Alignments for a candidate for PAH in Pseudomonas benzenivorans DSM 8628

GapMind for Amino acid biosynthesis

Alignments for a candidate for PAH in Pseudomonas benzenivorans DSM 8628

Align Phenylalanine 4-monooxygenase (EC 1.14.16.1) (characterized)
to candidate WP_090447112.1 BLS63_RS17720 phenylalanine 4-monooxygenase

Query= reanno::pseudo5_N2C3_1:AO356_03975
         (261 letters)



>NCBI__GCF_900100495.1:WP_090447112.1
          Length = 261

 Score =  471 bits (1211), Expect = e-138
 Identities = 221/261 (84%), Positives = 243/261 (93%)

Query: 1   MKQTQYVAREPDAQGFIHYTAEEHAVWNTLITRQLKVIEGRACQEYLDGIDKLGLPHDRI 60
           MK TQYVAR+PD  GFIHY+  EH VWNTLITRQLKV+EGRACQEYLDGI+++GLP +RI
Sbjct: 1   MKTTQYVARKPDESGFIHYSEAEHQVWNTLITRQLKVVEGRACQEYLDGIEQIGLPLERI 60

Query: 61  PQLDEINKVLGQTTGWQVARVPALIPFQTFFELLASKQFPVATFIRTREELDYLQEPDIF 120
           PQLDE+N+VL  TTGW+VARVPALIPFQTFFELLAS+QFPVATFIRT EELDYLQEPDIF
Sbjct: 61  PQLDEVNRVLQATTGWRVARVPALIPFQTFFELLASQQFPVATFIRTPEELDYLQEPDIF 120

Query: 121 HEIFGHCPLLTNPWFAEFTHTYGKLGLQASKEERVYLARLYWMTIEFGLVQTPQGRRIYG 180
           HEIFGHCP+LTNPWFAEFTHTYGKLGL A+KEERVYLARLYW+TIEFGLV T QGRRIYG
Sbjct: 121 HEIFGHCPMLTNPWFAEFTHTYGKLGLAATKEERVYLARLYWLTIEFGLVDTSQGRRIYG 180

Query: 181 GGILSSPKETVYCLSDEPEHQAFDPLEAMRTPYRIDILQPVYFVLPELKRLFDLAHEDIM 240
           GGILSSPKET+Y LSD+PEH  FDP+EAMRTPYRIDILQP+YFVLPELKRLF+LAHEDIM
Sbjct: 181 GGILSSPKETLYALSDQPEHLPFDPIEAMRTPYRIDILQPLYFVLPELKRLFELAHEDIM 240

Query: 241 GMVKRGRELGLHAPKFPPKAA 261
           GMV+R  ++GLHAPKFPPKAA
Sbjct: 241 GMVQRAMQMGLHAPKFPPKAA 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: 371
Number of extensions: 11
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 WP_090447112.1 BLS63_RS17720 (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.31045.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.9e-129  415.6   0.0   3.3e-129  415.4   0.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090447112.1  BLS63_RS17720 phenylalanine 4-mo


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447112.1  BLS63_RS17720 phenylalanine 4-monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  415.4   0.0  3.3e-129  3.3e-129       3     247 ..      11     254 ..       9     255 .. 0.99

  Alignments for each domain:
  == domain 1  score: 415.4 bits;  conditional E-value: 3.3e-129
                                 TIGR01267   3 tvaqdldryseeehavwatlidrqlkllegracdeyldGveklgldadripdleevneklraltGwkiv 71 
                                               +++ ++++yse eh+vw+tli+rqlk++egrac+eyldG+e++gl+++rip+l+evn++l+a+tGw+++
  lcl|NCBI__GCF_900100495.1:WP_090447112.1  11 PDESGFIHYSEAEHQVWNTLITRQLKVVEGRACQEYLDGIEQIGLPLERIPQLDEVNRVLQATTGWRVA 79 
                                               78899**************************************************************** PP

                                 TIGR01267  72 avpglipadvffehlanrrfpvttflrtpeeldylqepdvfhdlfGhvpllsnpvfadfleayGkkgvk 140
                                               +vp+lip+++ffe+la+++fpv+tf+rtpeeldylqepd+fh++fGh+p+l+np+fa+f+++yGk+g+ 
  lcl|NCBI__GCF_900100495.1:WP_090447112.1  80 RVPALIPFQTFFELLASQQFPVATFIRTPEELDYLQEPDIFHEIFGHCPMLTNPWFAEFTHTYGKLGLA 148
                                               ********************************************************************* PP

                                 TIGR01267 141 akalgaallarlywytvefGlvetaaglriyGaGilsskkelvyaleskeplrvafdllevmrtryrid 209
                                               a++++++ larlyw+t+efGlv+t++g riyG+Gilss+ke++ya  s++p++ +fd++e+mrt+yrid
  lcl|NCBI__GCF_900100495.1:WP_090447112.1 149 ATKEERVYLARLYWLTIEFGLVDTSQGRRIYGGGILSSPKETLYA-LSDQPEHLPFDPIEAMRTPYRID 216
                                               *********************************************.89********************* PP

                                 TIGR01267 210 klqkayfvlpslkrlfdaaqedfealvaeakdlkaldp 247
                                               +lq++yfvlp+lkrlf++a+ed++ +v++a+++++++p
  lcl|NCBI__GCF_900100495.1:WP_090447112.1 217 ILQPLYFVLPELKRLFELAHEDIMGMVQRAMQMGLHAP 254
                                               **********************************9997 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: 7.28
//
[ok]

This GapMind analysis is from Apr 10 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