Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_051378279.1 H566_RS23485 sugar phosphate isomerase/epimerase and 4-hydroxyphenylpyruvate domain-containing protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_456 (358 letters) >NCBI__GCF_000482785.1:WP_051378279.1 Length = 674 Score = 153 bits (387), Expect = 1e-41 Identities = 104/344 (30%), Positives = 156/344 (45%), Gaps = 11/344 (3%) Query: 8 PMGLMGFEFIEFA--SPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPHS 65 P + G F+EFA T L +F +GF + HRSK V L+RQG NL++NNEP S Sbjct: 328 PPRIDGTAFVEFAVDDGTEAALGRVFSALGFERAGEHRSKRVTLWRQGDTNLVINNEPGS 387 Query: 66 VASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAPL 125 AS F +HGPS+C +A R D Q+A RA GP E +PA++ + G+ L Sbjct: 388 FASEFFRQHGPSICAIALRTDDGQRAVNRATAFHLPRFEGRVGPHETTIPAVRTVDGSIL 447 Query: 126 YLIDRFGEGSSIYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYEKLFNF 185 Y + E +DIDF E +R GL +DH+ F Sbjct: 448 YFVSPELEARGFWDIDFRLAEPANR---AIGLGRVDHIAIAAPIESFDSAVLFQRAALGL 504 Query: 186 REIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAFL 245 ++ Y + S+A++ D +R+ LN S+ I + +G G+ H+AF Sbjct: 505 EPGDSLELTDPYGMVRSRALSNADRSLRVALNVSQSRST-VIARSVSSMHGAGVHHLAFD 563 Query: 246 TDDLVKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVDELQSRGILLDGASEQGDK 305 D+ + + G+ F+ PD YY+ L R +D L+ +L D + G+ Sbjct: 564 CADIFASVAAARGRGLAFLDI-PDNYYDDLAARFDIDAAVLDRLRMLRVLYDRDASGGE- 621 Query: 306 RLLLQIFSETLMGPVFFEFIQRKGD-DGFGEGNFKALFESIERD 348 L ++ G FFE +QR G DG+G N ++ RD Sbjct: 622 --FLHAYTPMFEGRFFFELVQRIGGYDGYGASNAPVRMAALARD 663 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: 604 Number of extensions: 33 Number of successful extensions: 3 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: 674 Length adjustment: 34 Effective length of query: 324 Effective length of database: 640 Effective search space: 207360 Effective search space used: 207360 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: 52 (24.6 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