Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_011882985.1 4-hydroxyphenylpyruvate dioxygenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_456 (358 letters) >NCBI__GCF_000016205.1:WP_011882985.1 Length = 365 Score = 418 bits (1074), Expect = e-121 Identities = 211/361 (58%), Positives = 268/361 (74%), Gaps = 15/361 (4%) Query: 5 YENPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPH 64 ++NP+G GFEFIE+ +P P L +FE MGFT +A HR KDV +YRQG IN I+N EP Sbjct: 6 WDNPVGTDGFEFIEYTAPDPKALGQLFERMGFTAIARHRHKDVTVYRQGDINFIINAEPD 65 Query: 65 SVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAP 124 S A FA HGPS+C +AFRV+D+ KAY+ ALELGA +TGPMELN+PAIKGIG + Sbjct: 66 SFAQRFARLHGPSICAIAFRVQDAAKAYRHALELGAWGFDNKTGPMELNIPAIKGIGDSL 125 Query: 125 LYLIDRF-GEGS---------SIYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAY 174 +Y +DR+ G+ SIYD+DF I G + NPVG GL IDHLTHNV+RGRM Sbjct: 126 IYFVDRWRGKNGAQPGAIGDISIYDVDFEPIPGANPNPVGHGLTYIDHLTHNVHRGRMQE 185 Query: 175 WAGFYEKLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQF 234 WA FYE+LFNFRE+RYFDI+G+ TG+ SKAMT+P G IRIP+NEE S+ AGQI+E+L + Sbjct: 186 WAEFYERLFNFREVRYFDIEGKVTGVKSKAMTSPCGKIRIPINEEGSETAGQIQEYLDAY 245 Query: 235 NGEGIQHVAFLTDDLVKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVDELQSRGI 294 +GEGIQH+A T+D+ D L+ G++ + DTYYE+++ R+PNHGE +DEL+ R I Sbjct: 246 HGEGIQHIALGTNDIYGAVDGLRGKGVKLLDT-IDTYYELVDRRVPNHGESLDELKKRKI 304 Query: 295 LLDGASEQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGV 354 L+DGA + LLLQIF+E +GP+FFE IQRKG+ GFGEGNFKALFESIE DQ+RRGV Sbjct: 305 LIDGARDD----LLLQIFTENQIGPIFFEIIQRKGNQGFGEGNFKALFESIELDQIRRGV 360 Query: 355 L 355 + Sbjct: 361 V 361 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: 540 Number of extensions: 28 Number of successful extensions: 4 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: 365 Length adjustment: 29 Effective length of query: 329 Effective length of database: 336 Effective search space: 110544 Effective search space used: 110544 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_011882985.1 (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.5342.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-125 403.4 0.0 7e-125 403.1 0.0 1.1 1 lcl|NCBI__GCF_000016205.1:WP_011882985.1 4-hydroxyphenylpyruvate dioxygen Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011882985.1 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.1 0.0 7e-125 7e-125 2 352 .. 14 360 .. 13 361 .. 0.93 Alignments for each domain: == domain 1 score: 403.1 bits; conditional E-value: 7e-125 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHG 70 gf+f+e++++d+k a+ +l+e++Gf+a+a+ +r+k++tv+rqg+i+++++ae+ s a++f++ HG lcl|NCBI__GCF_000016205.1:WP_011882985.1 14 GFEFIEYTAPDPK-ALGQLFERMGFTAIAR---HRHKDVTVYRQGDINFIINAEPDSF--AQRFARLHG 76 8************.***************8...*********************9999..********* PP TIGR01263 71 dgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekg....... 132 ++++++af+v+d+++a+++a+e ga +++++ +e++++aikgiGd+++++v+r + k+ lcl|NCBI__GCF_000016205.1:WP_011882985.1 77 PSICAIAFRVQDAAKAYRHALELGAWGFDNKTG--PMELNIPAIKGIGDSLIYFVDRWRGKNgaqpgai 143 ****************************99986..99*******************9875551222222 PP TIGR01263 133 ...silpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasa 198 si+++++ + ++ ++ + gl++iDH+++nv+rg+++++aefye++++f+e+++fdi++++++ lcl|NCBI__GCF_000016205.1:WP_011882985.1 144 gdiSIYDVDF--EPIPGANPNPVGHGLTYIDHLTHNVHRGRMQEWAEFYERLFNFREVRYFDIEGKVTG 210 2223444444..444456777899********************************************* PP TIGR01263 199 LkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkip 267 +kSk+++s++gk+++p+ne + ++ +QI+eyl++y+G+G+QH+Al t+di+ +v+ lr +gv++l++ lcl|NCBI__GCF_000016205.1:WP_011882985.1 211 VKSKAMTSPCGKIRIPINE-EGSETAGQIQEYLDAYHGEGIQHIALGTNDIYGAVDGLRGKGVKLLDTI 278 *******************.7889********************************************* PP TIGR01263 268 etYYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNf 336 +tYY+ +++rv++ + e+l+elk++kiL+D++ + lLLQiFt++ + g++FfEiIqRkg++GFGegNf lcl|NCBI__GCF_000016205.1:WP_011882985.1 279 DTYYELVDRRVPN-HGESLDELKKRKILIDGARDDLLLQIFTENQI--GPIFFEIIQRKGNQGFGEGNF 344 ************7.********************************..********************* PP TIGR01263 337 kaLfeaiEreqekrgv 352 kaLfe+iE +q++rgv lcl|NCBI__GCF_000016205.1:WP_011882985.1 345 KALFESIELDQIRRGV 360 **************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (365 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.98 // [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