Align phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate WP_036257263.1 DL86_RS00715 phenylalanine 4-monooxygenase
Query= BRENDA::P30967 (297 letters) >NCBI__GCF_000746085.1:WP_036257263.1 Length = 289 Score = 333 bits (854), Expect = 3e-96 Identities = 156/264 (59%), Positives = 199/264 (75%), Gaps = 1/264 (0%) Query: 26 DFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGLERLEVDADRVPDFNKLNQ 85 D+T+PQ + YS +H W LY RQ +LPGRACD F++GL L++ + +PDF +LN+ Sbjct: 17 DWTIPQGFESYSKAEHDVWIALYDRQATILPGRACDAFLQGLHALDLHGEGIPDFERLNR 76 Query: 86 KLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGHVP 145 +L A T W+IVAVP L+PDDVFF+HLANRRFP ++R QLDYLQEPD+FHD+FGHVP Sbjct: 77 RLCALTSWRIVAVPSLVPDDVFFDHLANRRFPAANFIRRADQLDYLQEPDIFHDVFGHVP 136 Query: 146 LLINPVFADYLEAYGKGGVKAKALGALPMLARLYWYTVEFGLINTPAGMRIYGAGILSSK 205 LL +PVFADY++AYG+GG++A LG L LARLYWYTVEFGL+ TPAG+RIYGAGI+SS+ Sbjct: 137 LLTDPVFADYMQAYGQGGLRALKLGRLHNLARLYWYTVEFGLLETPAGLRIYGAGIVSSR 196 Query: 206 SESIYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDAT-APDFAPLYLQ 264 SESI+ L+SASP+R+ F+L R+M T YRID FQ+ YFVI S + L DAT DF PLY Q Sbjct: 197 SESIFALESASPHRIRFNLERVMRTPYRIDDFQQIYFVIPSLQDLLDATIKTDFGPLYAQ 256 Query: 265 LADAQPWGAGDVAPDDLVLNAGDR 288 LA + P D+VL+ G + Sbjct: 257 LAGQADIAISGIEPGDVVLSRGSQ 280 Lambda K H 0.323 0.140 0.445 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: 346 Number of extensions: 9 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: 297 Length of database: 289 Length adjustment: 26 Effective length of query: 271 Effective length of database: 263 Effective search space: 71273 Effective search space used: 71273 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_036257263.1 DL86_RS00715 (phenylalanine 4-monooxygenase)
to HMM TIGR01267 (phhA: phenylalanine-4-hydroxylase (EC 1.14.16.1))
# 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.aa/TIGR01267.hmm # target sequence database: /tmp/gapView.2150.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01267 [M=248] Accession: TIGR01267 Description: Phe4hydrox_mono: phenylalanine-4-hydroxylase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-113 362.1 0.0 7.5e-113 361.8 0.0 1.0 1 lcl|NCBI__GCF_000746085.1:WP_036257263.1 DL86_RS00715 phenylalanine 4-mon Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000746085.1:WP_036257263.1 DL86_RS00715 phenylalanine 4-monooxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 361.8 0.0 7.5e-113 7.5e-113 1 242 [. 17 260 .. 17 265 .. 0.98 Alignments for each domain: == domain 1 score: 361.8 bits; conditional E-value: 7.5e-113 TIGR01267 1 dftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwk 69 d+t++q+++ ys+ eh vw +l+drq+ +l+gracd +l+G+ l+l+ + ipd+e +n++l alt w+ lcl|NCBI__GCF_000746085.1:WP_036257263.1 17 DWTIPQGFESYSKAEHDVWIALYDRQATILPGRACDAFLQGLHALDLHGEGIPDFERLNRRLCALTSWR 85 6799***************************************************************** PP TIGR01267 70 ivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkg 138 ivavp+l+p+dvff+hlanrrfp ++f+r ++ldylqepd+fhd+fGhvpll++pvfad+++ayG++g lcl|NCBI__GCF_000746085.1:WP_036257263.1 86 IVAVPSLVPDDVFFDHLANRRFPAANFIRRADQLDYLQEPDIFHDVFGHVPLLTDPVFADYMQAYGQGG 154 ********************************************************************* PP TIGR01267 139 vkakalgaa.llarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtry 206 ++a +lg+ larlywytvefGl+et+aglriyGaGi+ss +e+++ales++p+r+ f+l++vmrt+y lcl|NCBI__GCF_000746085.1:WP_036257263.1 155 LRALKLGRLhNLARLYWYTVEFGLLETPAGLRIYGAGIVSSRSESIFALESASPHRIRFNLERVMRTPY 223 ********989********************************************************** PP TIGR01267 207 ridklqkayfvlpslkrlfdaaqe.dfealvaeakdl 242 rid +q++yfv+psl+ l da+ + df +l+a+++ + lcl|NCBI__GCF_000746085.1:WP_036257263.1 224 RIDDFQQIYFVIPSLQDLLDATIKtDFGPLYAQLAGQ 260 ********************98766*******98865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (289 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: 00:00:00.00 # Mc/sec: 7.70 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
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