Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate N515DRAFT_0360 N515DRAFT_0360 4-hydroxyphenylpyruvate dioxygenase
Query= BRENDA::Q09PG8 (367 letters) >FitnessBrowser__Dyella79:N515DRAFT_0360 Length = 364 Score = 530 bits (1364), Expect = e-155 Identities = 257/354 (72%), Positives = 293/354 (82%), Gaps = 2/354 (0%) Query: 16 VATFENPMGIDGFEFVEFASPEPE--KLHELFRNLGFVQVARHKTRPIYNYRQNDCTFLI 73 V TFENPMGIDGFEFVEFA+P +LHELF ++GF V +HK RPI YRQ FL+ Sbjct: 11 VTTFENPMGIDGFEFVEFAAPAGRGAELHELFGSMGFTAVLKHKRRPITVYRQGGVNFLV 70 Query: 74 NEDPDSFAADFARVHGPSACGFAIRVNKLAEWVRVQALKNGAKSIADKETSKAVAAPVIE 133 NEDPDSFAA+FA HGP A GFAIR + A V + L NG +++ DKE SKAV APV++ Sbjct: 71 NEDPDSFAAEFAAQHGPCAAGFAIRFKQPAAEVYAKVLANGGEAVGDKEASKAVDAPVVK 130 Query: 134 GIGGCMLYIVDRYDDKGTIHDPDWEWLPGAQMMPKGFGLTFIDHLTHNVYFGNMSKWADY 193 GIG CMLY+VDRY DKG+I+D D+ +PG + P GFGLTFIDHLTHN+YFGNM KW+DY Sbjct: 131 GIGDCMLYLVDRYGDKGSIYDGDYAPIPGVEQNPAGFGLTFIDHLTHNLYFGNMQKWSDY 190 Query: 194 YERLFQFREIRYFDIKGAKTGLLSKAMTAPDGMVRIPLNESPDPKSQINEYLDQYRGEGI 253 YERLF FREIRYFDIKGAKTGL+SKAMTAPDG+VRIPLNES DPKSQINEYLD Y GEGI Sbjct: 191 YERLFNFREIRYFDIKGAKTGLVSKAMTAPDGIVRIPLNESSDPKSQINEYLDAYHGEGI 250 Query: 254 QHIACFTDDIYATVEAMRAHGIEFLDTPNAYYAVIDERIPNHGEDVARMKESRILIDADP 313 QHIACFTD+IY TVEAMRA G+ FLDTP+ Y+ VID RIPNHGEDV R+ ++ILIDADP Sbjct: 251 QHIACFTDNIYETVEAMRAKGVSFLDTPDTYFDVIDLRIPNHGEDVPRLARNKILIDADP 310 Query: 314 ETKKKLLLQIFTKNCVGPIFFEIIQRKGNTGFGEGNFQALFESIEREQMARGVL 367 ETK++ LLQIFT+N +GPIFFEIIQRKGN GFGEGNFQALFESIER+QM RGVL Sbjct: 311 ETKQRKLLQIFTQNNIGPIFFEIIQRKGNEGFGEGNFQALFESIERDQMRRGVL 364 Lambda K H 0.321 0.138 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: 616 Number of extensions: 28 Number of successful extensions: 2 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: 367 Length of database: 364 Length adjustment: 30 Effective length of query: 337 Effective length of database: 334 Effective search space: 112558 Effective search space used: 112558 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 (21.9 bits) S2: 49 (23.5 bits)
Align candidate N515DRAFT_0360 N515DRAFT_0360 (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.28151.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-117 378.8 0.0 1.9e-117 378.7 0.0 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 N515DRAFT_0360 4-hydroxyphenylpy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 N515DRAFT_0360 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.7 0.0 1.9e-117 1.9e-117 2 353 .] 22 364 .] 21 364 .] 0.96 Alignments for each domain: == domain 1 score: 378.7 bits; conditional E-value: 1.9e-117 TIGR01263 2 gfdfvefavgdak.qaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaafl 66 gf+fvefa++ + + +++l+ ++Gf+av k ++++ +tv+rqg +++++++ + s aa+f+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 22 GFEFVEFAAPAGRgAELHELFGSMGFTAVLK---HKRRPITVYRQGGVNFLVNEDPDSF--AAEFA 82 89*******98774789*************9...********************99999..***** PP TIGR01263 67 akHGdgvkdvafeved.veaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregek 131 a+HG+++++ a++ ++ +++++++ +++g eav ++e +k+v+++++kgiGd +l+lv+r+g+k lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 83 AQHGPCAAGFAIRFKQpAAEVYAKVLANGGEAVGDKEA--SKAVDAPVVKGIGDCMLYLVDRYGDK 146 *************9874789*************99986..689*********************** PP TIGR01263 132 gsilpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteas 197 gsi++g+ + +++++++ gl+ iDH+++n++ g+++k++++ye++++f+ei++fdik+ + lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 147 GSIYDGDYAPIPG--VEQNPAGFGLTFIDHLTHNLYFGNMQKWSDYYERLFNFREIRYFDIKGAKT 210 ******9976665..777789********************************************* PP TIGR01263 198 aLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargvef 263 +L+Sk++++++g v++plne s++ ksQI+eyl++y+G+G+QH+A t++i++tve++ra+gv f lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 211 GLVSKAMTAPDGIVRIPLNE--SSDPKSQINEYLDAYHGEGIQHIACFTDNIYETVEAMRAKGVSF 274 ********************..99****************************************** PP TIGR01263 264 lkipetYYdnlkervkklvkedleelkelkiLvDrd...eeGlLLQiFtkpvvdrgtlFfEiIqRk 326 l++p+tY+d ++ r+++ + ed+ +l ++kiL+D d ++ LLQiFt++ + g++FfEiIqRk lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 275 LDTPDTYFDVIDLRIPN-HGEDVPRLARNKILIDADpetKQRKLLQIFTQNNI--GPIFFEIIQRK 337 ****************7.******************876667***********..*********** PP TIGR01263 327 gakGFGegNfkaLfeaiEreqekrgvl 353 g++GFGegNf+aLfe+iEr+q +rgvl lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 338 GNEGFGEGNFQALFESIERDQMRRGVL 364 ************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (364 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: 7.64 // [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