Align phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate RR42_RS20365 RR42_RS20365 phenylalanine-4-hydroxylase
Query= BRENDA::P30967 (297 letters) >FitnessBrowser__Cup4G11:RR42_RS20365 Length = 310 Score = 426 bits (1095), Expect = e-124 Identities = 198/272 (72%), Positives = 228/272 (83%) Query: 26 DFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGLERLEVDADRVPDFNKLNQ 85 DFT+ QPL+RY+ DHA WA LY RQ +L GR CDEF++GL L ++ DRVP F++LN+ Sbjct: 39 DFTIAQPLERYTDTDHAVWAKLYDRQASMLRGRVCDEFLQGLSTLGMERDRVPSFDQLNE 98 Query: 86 KLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGHVP 145 LM ATGW++VAVPGL+PD VFFEHLANRRFP +WW+R+P QLDYLQEPD FHD+FGHVP Sbjct: 99 TLMRATGWQVVAVPGLVPDAVFFEHLANRRFPASWWMRKPEQLDYLQEPDCFHDVFGHVP 158 Query: 146 LLINPVFADYLEAYGKGGVKAKALGALPMLARLYWYTVEFGLINTPAGMRIYGAGILSSK 205 LLINPVFA+Y+EAYGKGG+KA +LGAL MLARLYWYTVEFGLI TP G+RIYGAGILSS+ Sbjct: 159 LLINPVFANYMEAYGKGGLKAASLGALDMLARLYWYTVEFGLIRTPEGLRIYGAGILSSQ 218 Query: 206 SESIYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDATAPDFAPLYLQL 265 ESIY LDSASPNR+GFD+ RIM TRYRIDTFQKTYFVIDSF QLFDAT PDFAPLY +L Sbjct: 219 GESIYSLDSASPNRIGFDVRRIMRTRYRIDTFQKTYFVIDSFDQLFDATRPDFAPLYEEL 278 Query: 266 ADAQPWGAGDVAPDDLVLNAGDRQGWADTEDV 297 GAGDV DLVL G R+GWAD++DV Sbjct: 279 RAQPTLGAGDVGQSDLVLQRGSREGWADSDDV 310 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: 372 Number of extensions: 6 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: 297 Length of database: 310 Length adjustment: 27 Effective length of query: 270 Effective length of database: 283 Effective search space: 76410 Effective search space used: 76410 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 RR42_RS20365 RR42_RS20365 (phenylalanine-4-hydroxylase)
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.24950.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-123 395.7 0.0 4.1e-123 395.4 0.0 1.1 1 lcl|FitnessBrowser__Cup4G11:RR42_RS20365 RR42_RS20365 phenylalanine-4-hyd Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS20365 RR42_RS20365 phenylalanine-4-hydroxylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 395.4 0.0 4.1e-123 4.1e-123 1 244 [. 39 283 .. 39 287 .. 0.98 Alignments for each domain: == domain 1 score: 395.4 bits; conditional E-value: 4.1e-123 TIGR01267 1 dftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwk 69 dft+aq+l+ry++++havwa l+drq+ +l+gr cde+l+G+ lg++ dr+p ++++ne l+++tGw+ lcl|FitnessBrowser__Cup4G11:RR42_RS20365 39 DFTIAQPLERYTDTDHAVWAKLYDRQASMLRGRVCDEFLQGLSTLGMERDRVPSFDQLNETLMRATGWQ 107 79******************************************************************* PP TIGR01267 70 ivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkg 138 +vavpgl+p++vffehlanrrfp ++++r+pe+ldylqepd fhd+fGhvpll+npvfa+++eayGk+g lcl|FitnessBrowser__Cup4G11:RR42_RS20365 108 VVAVPGLVPDAVFFEHLANRRFPASWWMRKPEQLDYLQEPDCFHDVFGHVPLLINPVFANYMEAYGKGG 176 ********************************************************************* PP TIGR01267 139 vkakalgaa.llarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtry 206 +ka lga +larlywytvefGl++t++glriyGaGilss+ e++y+l+s++p+r++fd+ ++mrtry lcl|FitnessBrowser__Cup4G11:RR42_RS20365 177 LKAASLGALdMLARLYWYTVEFGLIRTPEGLRIYGAGILSSQGESIYSLDSASPNRIGFDVRRIMRTRY 245 *******977*********************************************************** PP TIGR01267 207 ridklqkayfvlpslkrlfdaaqedfealvaeakdlka 244 rid++qk+yfv++s+++lfda+++df++l+ e++ + + lcl|FitnessBrowser__Cup4G11:RR42_RS20365 246 RIDTFQKTYFVIDSFDQLFDATRPDFAPLYEELRAQPT 283 ******************************99887655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (310 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: 8.10 // [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