Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate GFF767 Psest_0781 phenylalanine-4-hydroxylase, monomeric form
Query= reanno::pseudo13_GW456_L13:PfGW456L13_4394 (261 letters) >FitnessBrowser__psRCH2:GFF767 Length = 261 Score = 456 bits (1174), Expect = e-133 Identities = 215/261 (82%), Positives = 238/261 (91%) Query: 1 MKQTQYVAREPDAQGFIDYPAEEHAVWNTLITRQLKVIEGRACQEYLDGIEKLGLPHDRI 60 MK T YVAREPDAQG I YP EHAVW TL+ RQLK++EGRACQEYLDG+++L LPH+RI Sbjct: 1 MKTTHYVAREPDAQGHIHYPDAEHAVWQTLVERQLKLLEGRACQEYLDGLDQLALPHERI 60 Query: 61 PQLGEINKVLAETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120 PQLGEIN+VL TTGWQV RVPALIPFQ FFELLASK+FPVATFIRT +ELDYLQEPDIF Sbjct: 61 PQLGEINRVLEATTGWQVERVPALIPFQRFFELLASKRFPVATFIRTPQELDYLQEPDIF 120 Query: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLKASKEERVYLARLYWMTIEFGLLDTPQGQRIYG 180 HEIFGHCPLLTNPWFAEFTHTYG+LGLKASKEERVYLARLYWMT+EFGL+DTP G RIYG Sbjct: 121 HEIFGHCPLLTNPWFAEFTHTYGQLGLKASKEERVYLARLYWMTVEFGLVDTPAGLRIYG 180 Query: 181 GGILSSPKETVYSLSNEPEHQAFDPLECMRTPYRIDILQPLYFVLPNLKRLFDLAHEDIM 240 GGILSSPKET+YSLS+EPE Q FD +E MRTPYRIDILQPLYFVLP+LK+LFDLA +DIM Sbjct: 181 GGILSSPKETLYSLSDEPERQPFDAMEAMRTPYRIDILQPLYFVLPDLKQLFDLAQQDIM 240 Query: 241 GMVKQAMQMGLHTPKFPPKAA 261 MV++AM++GLH PKFPPKAA Sbjct: 241 AMVREAMRLGLHQPKFPPKAA 261 Lambda K H 0.322 0.140 0.435 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: 376 Number of extensions: 8 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: 261 Length of database: 261 Length adjustment: 25 Effective length of query: 236 Effective length of database: 236 Effective search space: 55696 Effective search space used: 55696 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: 47 (22.7 bits)
Align candidate GFF767 Psest_0781 (phenylalanine-4-hydroxylase, monomeric form)
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.7836.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-129 414.8 0.0 5.6e-129 414.6 0.0 1.0 1 lcl|FitnessBrowser__psRCH2:GFF767 Psest_0781 phenylalanine-4-hydro Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF767 Psest_0781 phenylalanine-4-hydroxylase, monomeric form # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 414.6 0.0 5.6e-129 5.6e-129 3 247 .. 11 254 .. 9 255 .. 0.99 Alignments for each domain: == domain 1 score: 414.6 bits; conditional E-value: 5.6e-129 TIGR01267 3 tvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwkivavpglip 78 ++aq++++y++ ehavw+tl++rqlkllegrac+eyldG+++l l+++rip+l e+n++l+a+tGw++ +vp+lip lcl|FitnessBrowser__psRCH2:GFF767 11 PDAQGHIHYPDAEHAVWQTLVERQLKLLEGRACQEYLDGLDQLALPHERIPQLGEINRVLEATTGWQVERVPALIP 86 789************************************************************************* PP TIGR01267 79 advffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvkakalgaallarlyw 154 ++ ffe+la++rfpv+tf+rtp+eldylqepd+fh++fGh+pll+np+fa+f+++yG++g+ka++++++ larlyw lcl|FitnessBrowser__psRCH2:GFF767 87 FQRFFELLASKRFPVATFIRTPQELDYLQEPDIFHEIFGHCPLLTNPWFAEFTHTYGQLGLKASKEERVYLARLYW 162 **************************************************************************** PP TIGR01267 155 ytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtryridklqkayfvlpslkrlfdaaqe 230 +tvefGlv+t+aglriyG+Gilss+ke++y+ s+ep+r++fd +e+mrt+yrid+lq++yfvlp+lk+lfd+aq+ lcl|FitnessBrowser__psRCH2:GFF767 163 MTVEFGLVDTPAGLRIYGGGILSSPKETLYS-LSDEPERQPFDAMEAMRTPYRIDILQPLYFVLPDLKQLFDLAQQ 237 *******************************.8******************************************* PP TIGR01267 231 dfealvaeakdlkaldp 247 d++a+v ea++l++++p lcl|FitnessBrowser__psRCH2:GFF767 238 DIMAMVREAMRLGLHQP 254 *************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (248 nodes) Target sequences: 1 (261 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: 9.42 // [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