Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate SM_b20581 SM_b20581 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::psRCH2:GFF3449 (361 letters) >FitnessBrowser__Smeli:SM_b20581 Length = 629 Score = 157 bits (397), Expect = 7e-43 Identities = 107/328 (32%), Positives = 166/328 (50%), Gaps = 12/328 (3%) Query: 17 GFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQH----DINIVLNGSPTG 72 G EFVEFTA AE E L +L MGF A HR K V L++Q +NIV+N G Sbjct: 289 GVEFVEFTADRAEA-ETLGSLLGTMGFHAVASHREKSVTLWRQGRDHGGVNIVINTEQQG 347 Query: 73 HVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEGIGGSLL 132 H+ HG SA A+ +V +A+ A + GA++ AN GE + + GIGG L+ Sbjct: 348 FAHSSYLVHGASAYAVGLKVPDASAAIERSRALGAEIFLPEANEGEGAMAAIRGIGGGLI 407 Query: 133 YLVDRYGDKSIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDVWSGFYERIANFR 192 Y +D D ++ +F + G TP A L+ IDH+ ++ ++ W FY I + Sbjct: 408 YFLDEADD--VWSREFVW-SGATPQ-GASPLLAIDHVAQSMQAEELPSWLLFYTSILDAD 463 Query: 193 EIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQHIALSTD 252 ++ DI + S+ + G +R+ +N + + ++ FI E G G+QH+A TD Sbjct: 464 KLAEVDIVDPAGLIRSQVVENASGTLRLTLNGADNHRTLAGHFIAESFGSGVQHVAFRTD 523 Query: 253 DIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAPGDDGILLQ 312 DI+A + +G + YY+ ++ R + D LR+ +IL D +DG Q Sbjct: 524 DIFAAADHMLRSGFRPLAISRNYYDDIEVRFGLEPDFVDRLRDESILYD--RDEDGEYFQ 581 Query: 313 IFTNTVIGPIFFEIIQRK-GNQGFGEGN 339 I+ T FFEI++R+ G +G+G N Sbjct: 582 IYGPTYGEGFFFEIVERRAGYRGYGAAN 609 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: 597 Number of extensions: 27 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: 629 Length adjustment: 33 Effective length of query: 328 Effective length of database: 596 Effective search space: 195488 Effective search space used: 195488 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