Alignments for a candidate for HPD in Paraburkholderia sp. CCGE1002

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Paraburkholderia sp. CCGE1002

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_013094328.1 BC1002_RS33040 4-hydroxyphenylpyruvate dioxygenase

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



>NCBI__GCF_000092885.1:WP_013094328.1
          Length = 357

 Score =  595 bits (1533), Expect = e-175
 Identities = 290/353 (82%), Positives = 317/353 (89%), Gaps = 2/353 (0%)

Query: 27  WDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTLVAKHRSKDVVLYRQNGINFILNREPH 86
           +DNPM LMGFEFVEF SP P VLE +FE++GFTLVA+HRSKDV+LYRQ  INFI+NRE +
Sbjct: 5   FDNPMQLMGFEFVEFASPVPNVLEPLFEQMGFTLVARHRSKDVLLYRQGEINFIVNRERN 64

Query: 87  SQAAYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTGPMELRLPAIKGIGGAP 146
           SQAAYF AEHGPSACG+AFRVKD+H+AY RAL LGAQPIEI TGPMELRLPAIKGIGGAP
Sbjct: 65  SQAAYFAAEHGPSACGMAFRVKDSHRAYARALSLGAQPIEIATGPMELRLPAIKGIGGAP 124

Query: 147 LYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLNLIDHLTHNVYRGRMGFWANFYEKLFG 206
           LYLIDRFEDGKSIYDIDFEFIEGV+RRPAGHGL L+DHLTHNVYRGRM +WANFYE LF 
Sbjct: 125 LYLIDRFEDGKSIYDIDFEFIEGVERRPAGHGLRLVDHLTHNVYRGRMTYWANFYETLFN 184

Query: 207 FREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEESKQGGGQIEEFLMQFNGEGIQHIAL 266
           FRE+RYFDI+GEYTGLTSKAMTAPDGKIRIPLNEES +G GQIEEFLM FNGEGIQHIA 
Sbjct: 185 FRELRYFDIEGEYTGLTSKAMTAPDGKIRIPLNEESGKGSGQIEEFLMAFNGEGIQHIAF 244

Query: 267 ICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTRLPGHGQPVPELQSRGILLDGTTADGT 326
           + D+L+ V+D L MAGV L T PN  YY+ L+TRLPGHGQPV ELQSRGILLDGTTADG+
Sbjct: 245 LTDDLIAVIDNLQMAGVPLMTGPNSYYYDALETRLPGHGQPVGELQSRGILLDGTTADGS 304

Query: 327 PRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEGNFKALFESLERDQIRRGVL 379
           PRLLLQIFS P+LGPVFFEFIQR+GD  +GFGEGNFKALFESLERDQI RG L
Sbjct: 305 PRLLLQIFSKPLLGPVFFEFIQRKGD--EGFGEGNFKALFESLERDQIERGTL 355


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: 650
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: 381
Length of database: 357
Length adjustment: 30
Effective length of query: 351
Effective length of database: 327
Effective search space:   114777
Effective search space used:   114777
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 WP_013094328.1 BC1002_RS33040 (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.27477.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.4e-120  388.2   0.0   2.7e-120  388.0   0.0    1.0  1  lcl|NCBI__GCF_000092885.1:WP_013094328.1  BC1002_RS33040 4-hydroxyphenylpy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013094328.1  BC1002_RS33040 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  388.0   0.0  2.7e-120  2.7e-120       1     353 []      12     355 ..      12     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 388.0 bits;  conditional E-value: 2.7e-120
                                 TIGR01263   1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakH 69 
                                               +gf+fvefa++ ++  ++ l+e++Gf++va+   +r+k++ ++rqgei+++++ e +s+  aa f+a+H
  lcl|NCBI__GCF_000092885.1:WP_013094328.1  12 MGFEFVEFASPVPN-VLEPLFEQMGFTLVAR---HRSKDVLLYRQGEINFIVNRERNSQ--AAYFAAEH 74 
                                               58*********999.9**************8...***********************99..******** PP

                                 TIGR01263  70 GdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgf 138
                                               G++++++af+v+d + a+++a++ ga++++ ++    +e++l+aikgiG++ l+l++r+++ +si++++
  lcl|NCBI__GCF_000092885.1:WP_013094328.1  75 GPSACGMAFRVKDSHRAYARALSLGAQPIEIATG--PMELRLPAIKGIGGAPLYLIDRFEDGKSIYDID 141
                                               ******************************9986..99******************************* PP

                                 TIGR01263 139 eevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasa 207
                                               +e+ e   +++++++ gl+ +DH+++nv+rg+++++a+fye +++f+e+++fdi++e+++L+Sk+++++
  lcl|NCBI__GCF_000092885.1:WP_013094328.1 142 FEFIEG--VERRPAGHGLRLVDHLTHNVYRGRMTYWANFYETLFNFRELRYFDIEGEYTGLTSKAMTAP 208
                                               ***998..667779******************************************************* PP

                                 TIGR01263 208 egkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlk 275
                                               +gk+++plne +s+k ++QIee+l++++G+G+QH+A++t+d+++ +++l+  gv +++ + + YYd l+
  lcl|NCBI__GCF_000092885.1:WP_013094328.1 209 DGKIRIPLNE-ESGKGSGQIEEFLMAFNGEGIQHIAFLTDDLIAVIDNLQMAGVPLMTgPNSYYYDALE 276
                                               **********.89*********************************************4445578**** PP

                                 TIGR01263 276 ervkklvkedleelkelkiLvDrd.eeG...lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLf 340
                                                r++  + +++ el++++iL+D+   +G   lLLQiF+kp+   g++FfE+IqRkg++GFGegNfkaLf
  lcl|NCBI__GCF_000092885.1:WP_013094328.1 277 TRLPG-HGQPVGELQSRGILLDGTtADGsprLLLQIFSKPLL--GPVFFEFIQRKGDEGFGEGNFKALF 342
                                               ****7.*****************98899999***********..************************* PP

                                 TIGR01263 341 eaiEreqekrgvl 353
                                               e++Er+q++rg+l
  lcl|NCBI__GCF_000092885.1:WP_013094328.1 343 ESLERDQIERGTL 355
                                               **********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (357 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: 10.10
//
[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