GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Pseudomonas fluorescens FW300-N1B4

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Pf1N1B4_5003 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

Query= reanno::pseudo3_N2E3:AO353_26925
         (358 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003
          Length = 358

 Score =  712 bits (1838), Expect = 0.0
 Identities = 349/358 (97%), Positives = 355/358 (99%)

Query: 1   MADLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGQINLILN 60
           MADLYENPMGLMGFEFIE ASPTPNTLEPIF+IMGFTKVATHRSKDVHLYRQGQINLILN
Sbjct: 1   MADLYENPMGLMGFEFIEFASPTPNTLEPIFQIMGFTKVATHRSKDVHLYRQGQINLILN 60

Query: 61  NEPHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGI 120
           NEP+SVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMEL+LPAIKGI
Sbjct: 61  NEPNSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELHLPAIKGI 120

Query: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180
           GGAPLYLIDRFGEGSSIYDIDFVFIEGVDR+PVGAGLKIIDHLTHNVYRGRMAYWANFYE
Sbjct: 121 GGAPLYLIDRFGEGSSIYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWANFYE 180

Query: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240
           KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ
Sbjct: 181 KLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQ 240

Query: 241 HVAFLSDDLIKTWDHLKKIGMRFMTAPPDTYYEMLEGRLPNHGEPVNELQARGILLDGSS 300
           HVAFLSDDLIKTWDHLK IGMRFMT PPDTYYEMLEGRLPNHGEPVNELQARGILLDGSS
Sbjct: 241 HVAFLSDDLIKTWDHLKSIGMRFMTPPPDTYYEMLEGRLPNHGEPVNELQARGILLDGSS 300

Query: 301 EAGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTE 358
           E+GDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLST+
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: 685
Number of extensions: 23
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 Pf1N1B4_5003 (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.22539.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                      -----------
   7.4e-130  419.5   0.0   8.3e-130  419.3   0.0    1.0  1  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003  4-hydroxyphenylpyruvate dioxygen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003  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 !  419.3   0.0  8.3e-130  8.3e-130       1     353 []      12     355 ..      12     355 .. 0.98

  Alignments for each domain:
  == domain 1  score: 419.3 bits;  conditional E-value: 8.3e-130
                                      TIGR01263   1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaa 64 
                                                    +gf+f+efa++ ++ +++ +++ +Gf++va+   +r+k+++++rqg+i+l+l++e++s   a+ 
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003  12 MGFEFIEFASPTPN-TLEPIFQIMGFTKVAT---HRSKDVHLYRQGQINLILNNEPNSV--ASY 69 
                                                    58***********9.***************9...***********************99..*** PP

                                      TIGR01263  65 flakHGdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlvere 128
                                                    f+a+HG++v+++af+v+d ++a+++a+e ga++++ ++    +e++l+aikgiG++ l+l++r+
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003  70 FAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETG--PMELHLPAIKGIGGAPLYLIDRF 131
                                                    ***********************************9986..99********************* PP

                                      TIGR01263 129 gekgsilpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdi 192
                                                    ge +si+++++ + e   +++++ ++gl+ iDH+++nv+rg++ ++a+fyek+++f+ei++fdi
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003 132 GEGSSIYDIDFVFIEG--VDRNPVGAGLKIIDHLTHNVYRGRMAYWANFYEKLFNFREIRYFDI 193
                                                    ***********99997..778889**************************************** PP

                                      TIGR01263 193 kteasaLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveel 256
                                                    k+e+++L+Sk++++++g++++plne +s+k  +QIee+l++++G+G+QH+A++++d++kt+++l
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003 194 KGEYTGLTSKAMTAPDGMIRIPLNE-ESSKGAGQIEEFLMQFNGEGIQHVAFLSDDLIKTWDHL 256
                                                    *************************.899*********************************** PP

                                      TIGR01263 257 rargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd.eeG...lLLQiFtkpvvdr 315
                                                    ++ g++f++ +p+tYY++l+ r+++ + e+++el++++iL+D++ e+G   lLLQiF+++++  
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003 257 KSIGMRFMTpPPDTYYEMLEGRLPN-HGEPVNELQARGILLDGSsESGdkrLLLQIFSETLM-- 317
                                                    *********999************7.*****************99999999***********.. PP

                                      TIGR01263 316 gtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                                    g++FfE+IqRkg++GFGegNfkaLfe+iEr+q++rgvl
  lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5003 318 GPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVL 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: 10.04
//
[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