Align phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate WP_057508987.1 ABB28_RS12815 phenylalanine 4-monooxygenase
Query= BRENDA::P30967 (297 letters) >NCBI__GCF_001431535.1:WP_057508987.1 Length = 297 Score = 375 bits (964), Expect = e-109 Identities = 179/269 (66%), Positives = 211/269 (78%), Gaps = 2/269 (0%) Query: 31 QPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGLERLEVDADRVPDFNKLNQKLMAA 90 QP D YSA+DHATW+TL++RQ LL GRAC EF++ + + + ADR+P F +LN+ L AA Sbjct: 29 QPWDSYSADDHATWSTLFKRQRDLLNGRACQEFLDAQDAMGMSADRIPRFEQLNEALAAA 88 Query: 91 TGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGHVPLLINP 150 TGW +V V GL+P+ FF+HLANRRFPVTWW+R P Q+DY+ EPD+FHDLFGHVPLL+NP Sbjct: 89 TGWTLVGVEGLLPELDFFDHLANRRFPVTWWIRRPDQIDYIAEPDMFHDLFGHVPLLMNP 148 Query: 151 VFADYLEAYGKGGVKAKALG--ALPMLARLYWYTVEFGLINTPAGMRIYGAGILSSKSES 208 VFADY+EAYG+GGVKA ALG AL L RLYWYTVEFGLINT G+RIYGAGI+SSK ES Sbjct: 149 VFADYMEAYGRGGVKAHALGPDALQNLTRLYWYTVEFGLINTADGLRIYGAGIVSSKGES 208 Query: 209 IYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDATAPDFAPLYLQLADA 268 +Y L+S +PNR+GFDL RIM TRYRIDTFQKTYFVIDSF+QL ATAPDF P+Y LAD Sbjct: 209 LYSLESPAPNRIGFDLERIMRTRYRIDTFQKTYFVIDSFEQLMQATAPDFTPIYASLADQ 268 Query: 269 QPWGAGDVAPDDLVLNAGDRQGWADTEDV 297 AG+V DD V G GWA DV Sbjct: 269 PQLPAGEVQADDRVFQRGTGAGWATGGDV 297 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: 388 Number of extensions: 15 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: 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_057508987.1 ABB28_RS12815 (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.29273.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-115 370.1 0.0 2.8e-115 369.8 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508987.1 ABB28_RS12815 phenylalanine 4-mo Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057508987.1 ABB28_RS12815 phenylalanine 4-monooxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 369.8 0.0 2.8e-115 2.8e-115 4 243 .. 27 269 .. 24 273 .. 0.97 Alignments for each domain: == domain 1 score: 369.8 bits; conditional E-value: 2.8e-115 TIGR01267 4 vaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwkiva 72 v+q++d ys+++ha+w+tl++rq ll+grac+e+ld + +g++adrip +e++ne l a+tGw +v lcl|NCBI__GCF_001431535.1:WP_057508987.1 27 VEQPWDSYSADDHATWSTLFKRQRDLLNGRACQEFLDAQDAMGMSADRIPRFEQLNEALAAATGWTLVG 95 789****************************************************************** PP TIGR01267 73 vpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvka 141 v gl+p+ ff+hlanrrfpvt+++r p+++dy+ epd+fhdlfGhvpll+npvfad++eayG++gvka lcl|NCBI__GCF_001431535.1:WP_057508987.1 96 VEGLLPELDFFDHLANRRFPVTWWIRRPDQIDYIAEPDMFHDLFGHVPLLMNPVFADYMEAYGRGGVKA 164 ********************************************************************* PP TIGR01267 142 kalgaa...llarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtryr 207 +alg + l+rlywytvefGl++ta+glriyGaGi+ssk e++y+les p+r++fdl+++mrtryr lcl|NCBI__GCF_001431535.1:WP_057508987.1 165 HALGPDalqNLTRLYWYTVEFGLINTADGLRIYGAGIVSSKGESLYSLESPAPNRIGFDLERIMRTRYR 233 ***98755579********************************************************** PP TIGR01267 208 idklqkayfvlpslkrlfdaaqedfealvaeakdlk 243 id++qk+yfv++s+++l++a+++df++++a ++d+ lcl|NCBI__GCF_001431535.1:WP_057508987.1 234 IDTFQKTYFVIDSFEQLMQATAPDFTPIYASLADQP 269 *******************************99985 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 6.77 // [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