Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Ga0059261_2984 Ga0059261_2984 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::psRCH2:GFF3449 (361 letters) >FitnessBrowser__Korea:Ga0059261_2984 Length = 345 Score = 351 bits (901), Expect = e-101 Identities = 192/352 (54%), Positives = 240/352 (68%), Gaps = 15/352 (4%) Query: 11 NPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVLNGSP 70 NP+G +GFEFVEFT+P+ + F Q+GF + +H +K + ++Q IN++LN Sbjct: 6 NPLGLNGFEFVEFTSPDPAA---MAAQFEQLGFVASHRHPTKNITRYKQGRINLMLNRDD 62 Query: 71 TGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEGIGGS 130 G V F +HGPSA AMAFRV + +A + + GA+ E + + GIGGS Sbjct: 63 AGRVAKFRGEHGPSASAMAFRVADPVKAMEWALAHGAERT-------EEDDTVILGIGGS 115 Query: 131 LLYLVDRYGDKSIYDVDFEYIEGRTPND--NAVGLMCIDHLTHNVMRGQMDVWSGFYERI 188 LY + D +Y+ ++ I G + N VGL +DHLTHNV RGQM VWS FY+ + Sbjct: 116 YLYFIQDGHD--LYE-NWAEIPGWQEAEAANNVGLDLLDHLTHNVRRGQMRVWSQFYKTL 172 Query: 189 ANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQHIA 248 F E +YFDI+G+ TGLFS+AM AP IRIP+NES DDKSQIEEFIREY GEGIQH+A Sbjct: 173 FGFEEQKYFDIKGQATGLFSQAMIAPDKAIRIPLNESQDDKSQIEEFIREYKGEGIQHLA 232 Query: 249 LSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAPGDDG 308 L+TDDIY TV +LRA GV T +TYYE VD RV GHGE + LR+ ILIDG G++G Sbjct: 233 LTTDDIYDTVERLRARGVRLQDTIETYYELVDKRVPGHGEDLERLRKNRILIDGNVGEEG 292 Query: 309 ILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVIKAD 360 ILLQIFT + GPIFFEIIQRKGN+GFG GNF+ALFESIE DQ+RRGVIK D Sbjct: 293 ILLQIFTENMFGPIFFEIIQRKGNEGFGNGNFQALFESIELDQIRRGVIKVD 344 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: 444 Number of extensions: 18 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 361 Length of database: 345 Length adjustment: 29 Effective length of query: 332 Effective length of database: 316 Effective search space: 104912 Effective search space used: 104912 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 Ga0059261_2984 Ga0059261_2984 (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.23539.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-117 376.5 0.1 9.8e-117 376.3 0.1 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_2984 Ga0059261_2984 4-hydroxyphenylpy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_2984 Ga0059261_2984 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 376.3 0.1 9.8e-117 9.8e-117 2 352 .. 12 340 .. 11 341 .. 0.95 Alignments for each domain: == domain 1 score: 376.3 bits; conditional E-value: 9.8e-117 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHG 70 gf+fvef+++d+ a++a +e+lGf a + + +k++t ++qg+i+l+l+ + + +a+f +HG lcl|FitnessBrowser__Korea:Ga0059261_2984 12 GFEFVEFTSPDPA-AMAAQFEQLGFVASHR---HPTKNITRYKQGRINLMLNRDDAGR--VAKFRGEHG 74 89***********.9999*******88776...**********************999..********* PP TIGR01263 71 dgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfe 139 ++++++af+v+d +a e a+++gae ++ + +i giG++ l++++ + +++++ lcl|FitnessBrowser__Korea:Ga0059261_2984 75 PSASAMAFRVADPVKAMEWALAHGAERTEEDD---------TVILGIGGSYLYFIQDG---HDLYENWA 131 **************************965554.........689***********985...45688877 PP TIGR01263 140 evsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasae 208 e+ + +e+ ++vgl+ +DH+++nv+rg+++ +++fy+ ++gf+e+k+fdik++a++L S+++ +++ lcl|FitnessBrowser__Korea:Ga0059261_2984 132 EIPGWQ-EAEAANNVGLDLLDHLTHNVRRGQMRVWSQFYKTLFGFEEQKYFDIKGQATGLFSQAMIAPD 199 777754.5555799******************************************************* PP TIGR01263 209 gkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdnlker 277 +++++plne s+++ksQIee+++ey+G+G+QHlAl+t+di++tve+lrargv++ ++ etYY+ +++r lcl|FitnessBrowser__Korea:Ga0059261_2984 200 KAIRIPLNE--SQDDKSQIEEFIREYKGEGIQHLALTTDDIYDTVERLRARGVRLQDTIETYYELVDKR 266 *********..9********************************************************* PP TIGR01263 278 vkklvkedleelkelkiLvDrd..eeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiE 344 v+ + edle+l++++iL+D++ eeG+LLQiFt++++ g++FfEiIqRkg++GFG+gNf+aLfe+iE lcl|FitnessBrowser__Korea:Ga0059261_2984 267 VPG-HGEDLERLRKNRILIDGNvgEEGILLQIFTENMF--GPIFFEIIQRKGNEGFGNGNFQALFESIE 332 **7.**********************************..***************************** PP TIGR01263 345 reqekrgv 352 +q++rgv lcl|FitnessBrowser__Korea:Ga0059261_2984 333 LDQIRRGV 340 ******98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (345 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: 10.07 // [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