Alignments for a candidate for PAH in Pseudomonas simiae WCS417

GapMind for Amino acid biosynthesis

Alignments for a candidate for PAH in Pseudomonas simiae WCS417

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate GFF3887 PS417_19900 phenylalanine 4-monooxygenase

Query= reanno::pseudo3_N2E3:AO353_18585
         (263 letters)



>FitnessBrowser__WCS417:GFF3887
          Length = 263

 Score =  511 bits (1316), Expect = e-150
 Identities = 243/263 (92%), Positives = 255/263 (96%)

Query: 1   MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVLEGRACQEYMDGIEKLGLPHDRI 60
           MKQTQYVAREPDAQGFIHY+ EEHAVWNTLITRQLKV+EGRACQEY+DGI+KLGLPHDRI
Sbjct: 1   MKQTQYVAREPDAQGFIHYSQEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI 60

Query: 61  PQLDEINKVLGETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120
           PQL EINKVL ETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF
Sbjct: 61  PQLGEINKVLAETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120

Query: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVDTPQGKRIYG 180
           HEIFGHCPLLTNPWFAEFTHTYGKLGL A+KE+RVYLARLYWMTIEFGLVDTP+G+RIYG
Sbjct: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLAATKEQRVYLARLYWMTIEFGLVDTPEGRRIYG 180

Query: 181 GGILSSPKETVYSLSGEPEHQAFDPLEAMRTPYRIDILQPLYFVLPNLKRLFDLAHEDIM 240
           GGILSSPKETVYSLS EPEHQ FDPLEAMRTPYRIDILQPLYFVLP+LKRLF++A EDIM
Sbjct: 181 GGILSSPKETVYSLSSEPEHQVFDPLEAMRTPYRIDILQPLYFVLPDLKRLFEVAQEDIM 240

Query: 241 GMVHQGMQLGLHAPKFPPKPKAA 263
           GMV +GMQLGLHAPKFPPKPKAA
Sbjct: 241 GMVERGMQLGLHAPKFPPKPKAA 263


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: 374
Number of extensions: 10
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: 263
Length of database: 263
Length adjustment: 25
Effective length of query: 238
Effective length of database: 238
Effective search space:    56644
Effective search space used:    56644
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 GFF3887 PS417_19900 (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.3414.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   1.4e-129  416.6   0.0   1.7e-129  416.4   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF3887  PS417_19900 phenylalanine 4-mono


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF3887  PS417_19900 phenylalanine 4-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  416.4   0.0  1.7e-129  1.7e-129       3     247 ..      11     254 ..       9     255 .. 0.99

  Alignments for each domain:
  == domain 1  score: 416.4 bits;  conditional E-value: 1.7e-129
                           TIGR01267   3 tvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwkivavpgli 77 
                                         ++aq++++ys+eehavw+tli+rqlk++egrac+eyldG++klgl++drip+l e+n++l ++tGw++++vp+li
  lcl|FitnessBrowser__WCS417:GFF3887  11 PDAQGFIHYSQEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRIPQLGEINKVLAETTGWQVARVPALI 85 
                                         789************************************************************************ PP

                           TIGR01267  78 padvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvkakalgaallarl 152
                                         p+++ffe+la+++fpv+tf+rt+eeldylqepd+fh++fGh+pll+np+fa+f+++yGk+g+ a++++++ larl
  lcl|FitnessBrowser__WCS417:GFF3887  86 PFQTFFELLASKQFPVATFIRTREELDYLQEPDIFHEIFGHCPLLTNPWFAEFTHTYGKLGLAATKEQRVYLARL 160
                                         *************************************************************************** PP

                           TIGR01267 153 ywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtryridklqkayfvlpslkrlfda 227
                                         yw+t+efGlv+t++g riyG+Gilss+ke+vy+  s+ep+++ fd+le+mrt+yrid+lq++yfvlp+lkrlf++
  lcl|FitnessBrowser__WCS417:GFF3887 161 YWMTIEFGLVDTPEGRRIYGGGILSSPKETVYS-LSSEPEHQVFDPLEAMRTPYRIDILQPLYFVLPDLKRLFEV 234
                                         *********************************.7889************************************* PP

                           TIGR01267 228 aqedfealvaeakdlkaldp 247
                                         aqed++ +v + ++l++++p
  lcl|FitnessBrowser__WCS417:GFF3887 235 AQEDIMGMVERGMQLGLHAP 254
                                         ***************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (248 nodes)
Target sequences:                          1  (263 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: 8.68
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

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

GapMind for Amino acid biosynthesis