Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate CA265_RS03130 CA265_RS03130 4-hydroxyphenylpyruvate dioxygenase
Query= BRENDA::Q53586 (381 letters) >FitnessBrowser__Pedo557:CA265_RS03130 Length = 376 Score = 371 bits (953), Expect = e-107 Identities = 195/371 (52%), Positives = 250/371 (67%), Gaps = 6/371 (1%) Query: 12 ARQADPFPVKGMDAVVFAVGNAKQAAHYYSTAFGMQLVAYSGPENGSRETASYVLTNGSA 71 ++ D P+ G D + F VGNAKQAAHYY TAFG Q +AY+GPE G R+ +SYVL G Sbjct: 11 SKAPDFLPINGTDYIEFYVGNAKQAAHYYKTAFGFQSLAYAGPETGVRDRSSYVLQQGKI 70 Query: 72 RFVLTSVIKPATPWGHFLADHVAEHGDGVVDLAIEVPDARAAHAYAIEHGARSVAEPYEL 131 R +LT+ +K P +A+HV +HGDGV LA+ V DA +A + GA+ P L Sbjct: 71 RLILTTALKSDHP----IAEHVKKHGDGVKVLALWVDDAYSAFEETTKRGAKPYLAPQTL 126 Query: 132 KDEHGTVVLAAIATYGKTRHTLVDRTGYDGPYLPGYVAAAPIVEPPAHRTFQAIDHCVGN 191 DE+G + ++ I TYG+T H ++R Y+G ++PGY +P A IDHCVGN Sbjct: 127 TDENGELKMSGIYTYGETVHMFIERKNYNGTFMPGYRVWESDYQP-ADAGLLYIDHCVGN 185 Query: 192 VELGRMNEWVGFYNKVMGFTNMKEFVGDDIATEYSALMSKVVADGTLKVKFPINEPALAK 251 V RMNE V +Y VMGF N+ F I TEYSALMSKV+++G KFPINEPA K Sbjct: 186 VGWNRMNEAVQWYEDVMGFVNILSFDDKQINTEYSALMSKVMSNGNGYSKFPINEPAEGK 245 Query: 252 KKSQIDEYLEFYGGAGVQHIALNTGDIVETVRTMRAAGVQFLDT-PDSYYDTLGEWVGDT 310 KKSQI+EYLE+Y G GVQHIA+ T DIV+TV+ ++A GV+FL P++YYD + + VG Sbjct: 246 KKSQIEEYLEYYEGEGVQHIAVATKDIVKTVKELKARGVEFLSAPPEAYYDMMPQRVGKI 305 Query: 311 RVPVDTLRELKILADRDEDGYLLQIFTKPVQDRPTVFFEIIERHGSMGFGKGNFKALFEA 370 + L L IL D DE+GYLLQIFTKPV+DRPT+FFE+I+R G+ FG GNFKALFE+ Sbjct: 306 DEEIALLESLGILVDCDEEGYLLQIFTKPVEDRPTLFFEVIQRKGAQSFGAGNFKALFES 365 Query: 371 IEREQEKRGNL 381 +EREQE RGNL Sbjct: 366 LEREQELRGNL 376 Lambda K H 0.318 0.136 0.403 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: 488 Number of extensions: 26 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: 381 Length of database: 376 Length adjustment: 30 Effective length of query: 351 Effective length of database: 346 Effective search space: 121446 Effective search space used: 121446 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate CA265_RS03130 CA265_RS03130 (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.22959.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-140 453.4 0.0 4e-140 453.2 0.0 1.0 1 lcl|FitnessBrowser__Pedo557:CA265_RS03130 CA265_RS03130 4-hydroxyphenylpyr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Pedo557:CA265_RS03130 CA265_RS03130 4-hydroxyphenylpyruvate dioxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.2 0.0 4e-140 4e-140 2 353 .] 21 376 .] 20 376 .] 0.98 Alignments for each domain: == domain 1 score: 453.2 bits; conditional E-value: 4e-140 TIGR01263 2 gfdfvefavgdakqaakalveklGfeavak...etgsrekastvlrqgeitlvltaelsssseaaafl 66 g d++ef+vg+akqaa+++ +++Gf+ +a+ etg r++ s+vl+qg+i+l+lt++l+s++++a+++ lcl|FitnessBrowser__Pedo557:CA265_RS03130 21 GTDYIEFYVGNAKQAAHYYKTAFGFQSLAYagpETGVRDRSSYVLQQGKIRLILTTALKSDHPIAEHV 88 689***************************************************************** PP TIGR01263 67 akHGdgvkdvafevedveaafeaavergaeavsapee.ed.ekevklaaikgiGdvvltlveregekg 132 +kHGdgvk +a+ v+d+ +afe+ +rga+++ ap++ +d ++e+k+ i ++G++v+ ++er++++g lcl|FitnessBrowser__Pedo557:CA265_RS03130 89 KKHGDGVKVLALWVDDAYSAFEETTKRGAKPYLAPQTlTDeNGELKMSGIYTYGETVHMFIERKNYNG 156 *************************************9888*************************** PP TIGR01263 133 silpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfd...ikteas 197 +++pg++ ++++ +++d+gl +iDH+vgnv ++++++++++ye+++gf +i sfd i+te+s lcl|FitnessBrowser__Pedo557:CA265_RS03130 157 TFMPGYRVWESD----YQPADAGLLYIDHCVGNVGWNRMNEAVQWYEDVMGFVNILSFDdkqINTEYS 220 *******99996....45689*********************************************** PP TIGR01263 198 aLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk 265 aL+Skv+ + +g k+p+nepa++kkksQIeeyle+yeG+GvQH+A+ t+divktv+el+argvefl+ lcl|FitnessBrowser__Pedo557:CA265_RS03130 221 ALMSKVMSNGNGYSKFPINEPAEGKKKSQIEEYLEYYEGEGVQHIAVATKDIVKTVKELKARGVEFLS 288 ******************************************************************** PP TIGR01263 266 .ipetYYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFG 332 +pe+YYd++ +rv+k ++e++ l++l+iLvD deeG+LLQiFtkpv dr+tlFfE+IqRkga+ FG lcl|FitnessBrowser__Pedo557:CA265_RS03130 289 aPPEAYYDMMPQRVGK-IDEEIALLESLGILVDCDEEGYLLQIFTKPVEDRPTLFFEVIQRKGAQSFG 355 99*************6.*************************************************** PP TIGR01263 333 egNfkaLfeaiEreqekrgvl 353 +gNfkaLfe++Ereqe rg+l lcl|FitnessBrowser__Pedo557:CA265_RS03130 356 AGNFKALFESLEREQELRGNL 376 ******************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (353 nodes) Target sequences: 1 (376 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: 7.31 // [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