Alignments for a candidate for PAH in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for PAH in Pseudomonas stutzeri RCH2

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.carbon/TIGR01267.hmm
# target sequence database:        /tmp/gapView.8517.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: 10.31
//
[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