Alignments for a candidate for HPD in Novosphingobium aromaticivorans DSM 12444

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Novosphingobium aromaticivorans DSM 12444

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_041550657.1 SARO_RS02975 4-hydroxyphenylpyruvate dioxygenase

Query= BRENDA::P80064
         (357 letters)



>NCBI__GCF_000013325.1:WP_041550657.1
          Length = 368

 Score =  528 bits (1360), Expect = e-155
 Identities = 254/360 (70%), Positives = 296/360 (82%), Gaps = 4/360 (1%)

Query: 2   DLYENPMGLMGFEFIELASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNE 61
           DL+ENP+GL GFEFIE ++P   +LEP+F  MGFT +A HRSK V L+RQG INLI N+E
Sbjct: 8   DLFENPLGLDGFEFIEFSAPEAGSLEPVFARMGFTHIANHRSKQVQLWRQGGINLIANHE 67

Query: 62  PHSVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGG 121
           P S A+YFAAEHGPS CGM +RV+++ KAY  A+E GA+P+ + TGPMEL LPAI+GIGG
Sbjct: 68  PRSPAAYFAAEHGPSACGMGWRVRNAAKAYATAIERGAEPVEVRTGPMELRLPAIRGIGG 127

Query: 122 APLYLIDRFGEGS----SIYDIDFVFLEGVDRHPVGAGLKIIDHLTHNVYRGRMAYWANF 177
           + +YLIDR+  G     SIYDIDF +L GVDRHPVGAG   IDHLTHNVY GRMA+WA+F
Sbjct: 128 SIIYLIDRYEGGQFGDLSIYDIDFEYLPGVDRHPVGAGFHTIDHLTHNVYGGRMAHWASF 187

Query: 178 YEKLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEG 237
           YE++F FREIRYFDIKGEYTGLTS+AMTAPDG IRIPLNEE+  G GQIEEFL  +NGEG
Sbjct: 188 YERVFGFREIRYFDIKGEYTGLTSRAMTAPDGKIRIPLNEEAKAGGGQIEEFLRAYNGEG 247

Query: 238 IQHVAFLSDDLIKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVGELQARGILLDG 297
           IQH+AF  DDL+  WD LK+IG  FM+ PP TYYEML+ RLP HGEPV ELQ RGILLDG
Sbjct: 248 IQHIAFACDDLLGGWDKLKAIGTPFMSPPPATYYEMLDERLPGHGEPVAELQKRGILLDG 307

Query: 298 SSESGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD 357
           S+E GD RLLLQIFSET +GPVFFEFIQRK D+GFGEGNF ALF+S+ERDQ+RRGVL T+
Sbjct: 308 STEEGDPRLLLQIFSETQIGPVFFEFIQRKRDEGFGEGNFTALFKSMERDQLRRGVLKTE 367


Lambda     K      H
   0.321    0.141    0.420 

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: 571
Number of extensions: 20
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: 357
Length of database: 368
Length adjustment: 29
Effective length of query: 328
Effective length of database: 339
Effective search space:   111192
Effective search space used:   111192
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 WP_041550657.1 SARO_RS02975 (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.462094.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-115  372.0   0.0   2.3e-115  371.8   0.0    1.0  1  NCBI__GCF_000013325.1:WP_041550657.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000013325.1:WP_041550657.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  371.8   0.0  2.3e-115  2.3e-115       2     353 .]      18     364 ..      17     364 .. 0.95

  Alignments for each domain:
  == domain 1  score: 371.8 bits;  conditional E-value: 2.3e-115
                             TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvk 74 
                                           gf+f+ef +++a  +++ ++ ++Gf+ +a+   +r+k++ ++rqg i+l+ ++e++s   aa f+a+HG++++
  NCBI__GCF_000013325.1:WP_041550657.1  18 GFEFIEFSAPEAG-SLEPVFARMGFTHIAN---HRSKQVQLWRQGGINLIANHEPRSP--AAYFAAEHGPSAC 84 
                                           8***********9.9**************9...*******************999998..************* PP

                             TIGR01263  75 dvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlvereg..ekg..silpgfeevse 143
                                           +++++v+++++a+++a+ergae+v+  +    +e++l+ai+giG+++++l++r++  + g  si+++++e   
  NCBI__GCF_000013325.1:WP_041550657.1  85 GMGWRVRNAAKAYATAIERGAEPVEVRTG--PMELRLPAIRGIGGSIIYLIDRYEggQFGdlSIYDIDFEYLP 155
                                           ***********************999985..99********************98443332268888887777 PP

                             TIGR01263 144 kaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklpln 216
                                              +++++ ++g+++iDH+++nv+ g++ ++a+fye+++gf+ei++fdik+e+++L+S+++++++gk+++pln
  NCBI__GCF_000013325.1:WP_041550657.1 156 G--VDRHPVGAGFHTIDHLTHNVYGGRMAHWASFYERVFGFREIRYFDIKGEYTGLTSRAMTAPDGKIRIPLN 226
                                           6..788889**************************************************************** PP

                             TIGR01263 217 epaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlkervkklvkedlee 288
                                           e + k   +QIee+l++y+G+G+QH+A+  +d++  +++l+a g+ f++ +p tYY++l+er++  + e++ e
  NCBI__GCF_000013325.1:WP_041550657.1 227 E-EAKAGGGQIEEFLRAYNGEGIQHIAFACDDLLGGWDKLKAIGTPFMSpPPATYYEMLDERLPG-HGEPVAE 297
                                           *.78999******************************************9999***********7.******* PP

                             TIGR01263 289 lkelkiLvDrd.eeG...lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                           l++++iL+D++ eeG   lLLQiF+++ +  g++FfE+IqRk+++GFGegNf aLf+++Er+q +rgvl
  NCBI__GCF_000013325.1:WP_041550657.1 298 LQKRGILLDGStEEGdprLLLQIFSETQI--GPVFFEFIQRKRDEGFGEGNFTALFKSMERDQLRRGVL 364
                                           **********9999***9**********9..***********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (368 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: 25.10
//
[ok]

This GapMind analysis is from Sep 24 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