Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_012851432.1 TCUR_RS05240 4-hydroxyphenylpyruvate dioxygenase
Query= BRENDA::Q53586 (381 letters) >NCBI__GCF_000024385.1:WP_012851432.1 Length = 364 Score = 535 bits (1378), Expect = e-157 Identities = 271/369 (73%), Positives = 303/369 (82%), Gaps = 8/369 (2%) Query: 15 ADPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSARFV 74 +D FPVKGMDAVVFAVGNA+QAAHYYSTAFGM+ VAY GPE G + A++VL +GS RFV Sbjct: 2 SDAFPVKGMDAVVFAVGNARQAAHYYSTAFGMRRVAYRGPETGCPDEAAHVLESGSVRFV 61 Query: 75 LTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYELKDE 134 L ++ T G HVAEHGDGVVDLAIEVPD AA+ +A+ GAR + EPY L+DE Sbjct: 62 LRGPVRAGTDLGR----HVAEHGDGVVDLAIEVPDVEAAYEHAVAAGARGLEEPYTLEDE 117 Query: 135 HGTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVAAAPIVEPPAHRTFQAIDHCVGNVEL 194 HG V LAAIA YG+TRHTLVDR+ Y GPYLPGYVAA PIVEPP R FQAIDHCVGNVE Sbjct: 118 HGKVHLAAIAAYGETRHTLVDRSNYSGPYLPGYVAADPIVEPPKRRYFQAIDHCVGNVE- 176 Query: 195 GRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAKKKS 254 RM+EWV FY++VMGFT+M EF+GDDIATEYSALMSKVVADGT KVKFPINEPA +KS Sbjct: 177 -RMDEWVDFYHRVMGFTDMAEFIGDDIATEYSALMSKVVADGTRKVKFPINEPADGPRKS 235 Query: 255 QIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDTPDSYYD--TLGEWVGDTRV 312 QI EYLEFYGG GVQHIAL T DI+ V M+AAGV+FLDTPDSYYD L +G+ RV Sbjct: 236 QIQEYLEFYGGPGVQHIALATNDILAAVDQMKAAGVEFLDTPDSYYDDPELRARIGEVRV 295 Query: 313 PVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEAIE 372 PV+ LR+ +IL DRDEDGYLLQIFT PVQDRPTVFFE+IERHGSMGFGKGNFKALFEAIE Sbjct: 296 PVEELRKRRILVDRDEDGYLLQIFTHPVQDRPTVFFELIERHGSMGFGKGNFKALFEAIE 355 Query: 373 REQEKRGNL 381 REQ +RGNL Sbjct: 356 REQARRGNL 364 Lambda K H 0.318 0.136 0.403 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: 613 Number of extensions: 25 Number of successful extensions: 4 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: 364 Length adjustment: 30 Effective length of query: 351 Effective length of database: 334 Effective search space: 117234 Effective search space used: 117234 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_012851432.1 TCUR_RS05240 (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.30547.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.6e-134 432.4 0.0 9.6e-134 432.2 0.0 1.0 1 lcl|NCBI__GCF_000024385.1:WP_012851432.1 TCUR_RS05240 4-hydroxyphenylpyru Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_012851432.1 TCUR_RS05240 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 432.2 0.0 9.6e-134 9.6e-134 2 353 .] 9 364 .] 8 364 .] 0.97 Alignments for each domain: == domain 1 score: 432.2 bits; conditional E-value: 9.6e-134 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavak...etgsrekastvlrqgeitlvltaelsssseaaafla 67 g+d v favg+a+qaa+++++++G+++va+ etg ++a++vl +g++++vl + + + + +++a lcl|NCBI__GCF_000024385.1:WP_012851432.1 9 GMDAVVFAVGNARQAAHYYSTAFGMRRVAYrgpETGCPDEAAHVLESGSVRFVLRGPVRAGTDLGRHVA 77 899****************************************************************** PP TIGR01263 68 kHGdgvkdvafevedveaafeaavergaeavsapee.ed.ekevklaaikgiGdvvltlveregekgsi 134 +HGdgv d+a+ev dveaa+e+av++ga+ +++p + ed +++v+laai ++G++++tlv+r++++g + lcl|NCBI__GCF_000024385.1:WP_012851432.1 78 EHGDGVVDLAIEVPDVEAAYEHAVAAGARGLEEPYTlEDeHGKVHLAAIAAYGETRHTLVDRSNYSGPY 146 ************************************9888***************************** PP TIGR01263 135 lpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfd...ikteasaLk 200 lpg+++ ++ + e+++ ++aiDH+vgnve +++++++fy++++gf+ +++f i te+saL+ lcl|NCBI__GCF_000024385.1:WP_012851432.1 147 LPGYVA---ADPIVEPPKRRYFQAIDHCVGNVE--RMDEWVDFYHRVMGFTDMAEFIgddIATEYSALM 210 ***996...4457888999**************..7********************8888********* PP TIGR01263 201 SkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipet 269 Skv+a+ + kvk+p+nepa++ +ksQI+eyle+y G+GvQH+Al t+di+++v++++a gvefl++p++ lcl|NCBI__GCF_000024385.1:WP_012851432.1 211 SKVVADGTRKVKFPINEPADGPRKSQIQEYLEFYGGPGVQHIALATNDILAAVDQMKAAGVEFLDTPDS 279 ********************************************************************* PP TIGR01263 270 YYdn..lkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNf 336 YYd+ l+ r+++ v+ ++eel++++iLvDrde+G+LLQiFt+pv+dr+t+FfE+I+R+g++GFG+gNf lcl|NCBI__GCF_000024385.1:WP_012851432.1 280 YYDDpeLRARIGE-VRVPVEELRKRRILVDRDEDGYLLQIFTHPVQDRPTVFFELIERHGSMGFGKGNF 347 ***6337788886.******************************************************* PP TIGR01263 337 kaLfeaiEreqekrgvl 353 kaLfeaiEreq++rg+l lcl|NCBI__GCF_000024385.1:WP_012851432.1 348 KALFEAIEREQARRGNL 364 ***************86 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: 10.21 // [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