Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Ac3H11_1849 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
Query= reanno::acidovorax_3H11:Ac3H11_1849 (381 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1849 Length = 381 Score = 779 bits (2012), Expect = 0.0 Identities = 381/381 (100%), Positives = 381/381 (100%) Query: 1 MTFINECRRHPMNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTL 60 MTFINECRRHPMNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTL Sbjct: 1 MTFINECRRHPMNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTL 60 Query: 61 VAKHRSKDVVLYRQNGINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHKAYNRALEL 120 VAKHRSKDVVLYRQNGINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHKAYNRALEL Sbjct: 61 VAKHRSKDVVLYRQNGINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHKAYNRALEL 120 Query: 121 GAQPIEIPTGPMELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLN 180 GAQPIEIPTGPMELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLN Sbjct: 121 GAQPIEIPTGPMELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLN 180 Query: 181 LIDHLTHNVYRGRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNE 240 LIDHLTHNVYRGRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNE Sbjct: 181 LIDHLTHNVYRGRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNE 240 Query: 241 ESKQGGGQIEEFLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTR 300 ESKQGGGQIEEFLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTR Sbjct: 241 ESKQGGGQIEEFLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTR 300 Query: 301 LPGHGQPVPELQSRGILLDGTTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEG 360 LPGHGQPVPELQSRGILLDGTTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEG Sbjct: 301 LPGHGQPVPELQSRGILLDGTTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEG 360 Query: 361 NFKALFESLERDQIRRGVLNA 381 NFKALFESLERDQIRRGVLNA Sbjct: 361 NFKALFESLERDQIRRGVLNA 381 Lambda K H 0.322 0.142 0.431 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: 767 Number of extensions: 31 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: 381 Length of database: 381 Length adjustment: 30 Effective length of query: 351 Effective length of database: 351 Effective search space: 123201 Effective search space used: 123201 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: 50 (23.9 bits)
Align candidate Ac3H11_1849 (4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))
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.27401.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.9e-115 370.2 0.0 7.9e-115 370.0 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 4-hydroxyphenylpyruvate dioxygen Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.0 0.0 7.9e-115 7.9e-115 1 353 [] 34 379 .. 34 379 .. 0.97 Alignments for each domain: == domain 1 score: 370.0 bits; conditional E-value: 7.9e-115 TIGR01263 1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelssssea 62 +gf+fvef+++++ ++a++eklGf++vak +r+k+++++rq+ i+++l+ e++s+ a lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 34 MGFEFVEFTSPQPG-VLEAVFEKLGFTLVAK---HRSKDVVLYRQNGINFILNREPHSQ--A 89 58***********9.9**************9...*************************..* PP TIGR01263 63 aaflakHGdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltl 124 a f a+HG++++++af+v+d+++a+++a+e ga++++ p+ +e++l+aikgiG++ l+l lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 90 AYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTG--PMELRLPAIKGIGGAPLYL 149 ***************************************96..99***************** PP TIGR01263 125 veregekgsilpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfke 186 ++r+++ +si+++++e+ e +++++++ gl+ iDH+++nv+rg+++ +a+fyek++gf+e lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 150 IDRFEDGKSIYDIDFEFIEG--VDRRPAGHGLNLIDHLTHNVYRGRMGFWANFYEKLFGFRE 209 ****************9997..788889********************************** PP TIGR01263 187 iksfdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlnted 248 i++fdi++e+++L+Sk++++++gk+++plne +sk+ +QIee+l++++G+G+QH+Al ++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 210 IRYFDIQGEYTGLTSKAMTAPDGKIRIPLNE-ESKQGGGQIEEFLMQFNGEGIQHIALICDN 270 *******************************.899*************************** PP TIGR01263 249 ivktveelrargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd.eeG...lLL 305 +++ v++l gv++ + + e YY++l+ r++ + +++ el++++iL+D+ +G lLL lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 271 LLDVVDKLGMAGVQLATaPNEVYYEMLDTRLPG-HGQPVPELQSRGILLDGTtADGtprLLL 331 *****************55567**********7.*****************988999999** PP TIGR01263 306 QiFtkpvvdrgtlFfEiIqRkga..kGFGegNfkaLfeaiEreqekrgvl 353 QiF+ p+ g++FfE+IqR+g+ +GFGegNfkaLfe++Er+q++rgvl lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 332 QIFSTPML--GPVFFEFIQREGDyrDGFGEGNFKALFESLERDQIRRGVL 379 ********..***********85338*********************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (381 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.07 // [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