Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Ac3H11_1225 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Query= reanno::pseudo6_N2E2:Pf6N2E2_456 (358 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1225 Length = 299 Score = 152 bits (383), Expect = 1e-41 Identities = 102/266 (38%), Positives = 146/266 (54%), Gaps = 16/266 (6%) Query: 7 NPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN----NE 62 NP+GL G EFIE+A+ P L E +GF VA HRS++V LYRQG +N+I+N NE Sbjct: 17 NPLGLQGIEFIEYATSRPQALGQALERLGFQPVARHRSREVLLYRQGDMNIIVNAHQDNE 76 Query: 63 PHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGG 122 V + A P + +AFRV ++ A++R LELGA +H E MELN+PAI G+G Sbjct: 77 RTGVHAPPALTETPVLAAIAFRVGNAAAAFRRVLELGAWAVHTEVEVMELNIPAIHGVGA 136 Query: 123 APLYLIDRFGEGSSIYDIDFVFIEGVD-RNPVGAGLKIIDHLTHNVYRGRMAYWAGFYEK 181 + +Y +DR+ E SIYD+DFV I V+ R P GL + + + GR A W FY + Sbjct: 137 SRIYFVDRWKE-FSIYDVDFVPIPTVNPRPPALQGLHLFG-VVQYIGLGRAADWIHFYSE 194 Query: 182 LFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQH 241 LF F E+ G T + + +P G + L E + + L E +Q Sbjct: 195 LFGFAELAPDQSFGVLT--HGRILASPCGTLHWQLIE-------PLVDALDADPEELLQR 245 Query: 242 VAFLTDDLVKTWDHLKSIGMRFMTAP 267 VAF T D++ T L++ G+ F+ +P Sbjct: 246 VAFGTPDVLATVQALRARGVEFVESP 271 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: 308 Number of extensions: 18 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: 299 Length adjustment: 28 Effective length of query: 330 Effective length of database: 271 Effective search space: 89430 Effective search space used: 89430 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: 48 (23.1 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