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.3927663.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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 26.04
//
[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:

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:

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:

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:

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