MEL +PAI G+G + +Y +DR+ D SIYD+DF I V++ PA GL+ + Sbjct: 120 VEVMELNIPAIHGVGTSRIYFVDRY-DKFSIYDVDFVPIPTVEQHPPAVAGLHFFG-IVQ 177 Query: 188 NVYRGRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKI-RIPLNEESKQGG 246 + R WA FY +LFGF E+ + P G+I R P S+ Sbjct: 178 YIGTDRTEDWAEFYRELFGFIEL----------PAEQRFGILPKGRILRSPCPASSRFYL 227 Query: 247 GQIE---EFLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQ 284 IE L + EG+Q I L C ++L V +LG GV+ Sbjct: 228 QLIEPDASVLEVESNEGLQRIGLGCPDVLAAVAELGKRGVE 268 Lambda K H 0.322 0.142 0.431 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: 358 Number of extensions: 15 Number of successful extensions: 5 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: 381 Length of database: 300 Length adjustment: 28 Effective length of query: 353 Effective length of database: 272 Effective search space: 96016 Effective search space used: 96016 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 (21.9 bits) S2: 49 (23.5 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