Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_028997136.1 H537_RS0105845 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::acidovorax_3H11:Ac3H11_1849 (381 letters) >NCBI__GCF_000430725.1:WP_028997136.1 Length = 359 Score = 595 bits (1533), Expect = e-175 Identities = 286/354 (80%), Positives = 318/354 (89%), Gaps = 2/354 (0%) Query: 27 WDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTLVAKHRSKDVVLYRQNGINFILNREPH 86 +DNPMGLMGFEFVEF SP PG+LEAVFEK+GFTLVAKHRSK+V+L+RQ INFI+N EP Sbjct: 5 FDNPMGLMGFEFVEFASPTPGLLEAVFEKMGFTLVAKHRSKNVLLFRQGDINFIVNNEPK 64 Query: 87 SQAAYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTGPMELRLPAIKGIGGAP 146 S AAYF AEHGPSACGLAFRVKD+HKAY ALE GAQP++IPTGPMELRLPAIKGIGGAP Sbjct: 65 SVAAYFAAEHGPSACGLAFRVKDSHKAYAMALEQGAQPVDIPTGPMELRLPAIKGIGGAP 124 Query: 147 LYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLNLIDHLTHNVYRGRMGFWANFYEKLFG 206 LYLIDRFEDGKSIYDIDFEF+EGV+RRP GHG +IDHLTHNVYRGRM +WA+FYEKLF Sbjct: 125 LYLIDRFEDGKSIYDIDFEFVEGVERRPVGHGFKVIDHLTHNVYRGRMAYWASFYEKLFN 184 Query: 207 FREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEESKQGGGQIEEFLMQFNGEGIQHIAL 266 FREIRYFDIQGEYTGLTSKAMTAPDG+IRIPLNEESKQG GQIEEFLMQFNGEGIQH+AL Sbjct: 185 FREIRYFDIQGEYTGLTSKAMTAPDGQIRIPLNEESKQGSGQIEEFLMQFNGEGIQHVAL 244 Query: 267 ICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTRLPGHGQPVPELQSRGILLDGTTADGT 326 + D++ + VDKL MAG+ + TAPN++YYEML RLPGHGQPV EL++RGILLDG T G Sbjct: 245 LTDDIFESVDKLQMAGIPVMTAPNDIYYEMLQERLPGHGQPVEELKARGILLDGNTQGGE 304 Query: 327 PRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEGNFKALFESLERDQIRRGVLN 380 RLLLQIFS + GPVFFEFIQR+GD DGFGEGNFKALF+S+ERDQIRRGVL+ Sbjct: 305 KRLLLQIFSQALFGPVFFEFIQRKGD--DGFGEGNFKALFQSMERDQIRRGVLD 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: 645 Number of extensions: 26 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: 359 Length adjustment: 30 Effective length of query: 351 Effective length of database: 329 Effective search space: 115479 Effective search space used: 115479 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_028997136.1 H537_RS0105845 (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.13770.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-123 398.4 0.0 2.2e-123 398.2 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_028997136.1 H537_RS0105845 4-hydroxyphenylpy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_028997136.1 H537_RS0105845 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 398.2 0.0 2.2e-123 2.2e-123 1 353 [] 12 355 .. 12 355 .. 0.97 Alignments for each domain: == domain 1 score: 398.2 bits; conditional E-value: 2.2e-123 TIGR01263 1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakH 69 +gf+fvefa++ + ++a++ek+Gf++vak +r+k++ ++rqg+i++++++e++s aa f+a+H lcl|NCBI__GCF_000430725.1:WP_028997136.1 12 MGFEFVEFASPTPG-LLEAVFEKMGFTLVAK---HRSKNVLLFRQGDINFIVNNEPKSV--AAYFAAEH 74 58***********9.9**************9...************************9..******** PP TIGR01263 70 GdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgf 138 G++++++af+v+d ++a++ a+e+ga++v+ p+ +e++l+aikgiG++ l+l++r+++ +si++++ lcl|NCBI__GCF_000430725.1:WP_028997136.1 75 GPSACGLAFRVKDSHKAYAMALEQGAQPVDIPTG--PMELRLPAIKGIGGAPLYLIDRFEDGKSIYDID 141 ********************************96..99******************************* PP TIGR01263 139 eevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasa 207 +e+ e +++++ + g++ iDH+++nv+rg++ ++a+fyek+++f+ei++fdi++e+++L+Sk+++++ lcl|NCBI__GCF_000430725.1:WP_028997136.1 142 FEFVEG--VERRPVGHGFKVIDHLTHNVYRGRMAYWASFYEKLFNFREIRYFDIQGEYTGLTSKAMTAP 208 ***998..667779******************************************************* PP TIGR01263 208 egkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlk 275 +g++++plne +sk+ ++QIee+l++++G+G+QH+Al+t+di+++v++l+ g+ +++ + + YY++l+ lcl|NCBI__GCF_000430725.1:WP_028997136.1 209 DGQIRIPLNE-ESKQGSGQIEEFLMQFNGEGIQHVALLTDDIFESVDKLQMAGIPVMTaPNDIYYEMLQ 276 **********.899********************************************55578****** PP TIGR01263 276 ervkklvkedleelkelkiLvDrdeeG....lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLf 340 er++ + +++eelk+++iL+D++ +G lLLQiF++ ++ g++FfE+IqRkg++GFGegNfkaLf lcl|NCBI__GCF_000430725.1:WP_028997136.1 277 ERLPG-HGQPVEELKARGILLDGNTQGgekrLLLQIFSQALF--GPVFFEFIQRKGDDGFGEGNFKALF 342 ****7.******************8888999***********..************************* PP TIGR01263 341 eaiEreqekrgvl 353 +++Er+q++rgvl lcl|NCBI__GCF_000430725.1:WP_028997136.1 343 QSMERDQIRRGVL 355 **********985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (359 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: 10.24 // [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