Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate GFF3998 Psest_4071 4-hydroxyphenylpyruvate dioxygenase and related hemolysins
Query= BRENDA::P80064 (357 letters) >FitnessBrowser__psRCH2:GFF3998 Length = 641 Score = 190 bits (482), Expect = 1e-52 Identities = 117/328 (35%), Positives = 166/328 (50%), Gaps = 11/328 (3%) Query: 12 GFEFIELASPTPNT--LEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPHSVASYF 69 G +F+E A P+ L + +GF V HRSKDV L+RQG IN++LN EP+S A + Sbjct: 296 GIDFLEFAVDEPHAVRLGSWLQQLGFAHVGQHRSKDVQLFRQGEINIVLNAEPYSFAHNY 355 Query: 70 AAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAPLYLIDR 129 HGPSVC MA ++ D A RA G QP GP E +PA++ G +YL++ Sbjct: 356 FEAHGPSVCAMALKIDDEASALARACAFGGQPYRGLIGPNERQIPAVRAPDGGLIYLLES 415 Query: 130 FGEGSSIYDIDFVFLEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYEKLFNFREIRY 189 G S YDIDF L V P GAGL+ IDH+ + +A W FY LF+F Sbjct: 416 GAPGQSNYDIDF-RLHAVT--PAGAGLQRIDHMATALPAESLASWVLFYRSLFDFEADDE 472 Query: 190 FDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAFLSDDLI 249 + Y + +AM +P G +R+PLN + I + L + G G+ HVAF DD+ Sbjct: 473 LLLPDPYGLMKCRAMRSPCGRVRLPLNTSQDRDT-VIAQALSSYRGAGVHHVAFACDDIF 531 Query: 250 KTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVGELQARGILLDGSSESGDKRLLLQ 309 ++ G+ + P + YY+ L R + EL +L D +E G+ L Sbjct: 532 AEVARAQAAGVPLLQIPRN-YYDDLAARFDFDDSLLAELARYNVLYDRDAEGGE---LFH 587 Query: 310 IFSETLMGPVFFEFIQR-KGDDGFGEGN 336 +++E G FFE +QR G G+G N Sbjct: 588 VYTEPFEGRFFFEILQRCNGYAGYGTPN 615 Lambda K H 0.321 0.141 0.420 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: 595 Number of extensions: 36 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: 357 Length of database: 641 Length adjustment: 33 Effective length of query: 324 Effective length of database: 608 Effective search space: 196992 Effective search space used: 196992 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: 51 (24.3 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