Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate BPHYT_RS33445 BPHYT_RS33445 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::acidovorax_3H11:Ac3H11_1849 (381 letters) >FitnessBrowser__BFirm:BPHYT_RS33445 Length = 377 Score = 261 bits (668), Expect = 2e-74 Identities = 154/360 (42%), Positives = 203/360 (56%), Gaps = 23/360 (6%) Query: 29 NPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTLVAKHRSKDVVLYRQNGINFILNREPHSQ 88 NP+G G EFVEF + P L F KLGF +A+H SKDV LYRQ + F++N EP S Sbjct: 21 NPLGTAGLEFVEFAARDPQALGETFTKLGFKAIARHISKDVTLYRQGEMQFLINAEPDSF 80 Query: 89 AAYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIE---IPTGPMELRLPAIKGIGGA 145 AA + E+G C + RV DA +A++RA+ELGA E I TG EL +PAI+GIG + Sbjct: 81 AARYAEEYGAGICAIGIRVADAQRAFDRAIELGAWAFEGEKIGTG--ELLIPAIQGIGDS 138 Query: 146 PLYLIDRFE---------DGKSIYDIDFEFIE----GVDRRPAGHGLNLIDHLTHNVYRG 192 +Y +DR+ SI+DIDF IE D AG+GL +DHLT V G Sbjct: 139 HIYFVDRWRGRGGQRGGLGDISIFDIDFRPIEIDTAHADLSHAGNGLVAVDHLTQTVGEG 198 Query: 193 RMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEESKQGGGQIEEF 252 RM W +FY L FREI + S+ M +P G IR+PL EE + E+ Sbjct: 199 RMQEWLDFYRDLLNFREIHELHANW-HVSAESRVMVSPCGAIRVPLYEEGTSRTNLMHEY 257 Query: 253 LMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTRLPGHGQPVPELQ 312 L GEG+QHIAL D++ V++L GV+ P YY+ LD RLPGHG + L+ Sbjct: 258 LPDHPGEGVQHIALATDDIFACVEQLLANGVEFVEPPPR-YYDQLDARLPGHGLDIVRLE 316 Query: 313 SRGILLDG-TTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEGNFKALFESLER 371 +L+DG +ADG P L Q F G +FFE +QR+G + GFGEGN AL ++ E+ Sbjct: 317 RTRVLVDGEISADGVPLLFFQTFVRRRAGEIFFEIVQRQGHH--GFGEGNLSALAKAREQ 374 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: 477 Number of extensions: 34 Number of successful extensions: 7 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: 377 Length adjustment: 30 Effective length of query: 351 Effective length of database: 347 Effective search space: 121797 Effective search space used: 121797 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: 50 (23.9 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