Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate H281DRAFT_03867 H281DRAFT_03867 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::psRCH2:GFF3449 (361 letters) >FitnessBrowser__Burk376:H281DRAFT_03867 Length = 377 Score = 265 bits (677), Expect = 1e-75 Identities = 146/360 (40%), Positives = 212/360 (58%), Gaps = 23/360 (6%) Query: 9 QHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVLNG 68 +HNP+GT G EFVEF + + + + + FT++GF A+H SK+V LF+Q ++N ++N Sbjct: 19 EHNPLGTAGLEFVEFASRDPQALGET---FTKLGFKAIARHISKDVTLFRQGEMNFLINA 75 Query: 69 SPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGA-KLVGSHANFGELNIPCVEGI 127 P +AE++G CA+ RV +A +A GA G GEL IP ++GI Sbjct: 76 EPDSFAARYAEEYGAGICAIGIRVADAQRAFDRAIELGAWAFEGERIGAGELLIPAIQGI 135 Query: 128 GGSLLYLVDRY----------GDKSIYDVDFEYIEGRTPNDN----AVGLMCIDHLTHNV 173 G S +Y VDR+ GD SI+D+DF I+ T + + GL+ +DHLT V Sbjct: 136 GDSHIYFVDRWRGRGGQRGGLGDISIFDIDFRPIQIDTAHADLSHAGTGLVAVDHLTQTV 195 Query: 174 MRGQMDVWSGFYERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQI- 232 G+M W FY + NFREI ++ SR M +PCG IRIP+ E ++ + Sbjct: 196 GEGRMQEWLDFYRDLLNFREIHELHANWHVSAE-SRVMVSPCGAIRIPLYEEGTRRTDLM 254 Query: 233 EEFIREYHGEGIQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDV 292 E++ ++ GEG+QH+AL+TDDI+A V QL ANGV+F+ P YYE++D R+ GHG + Sbjct: 255 HEYLPDHPGEGVQHLALATDDIFACVEQLLANGVEFVEPPPRYYEQLDARLPGHGLDVER 314 Query: 293 LRELNILIDGAPGDDGILL---QIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEE 349 L+ ++L+DG G DG+ L Q F G IFFEI+QR+G+ GFGEGN AL + E+ Sbjct: 315 LKRTHVLVDGEIGTDGVPLLFFQTFVRRGAGEIFFEIVQRQGHHGFGEGNLSALARAREQ 374 Lambda K H 0.320 0.139 0.412 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: 472 Number of extensions: 34 Number of successful extensions: 8 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: 361 Length of database: 377 Length adjustment: 30 Effective length of query: 331 Effective length of database: 347 Effective search space: 114857 Effective search space used: 114857 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 17 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