Align phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate Ga0059261_1314 Ga0059261_1314 Phenylalanine 4-hydroxylase (EC 1.14.16.1)
Query= BRENDA::P30967 (297 letters) >FitnessBrowser__Korea:Ga0059261_1314 Length = 288 Score = 314 bits (804), Expect = 2e-90 Identities = 154/266 (57%), Positives = 201/266 (75%), Gaps = 8/266 (3%) Query: 24 ANDFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGLERLEVDADRVPDFNKL 83 A D+T+PQ D ++AE+H W TL++RQ KLLPGRA ++ GLE L++ +P+F +L Sbjct: 16 AADWTIPQNWDAFTAEEHGVWDTLFERQIKLLPGRASKAYLHGLELLKLSDGGIPNFEEL 75 Query: 84 NQKLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGH 143 +++L+ TGW++VAVPGL+PDDVFF+H+ANRRF ++R P QLDYLQEPDVFHD+FGH Sbjct: 76 SERLVKLTGWQVVAVPGLVPDDVFFDHMANRRFVAGNFIRRPDQLDYLQEPDVFHDVFGH 135 Query: 144 VPLLINPVFADYLEAYGKGGVKAKALGALPMLARLYWYTVEFGLINTPAGMRIYGAGILS 203 VP+L +PVFADY+EAYG+GG +A LGAL L+RLYWYTVEFGLI +RIYG+GI+S Sbjct: 136 VPMLADPVFADYMEAYGRGGGRAMELGALKQLSRLYWYTVEFGLIEEAGDLRIYGSGIVS 195 Query: 204 SKSESIYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDATA-PDFAPLY 262 S +ES + L+S SPNR+GFDL R+M T YRID FQ+ YFVI SF+ L AT DFAPLY Sbjct: 196 SSAESRFALESDSPNRIGFDLKRVMRTEYRIDDFQQNYFVIPSFETLLRATVETDFAPLY 255 Query: 263 LQLADAQPWGAGDVAPDDLVLNAGDR 288 ++ AQP D+ ++V AGDR Sbjct: 256 AEIL-AQP----DIPIAEIV--AGDR 274 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: 310 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 297 Length of database: 288 Length adjustment: 26 Effective length of query: 271 Effective length of database: 262 Effective search space: 71002 Effective search space used: 71002 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 Ga0059261_1314 Ga0059261_1314 (Phenylalanine 4-hydroxylase (EC 1.14.16.1))
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.14803.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-109 350.4 0.0 2.8e-109 350.1 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_1314 Ga0059261_1314 Phenylalanine 4-h Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_1314 Ga0059261_1314 Phenylalanine 4-hydroxylase (EC 1.14.16.1) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 350.1 0.0 2.8e-109 2.8e-109 1 240 [. 18 259 .. 18 264 .. 0.98 Alignments for each domain: == domain 1 score: 350.1 bits; conditional E-value: 2.8e-109 TIGR01267 1 dftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwk 69 d+t++q++d +++eeh vw tl++rq+kll+gra + yl+G+e l+l+ ip++ee++e+l +ltGw+ lcl|FitnessBrowser__Korea:Ga0059261_1314 18 DWTIPQNWDAFTAEEHGVWDTLFERQIKLLPGRASKAYLHGLELLKLSDGGIPNFEELSERLVKLTGWQ 86 6799***************************************************************** PP TIGR01267 70 ivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkg 138 +vavpgl+p+dvff+h+anrrf +f+r p++ldylqepdvfhd+fGhvp+l++pvfad++eayG++g lcl|FitnessBrowser__Korea:Ga0059261_1314 87 VVAVPGLVPDDVFFDHMANRRFVAGNFIRRPDQLDYLQEPDVFHDVFGHVPMLADPVFADYMEAYGRGG 155 ********************************************************************* PP TIGR01267 139 vkakalgaa.llarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtry 206 ++a++lga +l+rlywytvefGl+e+a++lriyG+Gi+ss e+ +ales++p+r++fdl++vmrt+y lcl|FitnessBrowser__Korea:Ga0059261_1314 156 GRAMELGALkQLSRLYWYTVEFGLIEEAGDLRIYGSGIVSSSAESRFALESDSPNRIGFDLKRVMRTEY 224 *******9889********************************************************** PP TIGR01267 207 ridklqkayfvlpslkrlfdaaqe.dfealvaeak 240 rid +q+ yfv+ps++ l a+ e df++l+ae lcl|FitnessBrowser__Korea:Ga0059261_1314 225 RIDDFQQNYFVIPSFETLLRATVEtDFAPLYAEIL 259 *****************99988777******9865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (288 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: 8.74 // [ok]
This GapMind analysis is from Apr 09 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