Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate BWI76_RS16945 BWI76_RS16945 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::psRCH2:GFF3449 (361 letters) >FitnessBrowser__Koxy:BWI76_RS16945 Length = 617 Score = 137 bits (344), Expect = 1e-36 Identities = 102/315 (32%), Positives = 144/315 (45%), Gaps = 9/315 (2%) Query: 17 GFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVLNGSPTGHVHA 76 G EF+EF A A+ E L Q+GF E HRSK V L++ +V+N P Sbjct: 290 GLEFIEFAAAPAQAGE-LGQRLAQLGFAEEGSHRSKRVSLWRNGGARVVVNAQPHSWADH 348 Query: 77 FAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEGIGGSLLYLVD 136 F ++HG S CAMA RV +A + G A E IP V GSL+YL++ Sbjct: 349 FHQRHGVSLCAMALRVSQSAAIVERARAYGYATWQGDAGPNESPIPAVCAPDGSLIYLIE 408 Query: 137 RYGDKSIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDVWSGFYERIANFREIRY 196 GD IY DF TP D+ G IDHL + D W F+ + F Sbjct: 409 -VGD-DIYTRDFHLRANLTPRDDYQG---IDHLALGMEADSRDNWIIFFRSVFGFILEHE 463 Query: 197 FDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQHIALSTDDIYA 256 + + S A+ +P G IR+ +N S +QI + Y G G+QH A + D+ A Sbjct: 464 QTLPDPYGLVRSLAVRSPQGDIRLALNISQSRATQIARSVACYQGAGLQHAAFACRDLPA 523 Query: 257 TVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAPGDDGILLQIFTN 316 T+ L V+ + P YY+ + R G ++L+ IL D GD G L ++T Sbjct: 524 TLASLPQIAVEALPIPANYYDDLLARF-GEDAQVNLLKNHQILYD-CDGDGGEFLHLYTR 581 Query: 317 TV-IGPIFFEIIQRK 330 G FFE+ +R+ Sbjct: 582 PFSAGRFFFELTERR 596 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: 498 Number of extensions: 30 Number of successful extensions: 2 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: 617 Length adjustment: 33 Effective length of query: 328 Effective length of database: 584 Effective search space: 191552 Effective search space used: 191552 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 17 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