Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate RR42_RS32440 RR42_RS32440 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::pseudo5_N2C3_1:AO356_22845 (358 letters) >FitnessBrowser__Cup4G11:RR42_RS32440 Length = 346 Score = 256 bits (654), Expect = 6e-73 Identities = 147/345 (42%), Positives = 203/345 (58%), Gaps = 17/345 (4%) Query: 12 MGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPHSVASYFA 71 MG+EF+EFASP P L FE GF +A HR K+V L+RQG +N I++ EP S A+ +A Sbjct: 1 MGYEFVEFASPDPAALGRTFERFGFHAIAQHRHKNVKLFRQGEMNFIVDAEPDSFATRYA 60 Query: 72 AEHGPSVCGMAFRVKDSQLAYKRALELGAQPIHIET-GPMELNLPAIKGIGGAPLYLIDR 130 +E+G S+C + RV D+ A+ RA++ GA P T GPMELN+PAI+GIG + +Y IDR Sbjct: 61 SEYGLSICAVGIRVNDAATAFARAVDAGAWPFEAGTVGPMELNIPAIQGIGRSIIYFIDR 120 Query: 131 F--GEGS-------SIYDIDFVFL----EGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAG 177 + EG SIYD+DF L GAGL +DH+T V G + W Sbjct: 121 WRGKEGRPGDVGDISIYDVDFRALAHAATDTAATTAGAGLARVDHVTQAVDPGHLEEWLD 180 Query: 178 FYEKLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGE 237 FY K+ FREI + G + S+ + +P G+IRIP+ E+ ++ Q+E +L +GE Sbjct: 181 FYRKVLGFREIHEVN-AGWHVASDSRVLLSPCGLIRIPIYEKGTQRHDQMEHYLSGHHGE 239 Query: 238 GIQHVAFLTDDLIKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQSRGILLD 297 GIQH+A TDDL+ + L G+RF+ PP YY+ ++ R+P HG + L+ GIL+D Sbjct: 240 GIQHIALATDDLVASAAALARNGVRFV-EPPAAYYDTVDARVPGHGLDLAALRRYGILVD 298 Query: 298 GA-SEQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKAL 341 GA G + LQ F+ G FFE +QR GFGEGN AL Sbjct: 299 GALRADGTREAFLQAFARREAGEFFFEIVQRDNYHGFGEGNLPAL 343 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: 378 Number of extensions: 23 Number of successful extensions: 6 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: 346 Length adjustment: 29 Effective length of query: 329 Effective length of database: 317 Effective search space: 104293 Effective search space used: 104293 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: 49 (23.5 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