Align phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate BPHYT_RS19520 BPHYT_RS19520 phenylalanine 4-monooxygenase
Query= BRENDA::P30967 (297 letters) >FitnessBrowser__BFirm:BPHYT_RS19520 Length = 296 Score = 366 bits (940), Expect = e-106 Identities = 173/275 (62%), Positives = 204/275 (74%), Gaps = 3/275 (1%) Query: 26 DFTLPQPLDRYSAEDHATWATLYQRQCKLLPGRACDEFMEGLERLEVDADRVPDFNKLNQ 85 DFT+ QP +RY A DHA W LY RQ LL GR CDEF+ G++ + + DRVP F+++N Sbjct: 22 DFTIDQPTERYGAVDHAVWQQLYARQTALLKGRVCDEFLAGIDTIGMPPDRVPSFDEINA 81 Query: 86 KLMAATGWKIVAVPGLIPDDVFFEHLANRRFPVTWWLREPHQLDYLQEPDVFHDLFGHVP 145 KL ATGW+IVAVPGL+PD VFFEHLANRRFPVTWW+R P QLDYLQEPD FHDLFGHVP Sbjct: 82 KLAPATGWEIVAVPGLVPDQVFFEHLANRRFPVTWWMRRPDQLDYLQEPDCFHDLFGHVP 141 Query: 146 LLINPVFADYLEAYGKGGVKAKALGALPMLARLYWYTVEFGLIN---TPAGMRIYGAGIL 202 LLINPVFADY+ AYG+ + A GALP+LARLYWYTVEFGLI +P G++IYGAGI+ Sbjct: 142 LLINPVFADYMHAYGRAALAAHDAGALPLLARLYWYTVEFGLIRDAASPNGVKIYGAGIV 201 Query: 203 SSKSESIYCLDSASPNRVGFDLMRIMNTRYRIDTFQKTYFVIDSFKQLFDATAPDFAPLY 262 SSK E++Y SA+PNR+GF L R+M TRYRIDTFQKTYFVID F QLF DFAPL Sbjct: 202 SSKGETLYSQQSAAPNRLGFGLERVMRTRYRIDTFQKTYFVIDDFAQLFKVAQTDFAPLL 261 Query: 263 LQLADAQPWGAGDVAPDDLVLNAGDRQGWADTEDV 297 +L AGDV D V+ G ++GW D+ Sbjct: 262 AKLVAEPALAAGDVLEHDRVITRGSQEGWLADGDI 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: 370 Number of extensions: 13 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: 296 Length adjustment: 26 Effective length of query: 271 Effective length of database: 270 Effective search space: 73170 Effective search space used: 73170 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 BPHYT_RS19520 BPHYT_RS19520 (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.27049.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-115 370.3 0.0 2.2e-115 370.1 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS19520 BPHYT_RS19520 phenylalanine 4-mo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS19520 BPHYT_RS19520 phenylalanine 4-monooxygenase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.1 0.0 2.2e-115 2.2e-115 1 244 [. 22 269 .. 22 273 .. 0.97 Alignments for each domain: == domain 1 score: 370.1 bits; conditional E-value: 2.2e-115 TIGR01267 1 dftvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwki 70 dft++q+ +ry + +havw+ l+ rq+ ll+gr cde+l G++ +g++ dr+p ++e+n kl +tGw+i lcl|FitnessBrowser__BFirm:BPHYT_RS19520 22 DFTIDQPTERYGAVDHAVWQQLYARQTALLKGRVCDEFLAGIDTIGMPPDRVPSFDEINAKLAPATGWEI 91 79******************************************************************** PP TIGR01267 71 vavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvk 140 vavpgl+p++vffehlanrrfpvt+++r p++ldylqepd fhdlfGhvpll+npvfad+++ayG+ ++ lcl|FitnessBrowser__BFirm:BPHYT_RS19520 92 VAVPGLVPDQVFFEHLANRRFPVTWWMRRPDQLDYLQEPDCFHDLFGHVPLLINPVFADYMHAYGRAALA 161 ********************************************************************** PP TIGR01267 141 akalgaa.llarlywytvefGlvetaag...lriyGaGilsskkelvyaleskeplrvafdllevmrtry 206 a+ ga llarlywytvefGl+++aa ++iyGaGi+ssk e++y+ +s+ p+r +f l++vmrtry lcl|FitnessBrowser__BFirm:BPHYT_RS19520 162 AHDAGALpLLARLYWYTVEFGLIRDAASpngVKIYGAGIVSSKGETLYSQQSAAPNRLGFGLERVMRTRY 231 ******999**************987533339************************************** PP TIGR01267 207 ridklqkayfvlpslkrlfdaaqedfealvaeakdlka 244 rid++qk+yfv++++ +lf++aq+df++l+a++ a lcl|FitnessBrowser__BFirm:BPHYT_RS19520 232 RIDTFQKTYFVIDDFAQLFKVAQTDFAPLLAKLVAEPA 269 ******************************99876655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (296 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: 9.47 // [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