Alignments for a candidate for HPD in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Pseudomonas putida KT2440

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate PP_3433 PP_3433 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2935
         (358 letters)



>FitnessBrowser__Putida:PP_3433
          Length = 358

 Score =  666 bits (1719), Expect = 0.0
 Identities = 323/358 (90%), Positives = 342/358 (95%)

Query: 1   MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60
           MAD++ENPMGLMGFEFIELASPTP  LEP+F+I+GFTKVATHRSKDVHLYRQG INLILN
Sbjct: 1   MADIFENPMGLMGFEFIELASPTPGVLEPVFQILGFTKVATHRSKDVHLYRQGGINLILN 60

Query: 61  NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI 120
           NEP S+ASYFAAEHGPSVCGMAFRV+++ +AY RALELGAQP+ IETGPMEL LPAIKGI
Sbjct: 61  NEPKSIASYFAAEHGPSVCGMAFRVRNAHEAYARALELGAQPVEIETGPMELRLPAIKGI 120

Query: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180
           GGAPLYLIDRF EGSSIYDIDF FIEGVDR+PVGAGLKIIDHLTHNVYRGRMAYWA FYE
Sbjct: 121 GGAPLYLIDRFEEGSSIYDIDFNFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYE 180

Query: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240
           KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ
Sbjct: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240

Query: 241 HVAFLSDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPVDQLQARGILLDGSS 300
           HVAFL+DDL+KTWD LK +GMRFMTAPP+TYYEMLE RLP HGEPVDQLQARGILLDG+S
Sbjct: 241 HVAFLTDDLLKTWDALKGLGMRFMTAPPQTYYEMLEERLPGHGEPVDQLQARGILLDGAS 300

Query: 301 ESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD 358
           + GDKRLLLQIFSETL+GPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD
Sbjct: 301 QPGDKRLLLQIFSETLLGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD 358


Lambda     K      H
   0.321    0.141    0.419 

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: 635
Number of extensions: 18
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: 358
Length of database: 358
Length adjustment: 29
Effective length of query: 329
Effective length of database: 329
Effective search space:   108241
Effective search space used:   108241
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 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate PP_3433 PP_3433 (4-hydroxyphenylpyruvate dioxygenase)
to HMM TIGR01263 (hppD: 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))

# 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/TIGR01263.hmm
# target sequence database:        /tmp/gapView.8746.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01263  [M=353]
Accession:   TIGR01263
Description: 4HPPD: 4-hydroxyphenylpyruvate dioxygenase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   8.8e-125  402.8   0.0   9.9e-125  402.6   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3433  PP_3433 4-hydroxyphenylpyruvate 


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3433  PP_3433 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.6   0.0  9.9e-125  9.9e-125       1     353 []      12     355 ..      12     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 402.6 bits;  conditional E-value: 9.9e-125
                           TIGR01263   1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkd 75 
                                         +gf+f+e+a++ +   ++ +++ lGf++va+   +r+k+++++rqg i+l+l++e++s   a+ f+a+HG++v++
  lcl|FitnessBrowser__Putida:PP_3433  12 MGFEFIELASPTPG-VLEPVFQILGFTKVAT---HRSKDVHLYRQGGINLILNNEPKSI--ASYFAAEHGPSVCG 80 
                                         589**********9.9**************9...*********************9999..************** PP

                           TIGR01263  76 vafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkek 150
                                         +af+v+++++a+++a+e ga++v+ ++    +e++l+aikgiG++ l+l++r++e +si+++++++ e   ++++
  lcl|FitnessBrowser__Putida:PP_3433  81 MAFRVRNAHEAYARALELGAQPVEIETG--PMELRLPAIKGIGGAPLYLIDRFEEGSSIYDIDFNFIEG--VDRN 151
                                         ***********************99986..99*********************************9997..7788 PP

                           TIGR01263 151 ledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkks 225
                                         + ++gl+ iDH+++nv+rg++ ++a fyek+++f+ei++fdik+e+++L+Sk++++++g++++plne +s+k  +
  lcl|FitnessBrowser__Putida:PP_3433 152 PVGAGLKIIDHLTHNVYRGRMAYWAGFYEKLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNE-ESSKGAG 225
                                         89*****************************************************************.899**** PP

                           TIGR01263 226 QIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd 299
                                         QIee+l++++G+G+QH+A++t+d++kt+++l+  g++f++ +p+tYY++l+er++  + e++++l++++iL+D++
  lcl|FitnessBrowser__Putida:PP_3433 226 QIEEFLMQFNGEGIQHVAFLTDDLLKTWDALKGLGMRFMTaPPQTYYEMLEERLPG-HGEPVDQLQARGILLDGA 299
                                         ****************************************99*************7.*****************9 PP

                           TIGR01263 300 .eeG...lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                          + G   lLLQiF++++   g++FfE+IqRkg++GFGegNfkaLfe+iEr+q++rgvl
  lcl|FitnessBrowser__Putida:PP_3433 300 sQPGdkrLLLQIFSETLL--GPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVL 355
                                         7556777***********..***********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (358 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.28
//
[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