Alignments for a candidate for PAH in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for PAH in Pseudomonas fluorescens FW300-N2E2

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate Pf6N2E2_2630 Phenylalanine-4-hydroxylase (EC 1.14.16.1)

Query= reanno::pseudo6_N2E2:Pf6N2E2_2630
         (261 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2630
          Length = 261

 Score =  541 bits (1394), Expect = e-159
 Identities = 261/261 (100%), Positives = 261/261 (100%)

Query: 1   MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI 60
           MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI
Sbjct: 1   MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI 60

Query: 61  PQLDEINKVLGETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120
           PQLDEINKVLGETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF
Sbjct: 61  PQLDEINKVLGETTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120

Query: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVQTPQGRRIYG 180
           HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVQTPQGRRIYG
Sbjct: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVQTPQGRRIYG 180

Query: 181 GGILSSPKETVYCLSDEPEHQAFDPLEAMRTPYRIDILQPVYFVLPELKRLFDLAHEDIM 240
           GGILSSPKETVYCLSDEPEHQAFDPLEAMRTPYRIDILQPVYFVLPELKRLFDLAHEDIM
Sbjct: 181 GGILSSPKETVYCLSDEPEHQAFDPLEAMRTPYRIDILQPVYFVLPELKRLFDLAHEDIM 240

Query: 241 GMVKRGRELGLHAPKFPPKAA 261
           GMVKRGRELGLHAPKFPPKAA
Sbjct: 241 GMVKRGRELGLHAPKFPPKAA 261


Lambda     K      H
   0.323    0.141    0.439 

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: 425
Number of extensions: 13
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate Pf6N2E2_2630 (Phenylalanine-4-hydroxylase (EC 1.14.16.1))
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.12997.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   2.1e-131  422.6   0.0   2.4e-131  422.4   0.0    1.0  1  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2630  Phenylalanine-4-hydroxylase (EC 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2630  Phenylalanine-4-hydroxylase (EC 1.14.16.1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.4   0.0  2.4e-131  2.4e-131       3     247 ..      11     254 ..       9     255 .. 0.99

  Alignments for each domain:
  == domain 1  score: 422.4 bits;  conditional E-value: 2.4e-131
                                      TIGR01267   3 tvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklralt 66 
                                                    ++aq++++y++eehavw+tli+rqlk++egrac+eyldG++klgl++drip+l+e+n++l ++t
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2630  11 PDAQGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRIPQLDEINKVLGETT 74 
                                                    789************************************************************* PP

                                      TIGR01267  67 GwkivavpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadf 130
                                                    Gw++++vp+lip+++ffe+la+++fpv+tf+rt+eeldylqepd+fh++fGh+pll+np+fa+f
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2630  75 GWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIFHEIFGHCPLLTNPWFAEF 138
                                                    **************************************************************** PP

                                      TIGR01267 131 leayGkkgvkakalgaallarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrv 194
                                                    +++yGk+g++a++++++ larlyw+t+efGlv+t++g riyG+Gilss+ke+vy+  s+ep+++
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2630 139 THTYGKLGLQASKEERVYLARLYWMTIEFGLVQTPQGRRIYGGGILSSPKETVYC-LSDEPEHQ 201
                                                    *******************************************************.8******* PP

                                      TIGR01267 195 afdllevmrtryridklqkayfvlpslkrlfdaaqedfealvaeakdlkaldp 247
                                                    afd+le+mrt+yrid+lq++yfvlp+lkrlfd+a+ed++ +v++ ++l++++p
  lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2630 202 AFDPLEAMRTPYRIDILQPVYFVLPELKRLFDLAHEDIMGMVKRGRELGLHAP 254
                                                    **********************************************9999987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 8.50
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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

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 catabolism of small carbon sources