Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_013517522.1 ALIDE2_RS02940 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::acidovorax_3H11:Ac3H11_1849 (381 letters) >NCBI__GCF_000204645.1:WP_013517522.1 Length = 373 Score = 657 bits (1694), Expect = 0.0 Identities = 319/369 (86%), Positives = 342/369 (92%), Gaps = 2/369 (0%) Query: 12 MNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTLVAKHRSKDVVL 71 M AALP + A + AW+NPMGLMGFEFVEFTSPQPG+LE VFEKLGFTLVA+HRSKDV+L Sbjct: 1 MTAALPTQAARETTAWENPMGLMGFEFVEFTSPQPGLLEDVFEKLGFTLVARHRSKDVLL 60 Query: 72 YRQNGINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTGP 131 YRQN INFILNREPHSQAAYFGAEHGPSACGLAFRVKDAH+AY RALELGAQPIEIPTGP Sbjct: 61 YRQNQINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHRAYKRALELGAQPIEIPTGP 120 Query: 132 MELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLNLIDHLTHNVYR 191 MELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFE++EGV +RP GHGL IDHLTHNVYR Sbjct: 121 MELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEWLEGVPQRPEGHGLKEIDHLTHNVYR 180 Query: 192 GRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEESKQGGGQIEE 251 GRMGFWANFYEKLF FREIRYFDIQGEYTGLTSKAMTAPDG+IRIPLNEE++QGGGQIEE Sbjct: 181 GRMGFWANFYEKLFNFREIRYFDIQGEYTGLTSKAMTAPDGRIRIPLNEEARQGGGQIEE 240 Query: 252 FLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTRLPGHGQPVPEL 311 FLMQFNGEGIQHIAL+CD L DVVD+LG+AGV LA APN+VYYEMLD RLPGHGQ V L Sbjct: 241 FLMQFNGEGIQHIALVCDRLTDVVDRLGLAGVPLAPAPNDVYYEMLDKRLPGHGQDVAAL 300 Query: 312 QSRGILLDGTTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEGNFKALFESLER 371 Q+RGILLDG+TA G PRLLLQIFSTPMLGPVFFEFIQREGD +GFGEGNFKALFESLER Sbjct: 301 QARGILLDGSTAGGQPRLLLQIFSTPMLGPVFFEFIQREGD--EGFGEGNFKALFESLER 358 Query: 372 DQIRRGVLN 380 DQ+ RGV++ Sbjct: 359 DQVNRGVID 367 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: 686 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: 373 Length adjustment: 30 Effective length of query: 351 Effective length of database: 343 Effective search space: 120393 Effective search space used: 120393 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 WP_013517522.1 ALIDE2_RS02940 (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.17270.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-115 372.4 0.0 1.7e-115 372.2 0.0 1.0 1 lcl|NCBI__GCF_000204645.1:WP_013517522.1 ALIDE2_RS02940 4-hydroxyphenylpy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000204645.1:WP_013517522.1 ALIDE2_RS02940 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.2 0.0 1.7e-115 1.7e-115 1 352 [. 23 365 .. 23 366 .. 0.97 Alignments for each domain: == domain 1 score: 372.2 bits; conditional E-value: 1.7e-115 TIGR01263 1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakH 69 +gf+fvef+++++ ++ ++eklGf++va+ +r+k++ ++rq++i+++l+ e++s+ aa f a+H lcl|NCBI__GCF_000204645.1:WP_013517522.1 23 MGFEFVEFTSPQPG-LLEDVFEKLGFTLVAR---HRSKDVLLYRQNQINFILNREPHSQ--AAYFGAEH 85 58***********9.9**************8...*************************..******** PP TIGR01263 70 GdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgf 138 G++++++af+v+d++ a+++a+e ga++++ p+ +e++l+aikgiG++ l+l++r+++ +si++++ lcl|NCBI__GCF_000204645.1:WP_013517522.1 86 GPSACGLAFRVKDAHRAYKRALELGAQPIEIPTG--PMELRLPAIKGIGGAPLYLIDRFEDGKSIYDID 152 ********************************96..99******************************* PP TIGR01263 139 eevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasa 207 +e+ e + +++e+ gl++iDH+++nv+rg+++ +a+fyek+++f+ei++fdi++e+++L+Sk+++++ lcl|NCBI__GCF_000204645.1:WP_013517522.1 153 FEWLEG--VPQRPEGHGLKEIDHLTHNVYRGRMGFWANFYEKLFNFREIRYFDIQGEYTGLTSKAMTAP 219 ****98..778889******************************************************* PP TIGR01263 208 egkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlk 275 +g++++plne + + +QIee+l++++G+G+QH+Al+ + +++ v++l gv + + + + YY++l+ lcl|NCBI__GCF_000204645.1:WP_013517522.1 220 DGRIRIPLNE-EARQGGGQIEEFLMQFNGEGIQHIALVCDRLTDVVDRLGLAGVPLAPaPNDVYYEMLD 287 **********.788999*****************************************55678****** PP TIGR01263 276 ervkklvkedleelkelkiLvDrdeeG....lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLf 340 +r++ + +d+ l++++iL+D++ G lLLQiF+ p+ g++FfE+IqR+g++GFGegNfkaLf lcl|NCBI__GCF_000204645.1:WP_013517522.1 288 KRLPG-HGQDVAALQARGILLDGSTAGgqprLLLQIFSTPML--GPVFFEFIQREGDEGFGEGNFKALF 353 ****7.******************8888999***********..************************* PP TIGR01263 341 eaiEreqekrgv 352 e++Er+q++rgv lcl|NCBI__GCF_000204645.1:WP_013517522.1 354 ESLERDQVNRGV 365 **********98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (373 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: 11.93 // [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