Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_034997824.1 DL88_RS15125 sugar phosphate isomerase/epimerase and 4-hydroxyphenylpyruvate domain-containing protein
Query= reanno::pseudo5_N2C3_1:AO356_22845 (358 letters) >NCBI__GCF_000745425.1:WP_034997824.1 Length = 631 Score = 171 bits (433), Expect = 5e-47 Identities = 111/325 (34%), Positives = 168/325 (51%), Gaps = 9/325 (2%) Query: 15 EFIEFA--SPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPHSVASYFAA 72 EFIEFA + LE + + +GF K A HR+K+V ++ QG IN++LN EP S A F Sbjct: 294 EFIEFAVDENSLGRLEKVLKGLGFRKFAHHRTKNVVVWSQGGINIVLNCEPESFAHSFYI 353 Query: 73 EHGPSVCGMAFRVKDSQLAYKRALELGAQPIHIETGPMELNLPAIKGIGGAPLYLIDRFG 132 HG +VC + V D+ A +RA +L A P P ++ +PAI+G+G + +Y ID+ G Sbjct: 354 THGFAVCAICLSVDDAHAALERARKLLAVPFPQAVVPGQIEIPAIRGVGNSLIYFIDQKG 413 Query: 133 EGSSIYDIDFVFLEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYEKLFNFREIRYFD 192 + +++ IDF EG+D P L IDH++ + M W FY +F+ + D Sbjct: 414 DLQNLWSIDFE-QEGMDTAPEEDVLVNIDHISQSTEYDEMLSWLLFYTSIFDVEKTSGLD 472 Query: 193 IKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAFLTDDLIKT 252 I + S+ + +G +RI +N S FL +F G G QH+AF T+D+ Sbjct: 473 IADPAGLVRSQVVQNEEGTLRIAINGAQSLRT-MAGRFLNEFFGSGTQHIAFATNDIFAA 531 Query: 253 WDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQSRGILLDGASEQGDKRLLLQIF 312 +K+ G+ + PD YY+ L R V +L + GI+ D E G+ QI+ Sbjct: 532 AKQMKANGLTTLPI-PDNYYDDLMARFDFDEVFVGQLANHGIMYD-RDETGE---YFQIY 586 Query: 313 SETLMGPVFFEFIQRKGDDGFGEGN 337 S T FFE ++R+ GFG N Sbjct: 587 SHTFPDGFFFEIVERRHYTGFGAAN 611 Lambda K H 0.321 0.141 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: 564 Number of extensions: 28 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: 358 Length of database: 631 Length adjustment: 33 Effective length of query: 325 Effective length of database: 598 Effective search space: 194350 Effective search space used: 194350 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