Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_011445236.1 SARO_RS07950 sugar phosphate isomerase/epimerase and 4-hydroxyphenylpyruvate domain-containing protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_456 (358 letters) >NCBI__GCF_000013325.1:WP_011445236.1 Length = 621 Score = 142 bits (357), Expect = 3e-38 Identities = 98/328 (29%), Positives = 151/328 (46%), Gaps = 11/328 (3%) Query: 12 MGFEFIEFASP--TPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPHSVASY 69 +G EFIEFA+ L + +GF A HR+KDV ++QG IN+++N EP +A Sbjct: 285 LGVEFIEFAASHEEAEALGGMLRPLGFRPTARHRTKDVTRWQQGGINIVVNCEPEGLAHS 344 Query: 70 FAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAPLYLID 129 F HG SVC + V+D A RA L P E +P+++G+GG+ LY +D Sbjct: 345 FDVVHGASVCAIGLAVEDVPAALARAEFLRVPRFEQAVAPGEWPIPSVRGVGGSLLYFVD 404 Query: 130 RFGEGSSIYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYEKLFNFREIR 189 +++ +F ++ P L IDH+ + W FY LF+ + Sbjct: 405 A-ATREAMWAHEFP--HALEPLPEAPLLTSIDHIAQTMQYEEFLSWLLFYVALFDLEKTP 461 Query: 190 YFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAFLTDDL 249 +I + S+A+ + D +R LN S F+ + G G+QHVAF T D Sbjct: 462 QLEIADPMGLVQSQAVESADRSVRFTLN-GSLAAQSLTSRFVQNYFGAGVQHVAFATGDA 520 Query: 250 VKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVDELQSRGILLDGASEQGDKRLLL 309 + S G+ + A P Y++ LE R G D + + +L D E Sbjct: 521 FAASESAASKGLERL-AIPRNYHDDLEARWGLEGNLADRMAADDLLYDRDGEAE----YF 575 Query: 310 QIFSETLMGPVFFEFIQRKGDDGFGEGN 337 Q +S VFFE ++R+G +G+G N Sbjct: 576 QFYSRAFARRVFFEVVERRGYEGYGAAN 603 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: 547 Number of extensions: 37 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: 621 Length adjustment: 33 Effective length of query: 325 Effective length of database: 588 Effective search space: 191100 Effective search space used: 191100 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