Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_011882206.1 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2935 (358 letters) >NCBI__GCF_000016205.1:WP_011882206.1 Length = 375 Score = 260 bits (665), Expect = 4e-74 Identities = 146/356 (41%), Positives = 208/356 (58%), Gaps = 17/356 (4%) Query: 1 MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60 +AD NP+G+ G EF+E A+P P+ L FE +GF VA H SK+V LYRQG + ++N Sbjct: 15 VADPAANPLGMAGLEFVEFAAPVPDALAQRFEQLGFKAVARHVSKNVTLYRQGQMQFLIN 74 Query: 61 NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIE-TGPMELNLPAIKG 119 EP S A+ +A E+G VC + RV +++A++RA+ELGA E G EL +PAI+G Sbjct: 75 AEPDSFAARYAEEYGMGVCAIGLRVASARRAFERAIELGAWAFEGERVGVGELKIPAIQG 134 Query: 120 IGGAPLYLIDRF--------GEGS-SIYDIDF----VFIEGVDRHPVGAGLKIIDHLTHN 166 IG + LY +DR+ G G SI+DIDF + D H G GL+ +DH T Sbjct: 135 IGDSHLYFVDRWRGRDGQRGGVGDISIFDIDFRPIDIATAHADLHCEGTGLQQVDHFTQT 194 Query: 167 VYRGRMAYWANFYEKLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQ 226 V GRM W +FY L +FREI D + S+ M +P G +RIP+ EE ++ Sbjct: 195 VGAGRMREWLDFYHDLLHFREIHEIDAHW-HVSEESRVMVSPCGAVRIPVYEEGTRRTEL 253 Query: 227 IEEFLMQFNGEGIQHVAFLSDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPV 286 + +L GEG+QH+A +DD++ + D L++ G+ F+ PP YY+ ++ RLP HG + Sbjct: 254 MHAYLPDHPGEGVQHIALATDDIVASVDALRANGVDFV-EPPARYYDEVDARLPGHGVDL 312 Query: 287 DQLQARGILLDGS-SESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKAL 341 D L+ +L+DG G RL Q F + G +FFE +QR+G GFGEGN AL Sbjct: 313 DALRRCAVLVDGEIGADGVPRLFFQTFVKRRPGEIFFEIVQRQGHHGFGEGNLAAL 368 Lambda K H 0.321 0.141 0.419 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: 432 Number of extensions: 23 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: 358 Length of database: 375 Length adjustment: 30 Effective length of query: 328 Effective length of database: 345 Effective search space: 113160 Effective search space used: 113160 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: 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