Alignments for a candidate for HPD in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Shewanella sp. ANA-3

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate 7025322 Shewana3_2482 4-hydroxyphenylpyruvate dioxygenase (RefSeq)

Query= reanno::MR1:201123
         (346 letters)



>FitnessBrowser__ANA3:7025322
          Length = 346

 Score =  684 bits (1764), Expect = 0.0
 Identities = 335/346 (96%), Positives = 341/346 (98%)

Query: 1   MASELNPLGLLGIEFTEFASSDTDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNK 60
           MASELNPLGLLGIEFTEFAS D+DFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLN 
Sbjct: 1   MASELNPLGLLGIEFTEFASPDSDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNN 60

Query: 61  QREGFSAKFAKSHGPAICSMGWRVEDASFAHRVAVERGAKAADDSAKDLPYPAIYGIGDS 120
           +REGFSA+FAKSHGPAI SMGWRVEDASFAHRVAVERGAKA  DSAKDLPYPAIYGIGDS
Sbjct: 61  EREGFSAEFAKSHGPAISSMGWRVEDASFAHRVAVERGAKAVADSAKDLPYPAIYGIGDS 120

Query: 121 LIYFIDTFGANNNIYATDFEDLSEPVITQEKGFIEVDHLTNNVYKGTMEHWANFYKNIFG 180
           LIYFIDTFGA+NNIYATDFEDLSEPVITQEKGF+EVDHLTNNVYKGTMEHWANFYKNIFG
Sbjct: 121 LIYFIDTFGADNNIYATDFEDLSEPVITQEKGFVEVDHLTNNVYKGTMEHWANFYKNIFG 180

Query: 181 FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF 240
           FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF
Sbjct: 181 FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF 240

Query: 241 RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRDRIKHHQILVDGDESGYLL 300
           RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENR+RIKHHQILVDGDESGYLL
Sbjct: 241 RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRERIKHHQILVDGDESGYLL 300

Query: 301 QIFTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 346
           QIFTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL
Sbjct: 301 QIFTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 346


Lambda     K      H
   0.321    0.140    0.414 

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: 657
Number of extensions: 23
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: 346
Length of database: 346
Length adjustment: 29
Effective length of query: 317
Effective length of database: 317
Effective search space:   100489
Effective search space used:   100489
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 7025322 Shewana3_2482 (4-hydroxyphenylpyruvate dioxygenase (RefSeq))
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.11062.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.9e-122  395.1   0.1   2.1e-122  395.0   0.1    1.0  1  lcl|FitnessBrowser__ANA3:7025322  Shewana3_2482 4-hydroxyphenylpyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7025322  Shewana3_2482 4-hydroxyphenylpyruvate dioxygenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.0   0.1  2.1e-122  2.1e-122       2     353 .]      12     346 .]      11     346 .] 0.97

  Alignments for each domain:
  == domain 1  score: 395.0 bits;  conditional E-value: 2.1e-122
                         TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkdvaf 78 
                                       g++f efa++d +  +++++ ++Gf++++k    ++k++ +++q++i+++l++e +     a+f+++HG++++++++
  lcl|FitnessBrowser__ANA3:7025322  12 GIEFTEFASPDSD-FMHKVFIDFGFSLLKK---AKNKDILYYKQNDINFLLNNEREGF--SAEFAKSHGPAISSMGW 82 
                                       79**********9.9**************9...9**********************99..9**************** PP

                         TIGR01263  79 evedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkekledvg 155
                                       +ved++ a++ averga+av+++     k++ ++ai giGd+++++++++g +++i+ +++e  ++  +   ++++g
  lcl|FitnessBrowser__ANA3:7025322  83 RVEDASFAHRVAVERGAKAVADSA----KDLPYPAIYGIGDSLIYFIDTFGADNNIYATDFEDLSEPVI---TQEKG 152
                                       *********************997....58******************************987776544...4689* PP

                         TIGR01263 156 leaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyle 232
                                       + ++DH+++nv++g++e++a+fy++i+gf+e+++fdi++ ++aL+S++l+s++g++++p+ne+ ++++k+QI+eyl+
  lcl|FitnessBrowser__ANA3:7025322 153 FVEVDHLTNNVYKGTMEHWANFYKNIFGFTEVRYFDISGVQTALVSYALRSPDGSFCIPINEG-KGNDKNQIDEYLK 228
                                       **************************************************************5.99*********** PP

                         TIGR01263 233 eyeGaGvQHlAlntedivktveelrargveflkipetYYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFt 309
                                       ey+G+GvQHlA++++divk++++++ ++++ l+i  +YYd++ ++v++ v+e+ e++k+++iLvD+de+G+LLQiFt
  lcl|FitnessBrowser__ANA3:7025322 229 EYNGPGVQHLAFRSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQ-VTENRERIKHHQILVDGDESGYLLQIFT 304
                                       *********************************999***********7.**************************** PP

                         TIGR01263 310 kpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                       k+++  g++F+EiIqRk++ GFGegNf aLf++iEr+q +rgvl
  lcl|FitnessBrowser__ANA3:7025322 305 KNLF--GPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 346
                                       ****..***********************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (346 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: 11.23
//
[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