Align phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate WP_043291603.1 phenylalanine 4-monooxygenase
Query= BRENDA::P30967 (297 letters) >NCBI__GCF_000016205.1:WP_043291603.1 Length = 297 Score = 343 bits (879), Expect = 4e-99 Identities = 170/275 (61%), Positives = 200/275 (72%), Gaps = 4/275 (1%) Query: 26 DFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGLERLEVDADRVPDFNKLNQ 85 DFT+ QPL+RY DHA W LY RQ LL GRACD F+ GL ++ + ADRVP F +N+ Sbjct: 22 DFTIDQPLERYGQVDHAVWQQLYARQAALLRGRACDAFIGGLGKIRLPADRVPSFADVNR 81 Query: 86 KLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGHVP 145 +L ATGW+IVAVPGL+PD VFFEHLA+RRFPVTWW+R P QLDYLQEPD FHDLFGHVP Sbjct: 82 QLKPATGWEIVAVPGLVPDRVFFEHLAHRRFPVTWWMRRPDQLDYLQEPDCFHDLFGHVP 141 Query: 146 LLINPVFADYLEAYGKGGVK-AKALGALPMLARLYWYTVEFGLINTPA---GMRIYGAGI 201 LLI PVFADY++AYG+ + A AL LARLYWYTVEFGLI P G+ IYGAGI Sbjct: 142 LLIEPVFADYMQAYGRTALAVADDDAALARLARLYWYTVEFGLIRDPRGTNGLSIYGAGI 201 Query: 202 LSSKSESIYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDATAPDFAPL 261 +SSK ES+Y ++SA+PNR+GFDL R+M T+YRIDTFQKTYFVID F QLF D L Sbjct: 202 VSSKGESLYSVESAAPNRLGFDLERVMRTKYRIDTFQKTYFVIDDFAQLFALADVDARAL 261 Query: 262 YLQLADAQPWGAGDVAPDDLVLNAGDRQGWADTED 296 +LA AG V D+VL G +GW D +D Sbjct: 262 AERLAALPELSAGTVLDTDVVLQRGTGEGWPDDDD 296 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: 364 Number of extensions: 18 Number of successful extensions: 3 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: 297 Length adjustment: 26 Effective length of query: 271 Effective length of database: 271 Effective search space: 73441 Effective search space used: 73441 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_043291603.1 (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.10711.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-111 357.7 0.0 1.6e-111 357.4 0.0 1.0 1 lcl|NCBI__GCF_000016205.1:WP_043291603.1 phenylalanine 4-monooxygenase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_043291603.1 phenylalanine 4-monooxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 357.4 0.0 1.6e-111 1.6e-111 1 241 [. 22 267 .. 22 273 .. 0.97 Alignments for each domain: == domain 1 score: 357.4 bits; conditional E-value: 1.6e-111 TIGR01267 1 dftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwk 69 dft++q+l+ry + +havw+ l+ rq+ ll+gracd ++ G+ k+ l+adr+p + +vn++l+ +tGw+ lcl|NCBI__GCF_000016205.1:WP_043291603.1 22 DFTIDQPLERYGQVDHAVWQQLYARQAALLRGRACDAFIGGLGKIRLPADRVPSFADVNRQLKPATGWE 90 79******************************************************************* PP TIGR01267 70 ivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkg 138 ivavpgl+p+ vffehla rrfpvt+++r p++ldylqepd fhdlfGhvpll++pvfad+++ayG+++ lcl|NCBI__GCF_000016205.1:WP_043291603.1 91 IVAVPGLVPDRVFFEHLAHRRFPVTWWMRRPDQLDYLQEPDCFHDLFGHVPLLIEPVFADYMQAYGRTA 159 ********************************************************************* PP TIGR01267 139 vkakalgaa..llarlywytvefGlvetaag...lriyGaGilsskkelvyaleskeplrvafdllevm 202 + + +aa larlywytvefGl++++ g l iyGaGi+ssk e++y++es+ p+r +fdl++vm lcl|NCBI__GCF_000016205.1:WP_043291603.1 160 LAVADDDAAlaRLARLYWYTVEFGLIRDPRGtngLSIYGAGIVSSKGESLYSVESAAPNRLGFDLERVM 228 ***999988678***************987644589********************************* PP TIGR01267 203 rtryridklqkayfvlpslkrlfdaaqedfealvaeakd 241 rt+yrid++qk+yfv++++ +lf +a+ d al +++ lcl|NCBI__GCF_000016205.1:WP_043291603.1 229 RTKYRIDTFQKTYFVIDDFAQLFALADVDARALAERLAA 267 *********************************998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (297 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 12.12 // [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