Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate SMc03211 SMc03211 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::psRCH2:GFF3449 (361 letters) >FitnessBrowser__Smeli:SMc03211 Length = 370 Score = 367 bits (942), Expect = e-106 Identities = 190/357 (53%), Positives = 246/357 (68%), Gaps = 11/357 (3%) Query: 7 IEQHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVL 66 I NP GTDGFEFVEF P E +L LF +MG+T A+H++K++ +++Q DIN VL Sbjct: 13 ISAENPAGTDGFEFVEFAHPEPE---KLAELFGRMGYTPIARHKTKDITVWRQGDINYVL 69 Query: 67 NGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEG 126 N H F +HGP A +MA+RV +A A + ++GA+ + L++P + G Sbjct: 70 NAQAGSHAMRFVGEHGPCAPSMAWRVVDAKHAFEHAVAKGAEAYTGNNKC--LDVPAIVG 127 Query: 127 IGGSLLYLVDRYGDK-SIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDVWSGFY 185 IGGSLLY V+ YG+K S YD +FE++ R P VG +DHLTHNV RG MD W FY Sbjct: 128 IGGSLLYFVEAYGEKGSAYDAEFEWLGERDPKPPGVGFYYLDHLTHNVYRGNMDKWWAFY 187 Query: 186 ERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQ 245 + NF++I +FDI+G++TGL SRA+T+PCGKIRIP+NES DD SQIEE++++Y GEGIQ Sbjct: 188 RELFNFKQIHFFDIDGRITGLVSRAITSPCGKIRIPLNESKDDTSQIEEYLKKYKGEGIQ 247 Query: 246 HIALSTDDIYATVRQLRANGVDFMT-TPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAP 304 HIA+ T+ IY +L NG+ FM P+TYYE RV GH EP D +R ILIDG Sbjct: 248 HIAVGTEAIYDATDKLAENGLKFMPGPPETYYEMSHQRVHGHDEPIDRMRTHGILIDGEG 307 Query: 305 GDDG----ILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVI 357 +G ILLQIF+ TVIGPIFFE IQRKG++GFGEGNF+ALFESIE DQ+RRGV+ Sbjct: 308 VVNGGMTKILLQIFSRTVIGPIFFEFIQRKGDEGFGEGNFRALFESIEADQIRRGVL 364 Lambda K H 0.320 0.139 0.412 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: 475 Number of extensions: 20 Number of successful extensions: 6 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: 361 Length of database: 370 Length adjustment: 30 Effective length of query: 331 Effective length of database: 340 Effective search space: 112540 Effective search space used: 112540 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 SMc03211 SMc03211 (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.12416.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-125 404.8 0.0 2.5e-125 404.6 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc03211 SMc03211 4-hydroxyphenylpyruvate Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc03211 SMc03211 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 404.6 0.0 2.5e-125 2.5e-125 2 353 .] 23 364 .. 22 364 .. 0.97 Alignments for each domain: == domain 1 score: 404.6 bits; conditional E-value: 2.5e-125 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkdv 76 gf+fvefa+++++ ++++l+ ++G++ +a+ +++k++tv+rqg+i++vl+a+ s+ a++f+ +HG+++ ++ lcl|FitnessBrowser__Smeli:SMc03211 23 GFEFVEFAHPEPE-KLAELFGRMGYTPIAR---HKTKDITVWRQGDINYVLNAQAGSH--AMRFVGEHGPCAPSM 91 8***********9.99999**********8...*************************..*************** PP TIGR01263 77 afevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkekl 151 a++v d+++afe+av++gaea++ ++ k ++++ai giG+++l++ve++gekgs +++++e+ + + k+ lcl|FitnessBrowser__Smeli:SMc03211 92 AWRVVDAKHAFEHAVAKGAEAYTGNN----KCLDVPAIVGIGGSLLYFVEAYGEKGSAYDAEFEWLGE--RDPKP 160 *********************98886....79**********************************97..67778 PP TIGR01263 152 edvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkksQ 226 ++vg++++DH+++nv+rg+++k++ fy+++++fk+i+ fdi++++++L+S++++s++gk+++plne sk+++sQ lcl|FitnessBrowser__Smeli:SMc03211 161 PGVGFYYLDHLTHNVYRGNMDKWWAFYRELFNFKQIHFFDIDGRITGLVSRAITSPCGKIRIPLNE--SKDDTSQ 233 9*****************************************************************..9****** PP TIGR01263 227 IeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd. 299 Ieeyl++y+G+G+QH+A+ te i++++++l ++g++f++ +petYY++ ++rv+ ++e+++++++++iL+D++ lcl|FitnessBrowser__Smeli:SMc03211 234 IEEYLKKYKGEGIQHIAVGTEAIYDATDKLAENGLKFMPgPPETYYEMSHQRVHG-HDEPIDRMRTHGILIDGEg 307 ******************************************************7.******************9 PP TIGR01263 300 ..eeG...lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353 + G +LLQiF+++v+ g++FfE+IqRkg++GFGegNf+aLfe+iE +q++rgvl lcl|FitnessBrowser__Smeli:SMc03211 308 vvNGGmtkILLQIFSRTVI--GPIFFEFIQRKGDEGFGEGNFRALFESIEADQIRRGVL 364 966669999**********..***********************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (370 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.79 // [ok]
This GapMind analysis is from Sep 17 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