Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate GFF747 PGA1_c07610 4-hydroxyphenylpyruvate dioxygenase Hpd
Query= reanno::pseudo6_N2E2:Pf6N2E2_456 (358 letters) >FitnessBrowser__Phaeo:GFF747 Length = 366 Score = 348 bits (893), Expect = e-100 Identities = 177/354 (50%), Positives = 245/354 (69%), Gaps = 9/354 (2%) Query: 6 ENPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKD-VHLYRQGAINLILNNEPH 64 ENP G GFEF+EFA P P L +F MG+ VA H+SK + L++QG I +LN E Sbjct: 16 ENPAGTDGFEFVEFAHPDPQELRDLFARMGYELVARHKSKPGIELWQQGDITYVLNAEKG 75 Query: 65 SVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAP 124 S A F A+HGP M +RV D+QKA++ A+ GA+ E +++PAIKGIGG+ Sbjct: 76 SFAERFVADHGPCAPSMGWRVVDAQKAFEHAVSKGAEAY--EGDDKTMDVPAIKGIGGSL 133 Query: 125 LYLIDRFGEGSSIYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYEKLFN 184 +Y ID++ + +S Y+ +F ++ P G G +DHLTHNV++G M W FY +LFN Sbjct: 134 IYFIDQYYD-TSPYNTEFEWL--TQSKPRGVGFYYLDHLTHNVFKGNMDKWFRFYGELFN 190 Query: 185 FREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAF 244 F+EIR+FDI+G++TGL S+A+T+P G IRIP+NE+ + GQI +L ++NGEGIQH+A Sbjct: 191 FKEIRFFDIEGKFTGLLSRALTSPCGRIRIPINEDRGE-TGQIVSYLKKYNGEGIQHIAV 249 Query: 245 LTDDLVKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVDELQSRGILLDGAS--EQ 302 ++D+ D + G++FM APP +YYEM R+ H EP+D +Q GIL+DG + Sbjct: 250 GSEDIYGATDEISDRGIKFMPAPPASYYEMSHDRVIGHEEPLDRMQKHGILIDGEGVVDG 309 Query: 303 GDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLA 356 G+ ++LLQIFS+T++GP+FFEFIQRKGDDGFGEGNFKALFESIER+Q+ G LA Sbjct: 310 GETKILLQIFSKTVIGPIFFEFIQRKGDDGFGEGNFKALFESIEREQIANGELA 363 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: 508 Number of extensions: 33 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: 358 Length of database: 366 Length adjustment: 29 Effective length of query: 329 Effective length of database: 337 Effective search space: 110873 Effective search space used: 110873 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 GFF747 PGA1_c07610 (4-hydroxyphenylpyruvate dioxygenase Hpd)
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.12990.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-116 373.8 0.0 6.6e-116 373.6 0.0 1.0 1 lcl|FitnessBrowser__Phaeo:GFF747 PGA1_c07610 4-hydroxyphenylpyruv Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF747 PGA1_c07610 4-hydroxyphenylpyruvate dioxygenase Hpd # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 373.6 0.0 6.6e-116 6.6e-116 2 352 .. 23 361 .. 22 362 .. 0.95 Alignments for each domain: == domain 1 score: 373.6 bits; conditional E-value: 6.6e-116 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkdvaf 78 gf+fvefa++d++ ++ l+ ++G+e+va+ +++ + +++qg+it+vl+ae+ s a++f+a+HG+++ ++++ lcl|FitnessBrowser__Phaeo:GFF747 23 GFEFVEFAHPDPQ-ELRDLFARMGYELVAR--HKSKPGIELWQQGDITYVLNAEKGSF--AERFVADHGPCAPSMGW 94 8***********9.99*************8..66677899****************99..***************** PP TIGR01263 79 evedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkekledvg 155 +v d+++afe+av++gaea++ + k+++++aikgiG++++++++++ ++ s +++++e+ ++ +k+ +vg lcl|FitnessBrowser__Phaeo:GFF747 95 RVVDAQKAFEHAVSKGAEAYEGDD----KTMDVPAIKGIGGSLIYFIDQYYDT-SPYNTEFEWLTQ----SKPRGVG 162 *******************87764....79******************97666.677777878875....45689** PP TIGR01263 156 leaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyle 232 ++++DH+++nv +g+++k+ fy ++++fkei+ fdi++++++L S++l+s++g++++p+ne + +++QI yl+ lcl|FitnessBrowser__Phaeo:GFF747 163 FYYLDHLTHNVFKGNMDKWFRFYGELFNFKEIRFFDIEGKFTGLLSRALTSPCGRIRIPINE--DRGETGQIVSYLK 237 **************************************************************..8899********* PP TIGR01263 233 eyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd...eeG... 302 +y+G+G+QH+A+ +edi+ +++e+++rg++f++ +p +YY++ ++rv ++e+l+++++++iL+D++ + G lcl|FitnessBrowser__Phaeo:GFF747 238 KYNGEGIQHIAVGSEDIYGATDEISDRGIKFMPaPPASYYEMSHDRVIG-HEEPLDRMQKHGILIDGEgvvDGGetk 313 *********************************999************7.******************997666888 PP TIGR01263 303 lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgv 352 +LLQiF+k+v+ g++FfE+IqRkg++GFGegNfkaLfe+iEreq+ g+ lcl|FitnessBrowser__Phaeo:GFF747 314 ILLQIFSKTVI--GPIFFEFIQRKGDDGFGEGNFKALFESIEREQIANGE 361 ***********..********************************99887 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (366 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.20 // [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