Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate 6937404 Sama_1568 4-hydroxyphenylpyruvate dioxygenase (RefSeq)
Query= reanno::MR1:201123 (346 letters) >FitnessBrowser__SB2B:6937404 Length = 345 Score = 605 bits (1559), Expect = e-178 Identities = 293/346 (84%), Positives = 319/346 (92%), Gaps = 1/346 (0%) Query: 1 MASELNPLGLLGIEFTEFASSDTDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNK 60 MASE NPLGLLGIEFTEFA+ D DFMHKVF+DFGFS+LKK K KDI YY+QNDINFL+N+ Sbjct: 1 MASETNPLGLLGIEFTEFATPDNDFMHKVFLDFGFSMLKKHKEKDIYYYQQNDINFLMNR 60 Query: 61 QREGFSAKFAKSHGPAICSMGWRVEDASFAHRVAVERGAKAADDSAKDLPYPAIYGIGDS 120 R GFSA FAKSHGPAI SMGWRVEDA +A++ AVERGAKAA D KDLPYPAIYGIGDS Sbjct: 61 DRAGFSAGFAKSHGPAITSMGWRVEDAEYAYKHAVERGAKAAPDDVKDLPYPAIYGIGDS 120 Query: 121 LIYFIDTFGANNNIYATDFEDLSEPVITQEKGFIEVDHLTNNVYKGTMEHWANFYKNIFG 180 LIYFID FG ++NIYATDF DL EPVI QEKGF+EVDHLTNNVYKGTME W+NFYK++FG Sbjct: 121 LIYFIDRFG-DDNIYATDFVDLDEPVIVQEKGFMEVDHLTNNVYKGTMEQWSNFYKDVFG 179 Query: 181 FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF 240 FTEVRYFDI G QTAL+SYALRSPDGSFCIPINEGKG+D+NQIDEYL+EYNGPGVQHLAF Sbjct: 180 FTEVRYFDIKGSQTALISYALRSPDGSFCIPINEGKGDDRNQIDEYLREYNGPGVQHLAF 239 Query: 241 RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRDRIKHHQILVDGDESGYLL 300 RSRDIV SLDAMEGSSI LDIIPEYYDTIF+K+PQVTE+R+RIKHHQILVDGDE+GYLL Sbjct: 240 RSRDIVASLDAMEGSSIATLDIIPEYYDTIFEKLPQVTEDRERIKHHQILVDGDENGYLL 299 Query: 301 QIFTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 346 QIFTKNLFGPIFIEIIQRKNNLGFGEGNF ALF+SIERDQ+RRGVL Sbjct: 300 QIFTKNLFGPIFIEIIQRKNNLGFGEGNFKALFESIERDQVRRGVL 345 Lambda K H 0.321 0.140 0.414 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: 612 Number of extensions: 24 Number of successful extensions: 2 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: 346 Length of database: 345 Length adjustment: 29 Effective length of query: 317 Effective length of database: 316 Effective search space: 100172 Effective search space used: 100172 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 6937404 Sama_1568 (4-hydroxyphenylpyruvate dioxygenase (RefSeq))
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.20205.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.9e-124 399.6 0.1 8.9e-124 399.5 0.1 1.0 1 lcl|FitnessBrowser__SB2B:6937404 Sama_1568 4-hydroxyphenylpyruvat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6937404 Sama_1568 4-hydroxyphenylpyruvate dioxygenase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 399.5 0.1 8.9e-124 8.9e-124 2 353 .] 12 345 .] 11 345 .] 0.95 Alignments for each domain: == domain 1 score: 399.5 bits; conditional E-value: 8.9e-124 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkdvaf 78 g++f efa++d++ +++++ ++Gf++++k ++ek++++++q++i+++++ + a f+++HG++++++++ lcl|FitnessBrowser__SB2B:6937404 12 GIEFTEFATPDND-FMHKVFLDFGFSMLKK---HKEKDIYYYQQNDINFLMNRDRAGF--SAGFAKSHGPAITSMGW 82 79**********9.9**************9...*********************9999..9**************** PP TIGR01263 79 evedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkekledvg 155 +ved+e a+++averga+a+ + + k++ ++ai giGd+++++++r+g++ +i+ +++ ++ ++++g lcl|FitnessBrowser__SB2B:6937404 83 RVEDAEYAYKHAVERGAKAAPDDV----KDLPYPAIYGIGDSLIYFIDRFGDD-NIYATDFVDLDE---PVIVQEKG 151 *******************77776....68*********************99.555555543333...3445789* PP TIGR01263 156 leaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyle 232 + ++DH+++nv++g++e++++fy++++gf+e+++fdik++++aL S++l+s++g++++p+ne+ ++++++QI+eyl+ lcl|FitnessBrowser__SB2B:6937404 152 FMEVDHLTNNVYKGTMEQWSNFYKDVFGFTEVRYFDIKGSQTALISYALRSPDGSFCIPINEG-KGDDRNQIDEYLR 227 **************************************************************5.99*********** PP TIGR01263 233 eyeGaGvQHlAlntedivktveelrargveflkipetYYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFt 309 ey+G+GvQHlA++++div+++++++ ++++ l+i +YYd++ e++++ v+ed e++k+++iLvD+de+G+LLQiFt lcl|FitnessBrowser__SB2B:6937404 228 EYNGPGVQHLAFRSRDIVASLDAMEGSSIATLDIIPEYYDTIFEKLPQ-VTEDRERIKHHQILVDGDENGYLLQIFT 303 *********************************999***********7.**************************** PP TIGR01263 310 kpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353 k+++ g++F+EiIqRk++ GFGegNfkaLfe+iEr+q++rgvl lcl|FitnessBrowser__SB2B:6937404 304 KNLF--GPIFIEIIQRKNNLGFGEGNFKALFESIERDQVRRGVL 345 ****..***********************************985 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: 8.87 // [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