Alignments for a candidate for HPD in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Shewanella oneidensis MR-1

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate 201123 SO1962 4-hydroxyphenylpyruvate dioxygenase (NCBI ptt file)

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



>FitnessBrowser__MR1:201123
          Length = 346

 Score =  704 bits (1817), Expect = 0.0
 Identities = 346/346 (100%), Positives = 346/346 (100%)

Query: 1   MASELNPLGLLGIEFTEFASSDTDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNK 60
           MASELNPLGLLGIEFTEFASSDTDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNK
Sbjct: 1   MASELNPLGLLGIEFTEFASSDTDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNK 60

Query: 61  QREGFSAKFAKSHGPAICSMGWRVEDASFAHRVAVERGAKAADDSAKDLPYPAIYGIGDS 120
           QREGFSAKFAKSHGPAICSMGWRVEDASFAHRVAVERGAKAADDSAKDLPYPAIYGIGDS
Sbjct: 61  QREGFSAKFAKSHGPAICSMGWRVEDASFAHRVAVERGAKAADDSAKDLPYPAIYGIGDS 120

Query: 121 LIYFIDTFGANNNIYATDFEDLSEPVITQEKGFIEVDHLTNNVYKGTMEHWANFYKNIFG 180
           LIYFIDTFGANNNIYATDFEDLSEPVITQEKGFIEVDHLTNNVYKGTMEHWANFYKNIFG
Sbjct: 121 LIYFIDTFGANNNIYATDFEDLSEPVITQEKGFIEVDHLTNNVYKGTMEHWANFYKNIFG 180

Query: 181 FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF 240
           FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF
Sbjct: 181 FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF 240

Query: 241 RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRDRIKHHQILVDGDESGYLL 300
           RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRDRIKHHQILVDGDESGYLL
Sbjct: 241 RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRDRIKHHQILVDGDESGYLL 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: 672
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 201123 SO1962 (4-hydroxyphenylpyruvate dioxygenase (NCBI ptt file))
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.10339.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
     1e-122  396.0   0.2   1.1e-122  395.8   0.2    1.0  1  lcl|FitnessBrowser__MR1:201123  SO1962 4-hydroxyphenylpyruvate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__MR1:201123  SO1962 4-hydroxyphenylpyruvate dioxygenase (NCBI ptt file)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.8   0.2  1.1e-122  1.1e-122       2     353 .]      12     346 .]      11     346 .] 0.97

  Alignments for each domain:
  == domain 1  score: 395.8 bits;  conditional E-value: 1.1e-122
                       TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkdvafev 80 
                                     g++f efa++d++  +++++ ++Gf++++k    ++k++ +++q++i+++l+++ +     a+f+++HG+++++++++v
  lcl|FitnessBrowser__MR1:201123  12 GIEFTEFASSDTD-FMHKVFIDFGFSLLKK---AKNKDILYYKQNDINFLLNKQREGF--SAKFAKSHGPAICSMGWRV 84 
                                     79**********9.9**************9...9*********************999..9****************** PP

                       TIGR01263  81 edveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkekledvgleai 159
                                     ed++ a++ averga+a++++     k++ ++ai giGd+++++++++g +++i+ +++e  ++  +   ++++g++++
  lcl|FitnessBrowser__MR1:201123  85 EDASFAHRVAVERGAKAADDSA----KDLPYPAIYGIGDSLIYFIDTFGANNNIYATDFEDLSEPVI---TQEKGFIEV 156
                                     *****************99997....68******************************987776544...468****** PP

                       TIGR01263 160 DHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaG 238
                                     DH+++nv++g++e++a+fy++i+gf+e+++fdi++ ++aL+S++l+s++g++++p+ne+ ++++k+QI+eyl+ey+G+G
  lcl|FitnessBrowser__MR1:201123 157 DHLTNNVYKGTMEHWANFYKNIFGFTEVRYFDISGVQTALVSYALRSPDGSFCIPINEG-KGNDKNQIDEYLKEYNGPG 234
                                     **********************************************************5.99***************** PP

                       TIGR01263 239 vQHlAlntedivktveelrargveflkipetYYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgt 317
                                     vQHlA++++divk++++++ ++++ l+i  +YYd++ ++v++ v+e+ +++k+++iLvD+de+G+LLQiFtk+++  g+
  lcl|FitnessBrowser__MR1:201123 235 VQHLAFRSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQ-VTENRDRIKHHQILVDGDESGYLLQIFTKNLF--GP 310
                                     ***************************999***********7.********************************..** PP

                       TIGR01263 318 lFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                     +F+EiIqRk++ GFGegNf aLf++iEr+q +rgvl
  lcl|FitnessBrowser__MR1:201123 311 IFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 11.11
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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