Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_050463614.1 AKL27_RS14605 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_456 (358 letters) >NCBI__GCF_001189915.1:WP_050463614.1 Length = 361 Score = 601 bits (1550), Expect = e-177 Identities = 288/355 (81%), Positives = 320/355 (90%) Query: 1 MADLYENPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60 M+DL++NPMGL+GFEF+EFASP PN LEP+FE MGF+K+A HRSKDV LYRQGAIN I+N Sbjct: 1 MSDLFDNPMGLIGFEFVEFASPQPNVLEPVFESMGFSKIAKHRSKDVVLYRQGAINFIVN 60 Query: 61 NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI 120 NEP S+ASYFAAEHGPS CGMAFRVK++ +AY RALELGAQP+ I TGPMEL+LPAIKGI Sbjct: 61 NEPRSLASYFAAEHGPSACGMAFRVKNAHQAYARALELGAQPLEIPTGPMELHLPAIKGI 120 Query: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYE 180 GGAPLYLIDR+ EG SIYDIDF F EGVDR+P GAGLK+IDHLTHNVYRGRM+YWA FYE Sbjct: 121 GGAPLYLIDRYEEGKSIYDIDFEFFEGVDRHPQGAGLKLIDHLTHNVYRGRMSYWAAFYE 180 Query: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESS+G+GQIEEFLMQFNGEGIQ Sbjct: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSRGSGQIEEFLMQFNGEGIQ 240 Query: 241 HVAFLTDDLVKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVDELQSRGILLDGAS 300 H+A TDDL+ T D L++ G+ MTAPP TYYEMLEGRLP HGEP ELQ+RGILLDG + Sbjct: 241 HIALYTDDLISTLDQLRASGVPMMTAPPATYYEMLEGRLPGHGEPTAELQARGILLDGTT 300 Query: 301 EQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVL 355 + +RLLLQIFS T++GPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVL Sbjct: 301 GENGQRLLLQIFSNTVLGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVL 355 Lambda K H 0.321 0.141 0.421 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: 614 Number of extensions: 23 Number of successful extensions: 1 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: 358 Length of database: 361 Length adjustment: 29 Effective length of query: 329 Effective length of database: 332 Effective search space: 109228 Effective search space used: 109228 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate WP_050463614.1 AKL27_RS14605 (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.16061.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-125 405.7 0.0 1.3e-125 405.6 0.0 1.0 1 lcl|NCBI__GCF_001189915.1:WP_050463614.1 AKL27_RS14605 4-hydroxyphenylpyr Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001189915.1:WP_050463614.1 AKL27_RS14605 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.6 0.0 1.3e-125 1.3e-125 2 353 .] 13 355 .. 12 355 .. 0.98 Alignments for each domain: == domain 1 score: 405.6 bits; conditional E-value: 1.3e-125 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHG 70 gf+fvefa+++++ ++ ++e++Gf+++ak +r+k+++++rqg i++++++e++s a+ f+a+HG lcl|NCBI__GCF_001189915.1:WP_050463614.1 13 GFEFVEFASPQPN-VLEPVFESMGFSKIAK---HRSKDVVLYRQGAINFIVNNEPRSL--ASYFAAEHG 75 79**********9.9**************9...************************9..********* PP TIGR01263 71 dgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfe 139 ++++++af+v+++++a+++a+e ga++++ p+ +e++l+aikgiG++ l+l++r++e +si+++++ lcl|NCBI__GCF_001189915.1:WP_050463614.1 76 PSACGMAFRVKNAHQAYARALELGAQPLEIPTG--PMELHLPAIKGIGGAPLYLIDRYEEGKSIYDIDF 142 *******************************96..99******************************** PP TIGR01263 140 evsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasae 208 e+ e ++++++++gl+ iDH+++nv+rg+++++a fyek+++f+ei++fdik+e+++L+Sk++++++ lcl|NCBI__GCF_001189915.1:WP_050463614.1 143 EFFEG--VDRHPQGAGLKLIDHLTHNVYRGRMSYWAAFYEKLFNFREIRYFDIKGEYTGLTSKAMTAPD 209 *9997..677789******************************************************** PP TIGR01263 209 gkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlke 276 g++++plne +s++ ++QIee+l++++G+G+QH+Al t+d+++t+++lra+gv +++ +p tYY++l+ lcl|NCBI__GCF_001189915.1:WP_050463614.1 210 GMIRIPLNE-ESSRGSGQIEEFLMQFNGEGIQHIALYTDDLISTLDQLRASGVPMMTaPPATYYEMLEG 277 *********.899********************************************99********** PP TIGR01263 277 rvkklvkedleelkelkiLvDrd..eeG..lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfe 341 r++ + e+ el++++iL+D+ e+G lLLQiF+++v g++FfE+IqRkg++GFGegNfkaLfe lcl|NCBI__GCF_001189915.1:WP_050463614.1 278 RLPG-HGEPTAELQARGILLDGTtgENGqrLLLQIFSNTVL--GPVFFEFIQRKGDDGFGEGNFKALFE 343 ***7.*****************999***999**********..************************** PP TIGR01263 342 aiEreqekrgvl 353 +iEr+q++rgvl lcl|NCBI__GCF_001189915.1:WP_050463614.1 344 SIERDQVRRGVL 355 *********985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (361 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: 8.34 // [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