Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate PP_2554 PP_2554 putative 3-dehydroshikimate dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_22845 (358 letters) >FitnessBrowser__Putida:PP_2554 Length = 635 Score = 175 bits (444), Expect = 3e-48 Identities = 113/329 (34%), Positives = 166/329 (50%), Gaps = 13/329 (3%) Query: 13 GFEFIEFA--SPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPHSVASYF 70 G EF+EFA L + +GF + HRSK+V L RQG IN++LN EP+S F Sbjct: 295 GVEFLEFAVDEAVGARLGNWLKRLGFAEAGKHRSKEVQLLRQGDINIVLNAEPYSFGHNF 354 Query: 71 AAEHGPSVCGMAFRVKDSQLAYKRALELGAQPIHIETGPMELNLPAIKGIGGAPLYLIDR 130 HGPS+C A RVKD Q A KRA QP GP E +PA++ G+ LYL+++ Sbjct: 355 FEAHGPSLCATALRVKDQQAALKRATAFRGQPFRGLVGPNECEVPAVRAPDGSLLYLVEQ 414 Query: 131 FGEGSSIYDIDFVFLEGVDRNPVG-AGLKIIDHLTHNVYRGRMAYWAGFYEKLFNFREIR 189 G ++YD DF +D N GL+ IDH+ + + W FY+ LF+F Sbjct: 415 GTAGHTLYDTDF----SLDNNATATGGLRRIDHMALALPAESLDSWVLFYKSLFDFAADD 470 Query: 190 YFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAFLTDDL 249 + Y + S+A+ + G +R+PLN ++ I L + G G+ H+AF DD+ Sbjct: 471 EVVLPDPYGLVKSRALRSQCGTLRLPLNISENRNTA-IAHALSSYRGSGVHHIAFDCDDI 529 Query: 250 IKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQSRGILLDGASEQGDKRLLL 309 + K G+ + P + YY+ L R E ++EL +L D ++ G+ L Sbjct: 530 FREVARAKLAGVPLLEIPLN-YYDDLAARFDFDDEFLSELAYYNVLYDRDAQGGE---LF 585 Query: 310 QIFSETLMGPVFFEFIQRK-GDDGFGEGN 337 +++E FFE IQRK G G+G N Sbjct: 586 HVYTEPFEERFFFEIIQRKAGYAGYGAAN 614 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: 586 Number of extensions: 40 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: 635 Length adjustment: 33 Effective length of query: 325 Effective length of database: 602 Effective search space: 195650 Effective search space used: 195650 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