Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate GFF3887 PS417_19900 phenylalanine 4-monooxygenase
Query= reanno::pseudo3_N2E3:AO353_18585 (263 letters) >FitnessBrowser__WCS417:GFF3887 Length = 263 Score = 511 bits (1316), Expect = e-150 Identities = 243/263 (92%), Positives = 255/263 (96%) Query: 1 MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVLEGRACQEYMDGIEKLGLPHDRI 60 MKQTQYVAREPDAQGFIHY+ EEHAVWNTLITRQLKV+EGRACQEY+DGI+KLGLPHDRI Sbjct: 1 MKQTQYVAREPDAQGFIHYSQEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI 60 Query: 61 PQLDEINKVLGETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120 PQL EINKVL ETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF Sbjct: 61 PQLGEINKVLAETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120 Query: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVDTPQGKRIYG 180 HEIFGHCPLLTNPWFAEFTHTYGKLGL A+KE+RVYLARLYWMTIEFGLVDTP+G+RIYG Sbjct: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLAATKEQRVYLARLYWMTIEFGLVDTPEGRRIYG 180 Query: 181 GGILSSPKETVYSLSGEPEHQAFDPLEAMRTPYRIDILQPLYFVLPNLKRLFDLAHEDIM 240 GGILSSPKETVYSLS EPEHQ FDPLEAMRTPYRIDILQPLYFVLP+LKRLF++A EDIM Sbjct: 181 GGILSSPKETVYSLSSEPEHQVFDPLEAMRTPYRIDILQPLYFVLPDLKRLFEVAQEDIM 240 Query: 241 GMVHQGMQLGLHAPKFPPKPKAA 263 GMV +GMQLGLHAPKFPPKPKAA Sbjct: 241 GMVERGMQLGLHAPKFPPKPKAA 263 Lambda K H 0.322 0.140 0.435 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: 374 Number of extensions: 10 Number of successful extensions: 1 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: 263 Length of database: 263 Length adjustment: 25 Effective length of query: 238 Effective length of database: 238 Effective search space: 56644 Effective search space used: 56644 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: 47 (22.7 bits)
Align candidate GFF3887 PS417_19900 (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.carbon/TIGR01267.hmm # target sequence database: /tmp/gapView.4723.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-129 416.6 0.0 1.7e-129 416.4 0.0 1.0 1 lcl|FitnessBrowser__WCS417:GFF3887 PS417_19900 phenylalanine 4-mono Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__WCS417:GFF3887 PS417_19900 phenylalanine 4-monooxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 416.4 0.0 1.7e-129 1.7e-129 3 247 .. 11 254 .. 9 255 .. 0.99 Alignments for each domain: == domain 1 score: 416.4 bits; conditional E-value: 1.7e-129 TIGR01267 3 tvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwkivavpgli 77 ++aq++++ys+eehavw+tli+rqlk++egrac+eyldG++klgl++drip+l e+n++l ++tGw++++vp+li lcl|FitnessBrowser__WCS417:GFF3887 11 PDAQGFIHYSQEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRIPQLGEINKVLAETTGWQVARVPALI 85 789************************************************************************ PP TIGR01267 78 padvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvkakalgaallarl 152 p+++ffe+la+++fpv+tf+rt+eeldylqepd+fh++fGh+pll+np+fa+f+++yGk+g+ a++++++ larl lcl|FitnessBrowser__WCS417:GFF3887 86 PFQTFFELLASKQFPVATFIRTREELDYLQEPDIFHEIFGHCPLLTNPWFAEFTHTYGKLGLAATKEQRVYLARL 160 *************************************************************************** PP TIGR01267 153 ywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtryridklqkayfvlpslkrlfda 227 yw+t+efGlv+t++g riyG+Gilss+ke+vy+ s+ep+++ fd+le+mrt+yrid+lq++yfvlp+lkrlf++ lcl|FitnessBrowser__WCS417:GFF3887 161 YWMTIEFGLVDTPEGRRIYGGGILSSPKETVYS-LSSEPEHQVFDPLEAMRTPYRIDILQPLYFVLPDLKRLFEV 234 *********************************.7889************************************* PP TIGR01267 228 aqedfealvaeakdlkaldp 247 aqed++ +v + ++l++++p lcl|FitnessBrowser__WCS417:GFF3887 235 AQEDIMGMVERGMQLGLHAP 254 ***************99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (263 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.05 // [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