Alignments for a candidate for HPD in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Pseudomonas fluorescens GW456-L13

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate PfGW456L13_2935 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935
          Length = 358

 Score =  728 bits (1878), Expect = 0.0
 Identities = 358/358 (100%), Positives = 358/358 (100%)

Query: 1   MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60
           MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN
Sbjct: 1   MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILN 60

Query: 61  NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI 120
           NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI
Sbjct: 61  NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI 120

Query: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180
           GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE
Sbjct: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180

Query: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240
           KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ
Sbjct: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240

Query: 241 HVAFLSDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPVDQLQARGILLDGSS 300
           HVAFLSDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPVDQLQARGILLDGSS
Sbjct: 241 HVAFLSDDLIKTWDHLKSIGMRFMTAPPETYYEMLEGRLPNHGEPVDQLQARGILLDGSS 300

Query: 301 ESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD 358
           ESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD
Sbjct: 301 ESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD 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: 678
Number of extensions: 21
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 PfGW456L13_2935 (4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27))
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.25072.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   2.1e-129  418.0   0.0   2.3e-129  417.8   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935  4-hydroxyphenylpyruvate dioxygen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935  4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.8   0.0  2.3e-129  2.3e-129       1     353 []      12     355 ..      12     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 417.8 bits;  conditional E-value: 2.3e-129
                                               TIGR01263   1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltae 55 
                                                             +gf+f+e+a++ ++ +++ ++e +Gf++va+   +r+k+++++rqg i+l+l++e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935  12 MGFEFIELASPTPN-TLEPIFEIMGFTKVAT---HRSKDVHLYRQGAINLILNNE 62 
                                                             58***********9.***************9...********************* PP

                                               TIGR01263  56 lsssseaaaflakHGdgvkdvafevedveaafeaavergaeavsapeeedekevk 110
                                                             ++s   a+ f+a+HG++v+++af+v+d ++a+++a+e ga++++ ++    +e++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935  63 PHSV--ASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETG--PMELN 113
                                                             ***9..**************************************9986..99*** PP

                                               TIGR01263 111 laaikgiGdvvltlveregekgsilpgfeevsekaalkekledvgleaiDHvvgn 165
                                                             l+aikgiG++ l+l++r+ge +si+++++ + e   +++++ ++gl+ iDH+++n
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935 114 LPAIKGIGGAPLYLIDRFGEGSSIYDIDFVFIEG--VDRHPVGAGLKIIDHLTHN 166
                                                             *****************************99997..677789************* PP

                                               TIGR01263 166 vergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepas 220
                                                             v+rg++ ++a+fyek+++f+ei++fdik+e+++L+Sk++++++g++++plne +s
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935 167 VYRGRMAYWANFYEKLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNE-ES 220
                                                             ****************************************************.89 PP

                                               TIGR01263 221 kkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnl 274
                                                             +k  +QIee+l++++G+G+QH+A++++d++kt+++l++ g++f++ +petYY++l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935 221 SKGAGQIEEFLMQFNGEGIQHVAFLSDDLIKTWDHLKSIGMRFMTaPPETYYEML 275
                                                             9********************************************9********* PP

                                               TIGR01263 275 kervkklvkedleelkelkiLvDrd.eeG...lLLQiFtkpvvdrgtlFfEiIqR 325
                                                             + r+++ + e++++l++++iL+D++ e+G   lLLQiF+++++  g++FfE+IqR
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935 276 EGRLPN-HGEPVDQLQARGILLDGSsESGdkrLLLQIFSETLM--GPVFFEFIQR 327
                                                             *****7.*****************99999999***********..********** PP

                                               TIGR01263 326 kgakGFGegNfkaLfeaiEreqekrgvl 353
                                                             kg++GFGegNfkaLfe+iEr+q++rgvl
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2935 328 KGDDGFGEGNFKALFESIERDQVRRGVL 355
                                                             *************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.55
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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