Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_089299872.1 CHB84_RS02105 4-hydroxyphenylpyruvate dioxygenase
Query= BRENDA::Q53586 (381 letters) >NCBI__GCF_900188115.1:WP_089299872.1 Length = 399 Score = 491 bits (1265), Expect = e-143 Identities = 249/377 (66%), Positives = 292/377 (77%), Gaps = 9/377 (2%) Query: 10 DTARQADPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNG 69 D DPFPV+ MDAVVF VGNA QAA +Y AFGM LVAYSGPE G+ + ++VLT+G Sbjct: 27 DHDETTDPFPVRAMDAVVFVVGNATQAAWFYQAAFGMTLVAYSGPETGNSDHKAFVLTSG 86 Query: 70 SARFVLTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPY 129 SARFV+ ++P++P L DH HGDGVVDLA+EV D +A GA + EP+ Sbjct: 87 SARFVVKGGVQPSSP----LLDHHRRHGDGVVDLALEVADVDRCIEHARAMGATVLDEPH 142 Query: 130 ELKDEHGTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVA---AAPIVEPPAHRTFQAID 186 + DEHGTV AIATYG+TRHTLVDR+ Y GPYLPGYVA A E R FQA+D Sbjct: 143 DEHDEHGTVRTGAIATYGETRHTLVDRSRYAGPYLPGYVARHGAIERAEGAPRRLFQAVD 202 Query: 187 HCVGNVELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINE 246 HCVGNVELG M+ WV FY +VMGF NM EFVGDDIATEYSALMSKVVA+G +VKFP+NE Sbjct: 203 HCVGNVELGNMDYWVDFYRRVMGFVNMAEFVGDDIATEYSALMSKVVANGNHRVKFPLNE 262 Query: 247 PALAKKKSQIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDTPDSYYD--TLG 304 PA+AKK+SQIDEYL++YGGAG QHIAL T DI+ TVR MR AGV+FL+ PDSYYD L Sbjct: 263 PAVAKKRSQIDEYLDYYGGAGCQHIALATNDIISTVRHMRKAGVEFLNVPDSYYDDPELR 322 Query: 305 EWVGDTRVPVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNF 364 +G+ RVP++TL+E IL DRDEDGYLLQ+FTKP+ DRPTVFFE+IERHGS+GFGKGNF Sbjct: 323 ARIGEVRVPIETLQEHGILVDRDEDGYLLQLFTKPIGDRPTVFFELIERHGSLGFGKGNF 382 Query: 365 KALFEAIEREQEKRGNL 381 KALFEAIEREQ++RGNL Sbjct: 383 KALFEAIEREQQRRGNL 399 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: 657 Number of extensions: 27 Number of successful extensions: 5 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: 399 Length adjustment: 30 Effective length of query: 351 Effective length of database: 369 Effective search space: 129519 Effective search space used: 129519 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: 50 (23.9 bits)
Align candidate WP_089299872.1 CHB84_RS02105 (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.16242.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.3e-131 423.0 0.0 8.2e-131 422.6 0.0 1.1 1 lcl|NCBI__GCF_900188115.1:WP_089299872.1 CHB84_RS02105 4-hydroxyphenylpyr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188115.1:WP_089299872.1 CHB84_RS02105 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.6 0.0 8.2e-131 8.2e-131 2 353 .] 39 399 .] 38 399 .] 0.98 Alignments for each domain: == domain 1 score: 422.6 bits; conditional E-value: 8.2e-131 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavak...etgsrekastvlrqgeitlvltaelsssseaaafla 67 ++d v f+vg+a+qaa ++ ++G+++va+ etg++++++ vl++g++++v++ ++ss++ ++ + lcl|NCBI__GCF_900188115.1:WP_089299872.1 39 AMDAVVFVVGNATQAAWFYQAAFGMTLVAYsgpETGNSDHKAFVLTSGSARFVVKGGVQPSSPLLDHHR 107 5899***************************************************************** PP TIGR01263 68 kHGdgvkdvafevedveaafeaavergaeavsapee.ed.ekevklaaikgiGdvvltlveregekgsi 134 +HGdgv d+a+ev+dv+ + e+a + ga+++++p++ +d +++v++ ai ++G++++tlv+r++++g + lcl|NCBI__GCF_900188115.1:WP_089299872.1 108 RHGDGVVDLALEVADVDRCIEHARAMGATVLDEPHDeHDeHGTVRTGAIATYGETRHTLVDRSRYAGPY 176 **********************************997668***************************** PP TIGR01263 135 lpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfd...ikteasaLk 200 lpg+++ + + + +e + ++a+DH+vgnve g+++++++fy++++gf ++++f i te+saL+ lcl|NCBI__GCF_900188115.1:WP_089299872.1 177 LPGYVARHGAIERAEGAPRRLFQAVDHCVGNVELGNMDYWVDFYRRVMGFVNMAEFVgddIATEYSALM 245 ********************************************************8899********* PP TIGR01263 201 SkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipet 269 Skv+a+ +++vk+plnepa kk+sQI+eyl++y GaG QH+Al t+di++tv+++r+ gvefl++p++ lcl|NCBI__GCF_900188115.1:WP_089299872.1 246 SKVVANGNHRVKFPLNEPAVAKKRSQIDEYLDYYGGAGCQHIALATNDIISTVRHMRKAGVEFLNVPDS 314 ********************************************************************* PP TIGR01263 270 YYdn..lkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNf 336 YYd+ l+ r+++ v+ ++e+l+e++iLvDrde+G+LLQ+Ftkp+ dr+t+FfE+I+R+g+ GFG+gNf lcl|NCBI__GCF_900188115.1:WP_089299872.1 315 YYDDpeLRARIGE-VRVPIETLQEHGILVDRDEDGYLLQLFTKPIGDRPTVFFELIERHGSLGFGKGNF 382 ***6337788886.******************************************************* PP TIGR01263 337 kaLfeaiEreqekrgvl 353 kaLfeaiEreq++rg+l lcl|NCBI__GCF_900188115.1:WP_089299872.1 383 KALFEAIEREQQRRGNL 399 ***************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (399 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: 11.84 // [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