Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate AO356_22845 AO356_22845 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::pseudo5_N2C3_1:AO356_22845 (358 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_22845 Length = 358 Score = 728 bits (1879), Expect = 0.0 Identities = 358/358 (100%), Positives = 358/358 (100%) Query: 1 MADLYENPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60 MADLYENPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN Sbjct: 1 MADLYENPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60 Query: 61 NEPHSVASYFAAEHGPSVCGMAFRVKDSQLAYKRALELGAQPIHIETGPMELNLPAIKGI 120 NEPHSVASYFAAEHGPSVCGMAFRVKDSQLAYKRALELGAQPIHIETGPMELNLPAIKGI Sbjct: 61 NEPHSVASYFAAEHGPSVCGMAFRVKDSQLAYKRALELGAQPIHIETGPMELNLPAIKGI 120 Query: 121 GGAPLYLIDRFGEGSSIYDIDFVFLEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYE 180 GGAPLYLIDRFGEGSSIYDIDFVFLEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYE Sbjct: 121 GGAPLYLIDRFGEGSSIYDIDFVFLEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYE 180 Query: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ Sbjct: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240 Query: 241 HVAFLTDDLIKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQSRGILLDGAS 300 HVAFLTDDLIKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQSRGILLDGAS Sbjct: 241 HVAFLTDDLIKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQSRGILLDGAS 300 Query: 301 EQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLATE 358 EQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLATE Sbjct: 301 EQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLATE 358 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: 696 Number of extensions: 25 Number of successful extensions: 1 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: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 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)
Align candidate AO356_22845 AO356_22845 (4-hydroxyphenylpyruvate dioxygenase)
to HMM TIGR01263 (hppD: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR01263.hmm # target sequence database: /tmp/gapView.30200.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01263 [M=353] Accession: TIGR01263 Description: 4HPPD: 4-hydroxyphenylpyruvate dioxygenase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-129 418.0 0.0 2.4e-129 417.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22845 AO356_22845 4-hydroxyphenylpyruv Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22845 AO356_22845 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.8 0.0 2.4e-129 2.4e-129 1 353 [] 12 355 .. 12 355 .. 0.98 Alignments for each domain: == domain 1 score: 417.8 bits; conditional E-value: 2.4e-129 TIGR01263 1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaa 63 +gf+f+efa++ ++ +++ ++e +Gf++va+ +r+k+++++rqg i+l+l++e++s a+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22845 12 MGFEFIEFASPTPN-TLEPIFEIMGFTKVAT---HRSKDVHLYRQGAINLILNNEPHSV--AS 68 58***********9.***************9...************************9..** PP TIGR01263 64 aflakHGdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlve 126 f+a+HG++v+++af+v+d + a+++a+e ga++++ ++ +e++l+aikgiG++ l+l++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22845 69 YFAAEHGPSVCGMAFRVKDSQLAYKRALELGAQPIHIETG--PMELNLPAIKGIGGAPLYLID 129 ************************************9986..99******************* PP TIGR01263 127 regekgsilpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiks 189 r+ge +si+++++ + e +++++ ++gl+ iDH+++nv+rg++ ++a fyek+++f+ei++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22845 130 RFGEGSSIYDIDFVFLEG--VDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYEKLFNFREIRY 190 *************99997..778889************************************* PP TIGR01263 190 fdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivkt 252 fdik+e+++L+Sk++++++g++++plne +s+k +QIee+l++++G+G+QH+A++t+d++kt lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22845 191 FDIKGEYTGLTSKAMTAPDGMIRIPLNE-ESSKGAGQIEEFLMQFNGEGIQHVAFLTDDLIKT 252 ****************************.899******************************* PP TIGR01263 253 veelrargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd.eeG...lLLQiFtk 310 +++l++ g++f++ +p+tYY++l+ r+++ + e+++el++++iL+D++ e+G lLLQiF++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22845 253 WDHLKSIGMRFMTaPPDTYYEMLEGRLPN-HGEPVNELQSRGILLDGAsEQGdkrLLLQIFSE 314 *************9**************7.*****************99999999******** PP TIGR01263 311 pvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353 +++ g++FfE+IqRkg++GFGegNfkaLfe+iEr+q++rgvl lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22845 315 TLM--GPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVL 355 ***..***********************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (358 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.53 // [ok]
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