Align 4-hydroxyphenylpyruvate dioxygenase; 4HPPD; HPD; HPPDase; Legiolysin; EC 1.13.11.27 (characterized)
to candidate H281DRAFT_03214 H281DRAFT_03214 4-hydroxyphenylpyruvate dioxygenase
Query= SwissProt::P69053 (348 letters) >FitnessBrowser__Burk376:H281DRAFT_03214 Length = 627 Score = 162 bits (409), Expect = 3e-44 Identities = 105/324 (32%), Positives = 154/324 (47%), Gaps = 10/324 (3%) Query: 11 GFAFLEFSGPDRNKLH--QQFSEMGFQAVAHHKNQDITLFKQGEIQFIVNAASHCQAEAH 68 G+ FLEF+ D + H ++ F+ H+++D+TL++ G ++NA A A Sbjct: 293 GYQFLEFAVDDTTRAHLADWLGKLRFRQAGQHRSKDVTLYQHGAASIVLNAEPDSFANAF 352 Query: 69 ASTHGPGACAMGFKVKDAKAAFQHAIAHGGIAFQDAPHANHG-LPAIQAIGGSVIYFVDE 127 HG CA F+V DA AF+ A G F N LPA+QA GS+ YFVDE Sbjct: 353 FQQHGLSLCASAFRVNDANQAFERAAGFGYAPFSGQIGPNERVLPAVQAPDGSLNYFVDE 412 Query: 128 E-HQPFSHEWNITSSE---PVVGNGLTAIDHLTHNVYRGNMDKWASFYASIFNFQEIRFF 183 QP E + ++ P LT IDH+ V ++D W F + F FQ Sbjct: 413 TPDQPTLFEADFVLTDVNGPFEVGPLTRIDHVCLAVPANSLDTWVLFLRTAFGFQAEPGV 472 Query: 184 NIKGKMTGLVSRALGSPCGKIKIPLNESKDDLSQIEEFLHEYHGEGIQHIALNTNDIYKT 243 + + SRAL S G +++ LN S D + + E LH YHG G+ H+A +T+DI+ Sbjct: 473 LVPDPYGLVRSRALRSRDGSVRVVLNASVDHHTAVAEALHTYHGSGLNHVAFSTSDIFSA 532 Query: 244 VNGLRKQGVKFLDVPDTYYEMINDRLPWHKEPLNQLHAEKILIDGEADPKDGLLLQIFTE 303 + G+ L +P YYE + R + L L IL D D + G +TE Sbjct: 533 IPEFVADGLPVLRIPRNYYEDLAARYELPDDMLEALREHNILYD--RDERGGEFFHAYTE 590 Query: 304 NIFGPVFFEIIQRKGN-QGFGEGN 326 + F EI++R+G G+G N Sbjct: 591 QLDQRFFMEIVERRGGYDGYGASN 614 Lambda K H 0.320 0.138 0.421 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: 583 Number of extensions: 35 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: 348 Length of database: 627 Length adjustment: 33 Effective length of query: 315 Effective length of database: 594 Effective search space: 187110 Effective search space used: 187110 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