Alignments for a candidate for HPD in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Acidovorax sp. GW101-3H11

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate Ac3H11_1849 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27)

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



>FitnessBrowser__acidovorax_3H11:Ac3H11_1849
          Length = 381

 Score =  779 bits (2012), Expect = 0.0
 Identities = 381/381 (100%), Positives = 381/381 (100%)

Query: 1   MTFINECRRHPMNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTL 60
           MTFINECRRHPMNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTL
Sbjct: 1   MTFINECRRHPMNAALPQETAAQLQAWDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTL 60

Query: 61  VAKHRSKDVVLYRQNGINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHKAYNRALEL 120
           VAKHRSKDVVLYRQNGINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHKAYNRALEL
Sbjct: 61  VAKHRSKDVVLYRQNGINFILNREPHSQAAYFGAEHGPSACGLAFRVKDAHKAYNRALEL 120

Query: 121 GAQPIEIPTGPMELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLN 180
           GAQPIEIPTGPMELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLN
Sbjct: 121 GAQPIEIPTGPMELRLPAIKGIGGAPLYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLN 180

Query: 181 LIDHLTHNVYRGRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNE 240
           LIDHLTHNVYRGRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNE
Sbjct: 181 LIDHLTHNVYRGRMGFWANFYEKLFGFREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNE 240

Query: 241 ESKQGGGQIEEFLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTR 300
           ESKQGGGQIEEFLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTR
Sbjct: 241 ESKQGGGQIEEFLMQFNGEGIQHIALICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTR 300

Query: 301 LPGHGQPVPELQSRGILLDGTTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEG 360
           LPGHGQPVPELQSRGILLDGTTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEG
Sbjct: 301 LPGHGQPVPELQSRGILLDGTTADGTPRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEG 360

Query: 361 NFKALFESLERDQIRRGVLNA 381
           NFKALFESLERDQIRRGVLNA
Sbjct: 361 NFKALFESLERDQIRRGVLNA 381


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: 767
Number of extensions: 31
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: 381
Length of database: 381
Length adjustment: 30
Effective length of query: 351
Effective length of database: 351
Effective search space:   123201
Effective search space used:   123201
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 Ac3H11_1849 (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.12030.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
   6.9e-115  370.2   0.0   7.9e-115  370.0   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849  4-hydroxyphenylpyruvate dioxygen


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849  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 !  370.0   0.0  7.9e-115  7.9e-115       1     353 []      34     379 ..      34     379 .. 0.97

  Alignments for each domain:
  == domain 1  score: 370.0 bits;  conditional E-value: 7.9e-115
                                        TIGR01263   1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelssssea 62 
                                                      +gf+fvef+++++   ++a++eklGf++vak   +r+k+++++rq+ i+++l+ e++s+  a
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849  34 MGFEFVEFTSPQPG-VLEAVFEKLGFTLVAK---HRSKDVVLYRQNGINFILNREPHSQ--A 89 
                                                      58***********9.9**************9...*************************..* PP

                                        TIGR01263  63 aaflakHGdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltl 124
                                                      a f a+HG++++++af+v+d+++a+++a+e ga++++ p+    +e++l+aikgiG++ l+l
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849  90 AYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTG--PMELRLPAIKGIGGAPLYL 149
                                                      ***************************************96..99***************** PP

                                        TIGR01263 125 veregekgsilpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfke 186
                                                      ++r+++ +si+++++e+ e   +++++++ gl+ iDH+++nv+rg+++ +a+fyek++gf+e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 150 IDRFEDGKSIYDIDFEFIEG--VDRRPAGHGLNLIDHLTHNVYRGRMGFWANFYEKLFGFRE 209
                                                      ****************9997..788889********************************** PP

                                        TIGR01263 187 iksfdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlnted 248
                                                      i++fdi++e+++L+Sk++++++gk+++plne +sk+  +QIee+l++++G+G+QH+Al  ++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 210 IRYFDIQGEYTGLTSKAMTAPDGKIRIPLNE-ESKQGGGQIEEFLMQFNGEGIQHIALICDN 270
                                                      *******************************.899*************************** PP

                                        TIGR01263 249 ivktveelrargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd.eeG...lLL 305
                                                      +++ v++l   gv++ + + e YY++l+ r++  + +++ el++++iL+D+   +G   lLL
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 271 LLDVVDKLGMAGVQLATaPNEVYYEMLDTRLPG-HGQPVPELQSRGILLDGTtADGtprLLL 331
                                                      *****************55567**********7.*****************988999999** PP

                                        TIGR01263 306 QiFtkpvvdrgtlFfEiIqRkga..kGFGegNfkaLfeaiEreqekrgvl 353
                                                      QiF+ p+   g++FfE+IqR+g+  +GFGegNfkaLfe++Er+q++rgvl
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1849 332 QIFSTPML--GPVFFEFIQREGDyrDGFGEGNFKALFESLERDQIRRGVL 379
                                                      ********..***********85338*********************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (381 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: 7.51
//
[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