Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_090448693.1 BLS63_RS26010 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::pseudo3_N2E3:AO353_26925 (358 letters) >NCBI__GCF_900100495.1:WP_090448693.1 Length = 635 Score = 174 bits (440), Expect = 8e-48 Identities = 109/328 (33%), Positives = 164/328 (50%), Gaps = 11/328 (3%) Query: 13 GFEFIELA--SPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGQINLILNNEPHSVASYF 70 G EF+E A L E +GF + HRSKDV L RQG IN++LN EP+S A F Sbjct: 295 GVEFLEFAVDEAVGARLGDWLERLGFARAGQHRSKDVSLLRQGDINIVLNAEPYSFAHNF 354 Query: 71 AAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAPLYLIDR 130 HGPS+C A RVKD A +RA + QP GP E +PA++ G+ +YL+++ Sbjct: 355 FEAHGPSLCATALRVKDGAAALQRACDYRGQPYRGLVGPNEREIPAVRAPDGSLIYLVEQ 414 Query: 131 FGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYEKLFNFREIRY 190 G G +IYD DF G + GL+ IDH+ + + W FY+ + +F Sbjct: 415 AGAGQTIYDSDFSLDAGAE---AKGGLQRIDHMALALPADGLDSWVLFYKSVLDFEADDE 471 Query: 191 FDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAFLSDDLI 250 + Y + S+A+ + +R+PLN ++ I L + G G+ H+AF D+ Sbjct: 472 VVLPDPYGLVKSRALRSRCSSVRLPLNISENRNTA-IAHALSSYRGSGVHHIAFSCADIF 530 Query: 251 KTWDHLKKIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQARGILLDGSSEAGDKRLLLQ 310 + K+ G+ + P + YY+ L R E ++EL +L D ++ G+ L Sbjct: 531 QEVARAKEAGVPLLEIPLN-YYDDLAARFDFDDEFLSELAYYNVLYDRDAQGGE---LFH 586 Query: 311 IFSETLMGPVFFEFIQRK-GDDGFGEGN 337 +++E FFE IQRK G G+G N Sbjct: 587 VYTEAFEERFFFEIIQRKNGYVGYGAAN 614 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: 557 Number of extensions: 35 Number of successful extensions: 4 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: 635 Length adjustment: 33 Effective length of query: 325 Effective length of database: 602 Effective search space: 195650 Effective search space used: 195650 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 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