Alignments for a candidate for HPD in Pseudomonas stutzeri RCH2

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Pseudomonas stutzeri RCH2

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate GFF3449 Psest_3514 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::psRCH2:GFF3449
         (361 letters)



>FitnessBrowser__psRCH2:GFF3449
          Length = 361

 Score =  736 bits (1899), Expect = 0.0
 Identities = 361/361 (100%), Positives = 361/361 (100%)

Query: 1   MNAVNKIEQHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQH 60
           MNAVNKIEQHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQH
Sbjct: 1   MNAVNKIEQHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQH 60

Query: 61  DINIVLNGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELN 120
           DINIVLNGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELN
Sbjct: 61  DINIVLNGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELN 120

Query: 121 IPCVEGIGGSLLYLVDRYGDKSIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDV 180
           IPCVEGIGGSLLYLVDRYGDKSIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDV
Sbjct: 121 IPCVEGIGGSLLYLVDRYGDKSIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDV 180

Query: 181 WSGFYERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYH 240
           WSGFYERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYH
Sbjct: 181 WSGFYERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYH 240

Query: 241 GEGIQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILI 300
           GEGIQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILI
Sbjct: 241 GEGIQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILI 300

Query: 301 DGAPGDDGILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVIKAD 360
           DGAPGDDGILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVIKAD
Sbjct: 301 DGAPGDDGILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVIKAD 360

Query: 361 E 361
           E
Sbjct: 361 E 361


Lambda     K      H
   0.320    0.139    0.412 

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: 711
Number of extensions: 17
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: 361
Length of database: 361
Length adjustment: 29
Effective length of query: 332
Effective length of database: 332
Effective search space:   110224
Effective search space used:   110224
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 GFF3449 Psest_3514 (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.32318.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
     7e-128  413.0   0.0   7.9e-128  412.8   0.0    1.0  1  lcl|FitnessBrowser__psRCH2:GFF3449  Psest_3514 4-hydroxyphenylpyruva


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__psRCH2:GFF3449  Psest_3514 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  412.8   0.0  7.9e-128  7.9e-128       2     352 ..      17     356 ..      16     357 .. 0.97

  Alignments for each domain:
  == domain 1  score: 412.8 bits;  conditional E-value: 7.9e-128
                           TIGR01263   2 gfdfvefavgdak..qaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvk 74 
                                         gf+fvef++++a+  +++++l++++Gf++ ak   +r+k++++++q +i++vl+ +++ +  ++af++kHG++++
  lcl|FitnessBrowser__psRCH2:GFF3449  17 GFEFVEFTAPNAEgiEQLRTLFTQMGFTETAK---HRSKEVWLFQQHDINIVLNGSPTGH--VHAFAEKHGPSAC 86 
                                         8***********988899*************9...************************9..************* PP

                           TIGR01263  75 dvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalke 149
                                         ++af+v+++++a +   ++ga+ v ++ +   +e++++ ++giG+++l+lv+r+g+k si+++++e  e  + ++
  lcl|FitnessBrowser__psRCH2:GFF3449  87 AMAFRVKNAAQAAAYVESQGAKLVGSHAN--FGELNIPCVEGIGGSLLYLVDRYGDK-SIYDVDFEYIEGRTPND 158
                                         ***********************999985..799*********************99.9******9999865555 PP

                           TIGR01263 150 kledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkk 224
                                           + vgl  iDH+++nv rg+++ ++ fye+i +f+ei++fdi+++ ++L S+++++++gk+++p+ne  s ++k
  lcl|FitnessBrowser__psRCH2:GFF3449 159 --NAVGLMCIDHLTHNVMRGQMDVWSGFYERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINE--SADDK 229
                                         ..89****************************************************************..89*** PP

                           TIGR01263 225 sQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdnlkervkklvkedleelkelkiLvDrd 299
                                         sQIee+++ey+G+G+QH+Al+t+di++tv++lra+gv+f+++p+tYY++++ rv   + e+ + l+el+iL+D++
  lcl|FitnessBrowser__psRCH2:GFF3449 230 SQIEEFIREYHGEGIQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAG-HGEPTDVLRELNILIDGA 303
                                         *******************************************************7.****************** PP

                           TIGR01263 300 ..eeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgv 352
                                           ++G+LLQiFt++v+  g++FfEiIqRkg++GFGegNfkaLfe+iE++q +rgv
  lcl|FitnessBrowser__psRCH2:GFF3449 304 pgDDGILLQIFTNTVI--GPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGV 356
                                         ****************..***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (361 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: 8.20
//
[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