Alignments for a candidate for HPD in Alicycliphilus denitrificans K601

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Alicycliphilus denitrificans K601

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_013517522.1 ALIDE2_RS02940 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::acidovorax_3H11:Ac3H11_1849
         (381 letters)



>NCBI__GCF_000204645.1:WP_013517522.1
          Length = 373

 Score =  657 bits (1694), Expect = 0.0
 Identities = 319/369 (86%), Positives = 342/369 (92%), Gaps = 2/369 (0%)

Query: 12  MNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTLVAKHRSKDVVL 71
           M AALP + A +  AW+NPMGLMGFEFVEFTSPQPG+LE VFEKLGFTLVA+HRSKDV+L
Sbjct: 1   MTAALPTQAARETTAWENPMGLMGFEFVEFTSPQPGLLEDVFEKLGFTLVARHRSKDVLL 60

Query: 72  YRQNGINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTGP 131
           YRQN INFILNREPHSQAAYFGAEHGPSACGLAFRVKDAH+AY RALELGAQPIEIPTGP
Sbjct: 61  YRQNQINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHRAYKRALELGAQPIEIPTGP 120

Query: 132 MELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLNLIDHLTHNVYR 191
           MELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFE++EGV +RP GHGL  IDHLTHNVYR
Sbjct: 121 MELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEWLEGVPQRPEGHGLKEIDHLTHNVYR 180

Query: 192 GRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEESKQGGGQIEE 251
           GRMGFWANFYEKLF FREIRYFDIQGEYTGLTSKAMTAPDG+IRIPLNEE++QGGGQIEE
Sbjct: 181 GRMGFWANFYEKLFNFREIRYFDIQGEYTGLTSKAMTAPDGRIRIPLNEEARQGGGQIEE 240

Query: 252 FLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTRLPGHGQPVPEL 311
           FLMQFNGEGIQHIAL+CD L DVVD+LG+AGV LA APN+VYYEMLD RLPGHGQ V  L
Sbjct: 241 FLMQFNGEGIQHIALVCDRLTDVVDRLGLAGVPLAPAPNDVYYEMLDKRLPGHGQDVAAL 300

Query: 312 QSRGILLDGTTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEGNFKALFESLER 371
           Q+RGILLDG+TA G PRLLLQIFSTPMLGPVFFEFIQREGD  +GFGEGNFKALFESLER
Sbjct: 301 QARGILLDGSTAGGQPRLLLQIFSTPMLGPVFFEFIQREGD--EGFGEGNFKALFESLER 358

Query: 372 DQIRRGVLN 380
           DQ+ RGV++
Sbjct: 359 DQVNRGVID 367


Lambda     K      H
   0.322    0.142    0.431 

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: 686
Number of extensions: 25
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: 381
Length of database: 373
Length adjustment: 30
Effective length of query: 351
Effective length of database: 343
Effective search space:   120393
Effective search space used:   120393
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: 50 (23.9 bits)

Align candidate WP_013517522.1 ALIDE2_RS02940 (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.25115.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.5e-115  372.4   0.0   1.7e-115  372.2   0.0    1.0  1  lcl|NCBI__GCF_000204645.1:WP_013517522.1  ALIDE2_RS02940 4-hydroxyphenylpy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204645.1:WP_013517522.1  ALIDE2_RS02940 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  372.2   0.0  1.7e-115  1.7e-115       1     352 [.      23     365 ..      23     366 .. 0.97

  Alignments for each domain:
  == domain 1  score: 372.2 bits;  conditional E-value: 1.7e-115
                                 TIGR01263   1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakH 69 
                                               +gf+fvef+++++   ++ ++eklGf++va+   +r+k++ ++rq++i+++l+ e++s+  aa f a+H
  lcl|NCBI__GCF_000204645.1:WP_013517522.1  23 MGFEFVEFTSPQPG-LLEDVFEKLGFTLVAR---HRSKDVLLYRQNQINFILNREPHSQ--AAYFGAEH 85 
                                               58***********9.9**************8...*************************..******** PP

                                 TIGR01263  70 GdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgf 138
                                               G++++++af+v+d++ a+++a+e ga++++ p+    +e++l+aikgiG++ l+l++r+++ +si++++
  lcl|NCBI__GCF_000204645.1:WP_013517522.1  86 GPSACGLAFRVKDAHRAYKRALELGAQPIEIPTG--PMELRLPAIKGIGGAPLYLIDRFEDGKSIYDID 152
                                               ********************************96..99******************************* PP

                                 TIGR01263 139 eevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasa 207
                                               +e+ e   + +++e+ gl++iDH+++nv+rg+++ +a+fyek+++f+ei++fdi++e+++L+Sk+++++
  lcl|NCBI__GCF_000204645.1:WP_013517522.1 153 FEWLEG--VPQRPEGHGLKEIDHLTHNVYRGRMGFWANFYEKLFNFREIRYFDIQGEYTGLTSKAMTAP 219
                                               ****98..778889******************************************************* PP

                                 TIGR01263 208 egkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlk 275
                                               +g++++plne +  +  +QIee+l++++G+G+QH+Al+ + +++ v++l   gv + + + + YY++l+
  lcl|NCBI__GCF_000204645.1:WP_013517522.1 220 DGRIRIPLNE-EARQGGGQIEEFLMQFNGEGIQHIALVCDRLTDVVDRLGLAGVPLAPaPNDVYYEMLD 287
                                               **********.788999*****************************************55678****** PP

                                 TIGR01263 276 ervkklvkedleelkelkiLvDrdeeG....lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLf 340
                                               +r++  + +d+  l++++iL+D++  G    lLLQiF+ p+   g++FfE+IqR+g++GFGegNfkaLf
  lcl|NCBI__GCF_000204645.1:WP_013517522.1 288 KRLPG-HGQDVAALQARGILLDGSTAGgqprLLLQIFSTPML--GPVFFEFIQREGDEGFGEGNFKALF 353
                                               ****7.******************8888999***********..************************* PP

                                 TIGR01263 341 eaiEreqekrgv 352
                                               e++Er+q++rgv
  lcl|NCBI__GCF_000204645.1:WP_013517522.1 354 ESLERDQVNRGV 365
                                               **********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (373 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: 8.48
//
[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