Alignments for a candidate for HPD in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Dyella japonica UNC79MFTsu3.2

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate N515DRAFT_0360 N515DRAFT_0360 4-hydroxyphenylpyruvate dioxygenase

Query= BRENDA::Q09PG8
         (367 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0360
          Length = 364

 Score =  530 bits (1364), Expect = e-155
 Identities = 257/354 (72%), Positives = 293/354 (82%), Gaps = 2/354 (0%)

Query: 16  VATFENPMGIDGFEFVEFASPEPE--KLHELFRNLGFVQVARHKTRPIYNYRQNDCTFLI 73
           V TFENPMGIDGFEFVEFA+P     +LHELF ++GF  V +HK RPI  YRQ    FL+
Sbjct: 11  VTTFENPMGIDGFEFVEFAAPAGRGAELHELFGSMGFTAVLKHKRRPITVYRQGGVNFLV 70

Query: 74  NEDPDSFAADFARVHGPSACGFAIRVNKLAEWVRVQALKNGAKSIADKETSKAVAAPVIE 133
           NEDPDSFAA+FA  HGP A GFAIR  + A  V  + L NG +++ DKE SKAV APV++
Sbjct: 71  NEDPDSFAAEFAAQHGPCAAGFAIRFKQPAAEVYAKVLANGGEAVGDKEASKAVDAPVVK 130

Query: 134 GIGGCMLYIVDRYDDKGTIHDPDWEWLPGAQMMPKGFGLTFIDHLTHNVYFGNMSKWADY 193
           GIG CMLY+VDRY DKG+I+D D+  +PG +  P GFGLTFIDHLTHN+YFGNM KW+DY
Sbjct: 131 GIGDCMLYLVDRYGDKGSIYDGDYAPIPGVEQNPAGFGLTFIDHLTHNLYFGNMQKWSDY 190

Query: 194 YERLFQFREIRYFDIKGAKTGLLSKAMTAPDGMVRIPLNESPDPKSQINEYLDQYRGEGI 253
           YERLF FREIRYFDIKGAKTGL+SKAMTAPDG+VRIPLNES DPKSQINEYLD Y GEGI
Sbjct: 191 YERLFNFREIRYFDIKGAKTGLVSKAMTAPDGIVRIPLNESSDPKSQINEYLDAYHGEGI 250

Query: 254 QHIACFTDDIYATVEAMRAHGIEFLDTPNAYYAVIDERIPNHGEDVARMKESRILIDADP 313
           QHIACFTD+IY TVEAMRA G+ FLDTP+ Y+ VID RIPNHGEDV R+  ++ILIDADP
Sbjct: 251 QHIACFTDNIYETVEAMRAKGVSFLDTPDTYFDVIDLRIPNHGEDVPRLARNKILIDADP 310

Query: 314 ETKKKLLLQIFTKNCVGPIFFEIIQRKGNTGFGEGNFQALFESIEREQMARGVL 367
           ETK++ LLQIFT+N +GPIFFEIIQRKGN GFGEGNFQALFESIER+QM RGVL
Sbjct: 311 ETKQRKLLQIFTQNNIGPIFFEIIQRKGNEGFGEGNFQALFESIERDQMRRGVL 364


Lambda     K      H
   0.321    0.138    0.421 

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: 616
Number of extensions: 28
Number of successful extensions: 2
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: 367
Length of database: 364
Length adjustment: 30
Effective length of query: 337
Effective length of database: 334
Effective search space:   112558
Effective search space used:   112558
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 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate N515DRAFT_0360 N515DRAFT_0360 (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.10582.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   1.7e-117  378.8   0.0   1.9e-117  378.7   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_0360  N515DRAFT_0360 4-hydroxyphenylpy


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_0360  N515DRAFT_0360 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  378.7   0.0  1.9e-117  1.9e-117       2     353 .]      22     364 .]      21     364 .] 0.96

  Alignments for each domain:
  == domain 1  score: 378.7 bits;  conditional E-value: 1.9e-117
                                    TIGR01263   2 gfdfvefavgdak.qaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaafl 66 
                                                  gf+fvefa++  + + +++l+ ++Gf+av k   ++++ +tv+rqg +++++++ + s   aa+f+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0360  22 GFEFVEFAAPAGRgAELHELFGSMGFTAVLK---HKRRPITVYRQGGVNFLVNEDPDSF--AAEFA 82 
                                                  89*******98774789*************9...********************99999..***** PP

                                    TIGR01263  67 akHGdgvkdvafeved.veaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregek 131
                                                  a+HG+++++ a++ ++ +++++++ +++g eav ++e   +k+v+++++kgiGd +l+lv+r+g+k
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0360  83 AQHGPCAAGFAIRFKQpAAEVYAKVLANGGEAVGDKEA--SKAVDAPVVKGIGDCMLYLVDRYGDK 146
                                                  *************9874789*************99986..689*********************** PP

                                    TIGR01263 132 gsilpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteas 197
                                                  gsi++g+ +      +++++++ gl+ iDH+++n++ g+++k++++ye++++f+ei++fdik+  +
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 147 GSIYDGDYAPIPG--VEQNPAGFGLTFIDHLTHNLYFGNMQKWSDYYERLFNFREIRYFDIKGAKT 210
                                                  ******9976665..777789********************************************* PP

                                    TIGR01263 198 aLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargvef 263
                                                  +L+Sk++++++g v++plne  s++ ksQI+eyl++y+G+G+QH+A  t++i++tve++ra+gv f
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 211 GLVSKAMTAPDGIVRIPLNE--SSDPKSQINEYLDAYHGEGIQHIACFTDNIYETVEAMRAKGVSF 274
                                                  ********************..99****************************************** PP

                                    TIGR01263 264 lkipetYYdnlkervkklvkedleelkelkiLvDrd...eeGlLLQiFtkpvvdrgtlFfEiIqRk 326
                                                  l++p+tY+d ++ r+++ + ed+ +l ++kiL+D d   ++  LLQiFt++ +  g++FfEiIqRk
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 275 LDTPDTYFDVIDLRIPN-HGEDVPRLARNKILIDADpetKQRKLLQIFTQNNI--GPIFFEIIQRK 337
                                                  ****************7.******************876667***********..*********** PP

                                    TIGR01263 327 gakGFGegNfkaLfeaiEreqekrgvl 353
                                                  g++GFGegNf+aLfe+iEr+q +rgvl
  lcl|FitnessBrowser__Dyella79:N515DRAFT_0360 338 GNEGFGEGNFQALFESIERDQMRRGVL 364
                                                  ************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (364 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.46
//
[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