Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_011800530.1 PNAP_RS05610 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::acidovorax_3H11:Ac3H11_1849 (381 letters) >NCBI__GCF_000015505.1:WP_011800530.1 Length = 360 Score = 612 bits (1579), Expect = e-180 Identities = 298/354 (84%), Positives = 320/354 (90%), Gaps = 2/354 (0%) Query: 27 WDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTLVAKHRSKDVVLYRQNGINFILNREPH 86 +DNPMGLMGFEFVEF SP PGVLE VFE++GFTLVA+HRSKDVVLYRQ INFI+NREP Sbjct: 5 FDNPMGLMGFEFVEFASPTPGVLEPVFERMGFTLVARHRSKDVVLYRQGDINFIVNREPK 64 Query: 87 SQAAYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTGPMELRLPAIKGIGGAP 146 S A YF AEHGPSACG+AFRVKDAH AYNRALELGAQPI+IPTGPMELRLPAIKGIGGAP Sbjct: 65 SVAGYFAAEHGPSACGMAFRVKDAHLAYNRALELGAQPIDIPTGPMELRLPAIKGIGGAP 124 Query: 147 LYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLNLIDHLTHNVYRGRMGFWANFYEKLFG 206 LYLIDRFEDGKSIYDIDF F++GVDR P GHGL LIDHLTHNVYRGRM FW FYEKLF Sbjct: 125 LYLIDRFEDGKSIYDIDFVFLDGVDRHPPGHGLKLIDHLTHNVYRGRMAFWGGFYEKLFN 184 Query: 207 FREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEESKQGGGQIEEFLMQFNGEGIQHIAL 266 FREIRYFDIQGEYTGLTS+AMTAPDGKIRIPLNEESKQGGGQIEEFL++FNGEGIQHIAL Sbjct: 185 FREIRYFDIQGEYTGLTSRAMTAPDGKIRIPLNEESKQGGGQIEEFLLKFNGEGIQHIAL 244 Query: 267 ICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTRLPGHGQPVPELQSRGILLDGTTADGT 326 ICD+LL VDKL +AGV L TAP++ YYEM+D RLPGHGQPV ELQ+RGILLDG+T GT Sbjct: 245 ICDDLLATVDKLQLAGVPLMTAPSDSYYEMIDARLPGHGQPVAELQTRGILLDGSTEGGT 304 Query: 327 PRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEGNFKALFESLERDQIRRGVLN 380 PRLLLQIFS P LGPVFFEFIQR+GD +GFGEGNFKALFESLERDQI RG L+ Sbjct: 305 PRLLLQIFSQPQLGPVFFEFIQRKGD--EGFGEGNFKALFESLERDQIERGALS 356 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: 648 Number of extensions: 25 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: 381 Length of database: 360 Length adjustment: 30 Effective length of query: 351 Effective length of database: 330 Effective search space: 115830 Effective search space used: 115830 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 WP_011800530.1 PNAP_RS05610 (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.675737.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.6e-118 380.4 0.0 6.4e-118 380.2 0.0 1.0 1 NCBI__GCF_000015505.1:WP_011800530.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000015505.1:WP_011800530.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 380.2 0.0 6.4e-118 6.4e-118 1 352 [. 12 354 .. 12 355 .. 0.97 Alignments for each domain: == domain 1 score: 380.2 bits; conditional E-value: 6.4e-118 TIGR01263 1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgv 73 +gf+fvefa++ + ++ ++e++Gf++va+ +r+k+++++rqg+i+++++ e++s a f+a+HG+++ NCBI__GCF_000015505.1:WP_011800530.1 12 MGFEFVEFASPTPG-VLEPVFERMGFTLVAR---HRSKDVVLYRQGDINFIVNREPKSV--AGYFAAEHGPSA 78 58***********9.9**************8...************************9..************ PP TIGR01263 74 kdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaa 146 +++af+v+d++ a+++a+e ga++++ p+ +e++l+aikgiG++ l+l++r+++ +si+++++ + + NCBI__GCF_000015505.1:WP_011800530.1 79 CGMAFRVKDAHLAYNRALELGAQPIDIPTG--PMELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFVFLDG-- 147 ****************************96..99********************************99987.. PP TIGR01263 147 lkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepa 219 +++++++ gl+ iDH+++nv+rg++ + fyek+++f+ei++fdi++e+++L+S+++++++gk+++plne + NCBI__GCF_000015505.1:WP_011800530.1 148 VDRHPPGHGLKLIDHLTHNVYRGRMAFWGGFYEKLFNFREIRYFDIQGEYTGLTSRAMTAPDGKIRIPLNE-E 219 777789*****************************************************************.8 PP TIGR01263 220 skkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlkervkklvkedleelke 291 sk+ +QIee+l +++G+G+QH+Al +d+++tv++l+ gv +++ + ++YY++++ r++ + +++ el++ NCBI__GCF_000015505.1:WP_011800530.1 220 SKQGGGQIEEFLLKFNGEGIQHIALICDDLLATVDKLQLAGVPLMTaPSDSYYEMIDARLPG-HGQPVAELQT 291 99********************************************67789**********7.********** PP TIGR01263 292 lkiLvDrdeeG....lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgv 352 ++iL+D++ eG lLLQiF++p g++FfE+IqRkg++GFGegNfkaLfe++Er+q++rg+ NCBI__GCF_000015505.1:WP_011800530.1 292 RGILLDGSTEGgtprLLLQIFSQPQL--GPVFFEFIQRKGDEGFGEGNFKALFESLERDQIERGA 354 ********6666**99*********9..***********************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (360 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: 00:00:00.00 # Mc/sec: 14.00 // [ok]
This GapMind analysis is from Sep 24 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