GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HPD in Cupriavidus basilensis 4G11

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate RR42_RS33500 RR42_RS33500 4-hydroxyphenylpyruvate dioxygenase

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



>FitnessBrowser__Cup4G11:RR42_RS33500
          Length = 357

 Score =  587 bits (1514), Expect = e-172
 Identities = 285/353 (80%), Positives = 313/353 (88%), Gaps = 2/353 (0%)

Query: 27  WDNPMGLMGFEFVEFTSPQPGVLEAVFEKLGFTLVAKHRSKDVVLYRQNGINFILNREPH 86
           ++NPM LMGFEFVEF SP P +LE +FE++GFTLVA+HRSKDVVLYRQ  INFI+NREPH
Sbjct: 5   FENPMQLMGFEFVEFASPTPNLLEPIFEQMGFTLVARHRSKDVVLYRQGDINFIVNREPH 64

Query: 87  SQAAYFGAEHGPSACGLAFRVKDAHKAYNRALELGAQPIEIPTGPMELRLPAIKGIGGAP 146
           S AAYF AEHGPSACG+AFRVKD+HKAY RALELGAQP+EI TGPMELRLPAIKGIGGAP
Sbjct: 65  SPAAYFAAEHGPSACGMAFRVKDSHKAYARALELGAQPVEIATGPMELRLPAIKGIGGAP 124

Query: 147 LYLIDRFEDGKSIYDIDFEFIEGVDRRPAGHGLNLIDHLTHNVYRGRMGFWANFYEKLFG 206
           LYLIDRFE+GKSIYDIDFEFI+GVDR P G GL LIDHLTHNVYRGRM +WANFYEKLF 
Sbjct: 125 LYLIDRFEEGKSIYDIDFEFIDGVDRHPVGLGLRLIDHLTHNVYRGRMAYWANFYEKLFN 184

Query: 207 FREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEESKQGGGQIEEFLMQFNGEGIQHIAL 266
           FREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEES +G GQIEEFLM FNGEGIQHIA 
Sbjct: 185 FREIRYFDIQGEYTGLTSKAMTAPDGKIRIPLNEESSKGSGQIEEFLMAFNGEGIQHIAF 244

Query: 267 ICDNLLDVVDKLGMAGVQLATAPNEVYYEMLDTRLPGHGQPVPELQSRGILLDGTTADGT 326
           + DNL++V+D L MAGV L TAPN+ YY+ L+ RLPGHGQPV +L++RGIL+DGTT  G 
Sbjct: 245 LTDNLIEVIDSLQMAGVPLMTAPNDYYYDGLEARLPGHGQPVDQLKARGILVDGTTEGGK 304

Query: 327 PRLLLQIFSTPMLGPVFFEFIQREGDYRDGFGEGNFKALFESLERDQIRRGVL 379
           PRLLLQIFS   LGPVFFEFIQR+GD  +GFGEGNFKALFESLERDQI RG L
Sbjct: 305 PRLLLQIFSKASLGPVFFEFIQRKGD--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: 641
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 RR42_RS33500 RR42_RS33500 (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.29021.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.5e-122  393.3   0.0   7.4e-122  393.2   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS33500  RR42_RS33500 4-hydroxyphenylpyru


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS33500  RR42_RS33500 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  393.2   0.0  7.4e-122  7.4e-122       1     353 []      12     355 ..      12     355 .. 0.97

  Alignments for each domain:
  == domain 1  score: 393.2 bits;  conditional E-value: 7.4e-122
                                 TIGR01263   1 kgfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakH 69 
                                               +gf+fvefa++ ++  ++ ++e++Gf++va+   +r+k+++++rqg+i+++++ e++s   aa f+a+H
  lcl|FitnessBrowser__Cup4G11:RR42_RS33500  12 MGFEFVEFASPTPN-LLEPIFEQMGFTLVAR---HRSKDVVLYRQGDINFIVNREPHSP--AAYFAAEH 74 
                                               58***********9.9**************8...*********************9999..******** PP

                                 TIGR01263  70 GdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgf 138
                                               G++++++af+v+d ++a+++a+e ga++v+ ++    +e++l+aikgiG++ l+l++r++e +si++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS33500  75 GPSACGMAFRVKDSHKAYARALELGAQPVEIATG--PMELRLPAIKGIGGAPLYLIDRFEEGKSIYDID 141
                                               ******************************9986..99******************************* PP

                                 TIGR01263 139 eevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasa 207
                                               +e+ +   +++++ + gl+ iDH+++nv+rg++ ++a+fyek+++f+ei++fdi++e+++L+Sk+++++
  lcl|FitnessBrowser__Cup4G11:RR42_RS33500 142 FEFIDG--VDRHPVGLGLRLIDHLTHNVYRGRMAYWANFYEKLFNFREIRYFDIQGEYTGLTSKAMTAP 208
                                               **9997..677789******************************************************* PP

                                 TIGR01263 208 egkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkip.etYYdnlk 275
                                               +gk+++plne +s+k ++QIee+l++++G+G+QH+A++t+++++ +++l+  gv +++ p + YYd l+
  lcl|FitnessBrowser__Cup4G11:RR42_RS33500 209 DGKIRIPLNE-ESSKGSGQIEEFLMAFNGEGIQHIAFLTDNLIEVIDSLQMAGVPLMTAPnDYYYDGLE 276
                                               **********.899********************************************6615678**** PP

                                 TIGR01263 276 ervkklvkedleelkelkiLvDrdeeG....lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLf 340
                                                r++  + +++++lk+++iLvD+  eG    lLLQiF+k     g++FfE+IqRkg++GFGegNfkaLf
  lcl|FitnessBrowser__Cup4G11:RR42_RS33500 277 ARLPG-HGQPVDQLKARGILVDGTTEGgkprLLLQIFSKASL--GPVFFEFIQRKGDEGFGEGNFKALF 342
                                               ****7.******************6666*************9..************************* PP

                                 TIGR01263 341 eaiEreqekrgvl 353
                                               e++Er+q++rg+l
  lcl|FitnessBrowser__Cup4G11:RR42_RS33500 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: 8.92
//
[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:

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:

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:

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:

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