Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_012334472.1 M446_RS22850 sugar phosphate isomerase/epimerase and 4-hydroxyphenylpyruvate domain-containing protein
Query= reanno::psRCH2:GFF3449 (361 letters) >NCBI__GCF_000019365.1:WP_012334472.1 Length = 637 Score = 192 bits (487), Expect = 3e-53 Identities = 118/326 (36%), Positives = 177/326 (54%), Gaps = 7/326 (2%) Query: 16 DGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVLNGSPTGHVH 75 +G EF+EF A + E ++ + +GF TA+HRSK V + Q IN+V+N G H Sbjct: 297 EGIEFIEF-AMDEEEARAFESVLSGLGFARTARHRSKAVTRWSQGAINLVVNTEKEGFAH 355 Query: 76 AFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEGIGGSLLYLV 135 +F HG S CA+A RV +A A + + GEL+IP V G+GGSLLYLV Sbjct: 356 SFQVTHGASVCAVALRVDDAGAALERARALLDEPFRQAVAPGELDIPAVRGVGGSLLYLV 415 Query: 136 DRY-GDKSIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDVWSGFYERIANFREI 194 DR G ++DVDFE + GL+ +DHL ++ +M W FY + + ++ Sbjct: 416 DRRSGLDRLWDVDFEPLAPEPVR--GAGLVAVDHLAQSMRHEEMLTWLLFYTGLFDLAKL 473 Query: 195 RYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQHIALSTDDI 254 D+ + S+A+ AP +R+ +N S ++ F+ E G G+QH+AL+TDDI Sbjct: 474 PVQDVVDPGGVVESQAVEAPGAALRLVLNASQSSRTLSSRFLSEALGGGVQHVALATDDI 533 Query: 255 YATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAPGDDGILLQIF 314 ATV LRA GV + P+ YY+ ++ R E LR+ NIL D G + Q++ Sbjct: 534 VATVASLRAAGVALLPIPENYYDDLEARTDLPPETLARLRDGNILYDREGGAE--FFQVY 591 Query: 315 TNTVIGPIF-FEIIQRKGNQGFGEGN 339 T ++G F FEI++R+G +G+G N Sbjct: 592 TRGLLGGGFAFEIVERRGYRGYGAAN 617 Lambda K H 0.320 0.139 0.412 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: 495 Number of extensions: 30 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: 361 Length of database: 637 Length adjustment: 34 Effective length of query: 327 Effective length of database: 603 Effective search space: 197181 Effective search space used: 197181 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