Alignments for a candidate for HPD in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Shewanella loihica PV-4

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate 5209702 Shew_2155 4-hydroxyphenylpyruvate dioxygenase (RefSeq)

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



>FitnessBrowser__PV4:5209702
          Length = 346

 Score =  608 bits (1567), Expect = e-179
 Identities = 296/346 (85%), Positives = 314/346 (90%)

Query: 1   MASELNPLGLLGIEFTEFASSDTDFMHKVFIDFGFSLLKKAKNKDILYYKQNDINFLLNK 60
           MASE NPLGLLGIEFTEF + D DFMHKVFIDFGFS LKK K KDI+YYKQNDINFLLN 
Sbjct: 1   MASEQNPLGLLGIEFTEFCTPDLDFMHKVFIDFGFSKLKKHKQKDIVYYKQNDINFLLNN 60

Query: 61  QREGFSAKFAKSHGPAICSMGWRVEDASFAHRVAVERGAKAADDSAKDLPYPAIYGIGDS 120
           ++ GFSA+FAK HG AI SMGWRVEDA FA   AV RGAK A D  KDLPYPAIYGIGDS
Sbjct: 61  EKSGFSAEFAKKHGAAISSMGWRVEDAKFAFEGAVARGAKPAGDEVKDLPYPAIYGIGDS 120

Query: 121 LIYFIDTFGANNNIYATDFEDLSEPVITQEKGFIEVDHLTNNVYKGTMEHWANFYKNIFG 180
           LIYFIDTFGA+NNIYATDF DL  P I QEKGFIEVDHLTNNVYKGTMEHW+NFYK+IFG
Sbjct: 121 LIYFIDTFGADNNIYATDFVDLENPEIVQEKGFIEVDHLTNNVYKGTMEHWSNFYKDIFG 180

Query: 181 FTEVRYFDISGVQTALVSYALRSPDGSFCIPINEGKGNDKNQIDEYLKEYNGPGVQHLAF 240
           FTEVRYFDI G QTAL+SYALRSPDGSFCIPINEGKG+D+NQIDEYL+EY+GPGVQHLAF
Sbjct: 181 FTEVRYFDIKGSQTALISYALRSPDGSFCIPINEGKGDDRNQIDEYLREYDGPGVQHLAF 240

Query: 241 RSRDIVKSLDAMEGSSIQCLDIIPEYYDTIFDKVPQVTENRDRIKHHQILVDGDESGYLL 300
           RSRDIV SLDAMEGSSIQ LDIIPEYYDTIFDK+PQVTE+R+RIKHHQILVDGDE GYLL
Sbjct: 241 RSRDIVASLDAMEGSSIQTLDIIPEYYDTIFDKLPQVTEDRERIKHHQILVDGDEDGYLL 300

Query: 301 QIFTKNLFGPIFIEIIQRKNNLGFGEGNFTALFQSIERDQMRRGVL 346
           QIFTKNLFGPIFIEIIQRKNNLGFGEGNF ALF+SIERDQ+RRGVL
Sbjct: 301 QIFTKNLFGPIFIEIIQRKNNLGFGEGNFKALFESIERDQVRRGVL 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: 618
Number of extensions: 22
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 5209702 Shew_2155 (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.19807.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   4.5e-126  407.0   0.1     5e-126  406.9   0.1    1.0  1  lcl|FitnessBrowser__PV4:5209702  Shew_2155 4-hydroxyphenylpyruvat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5209702  Shew_2155 4-hydroxyphenylpyruvate dioxygenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  406.9   0.1    5e-126    5e-126       2     353 .]      12     346 .]      11     346 .] 0.97

  Alignments for each domain:
  == domain 1  score: 406.9 bits;  conditional E-value: 5e-126
                        TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkdvafe 79 
                                      g++f ef ++d +  +++++ ++Gf++++k   +++k++++++q++i+++l++e+s     a+f++kHG ++++++++
  lcl|FitnessBrowser__PV4:5209702  12 GIEFTEFCTPDLD-FMHKVFIDFGFSKLKK---HKQKDIVYYKQNDINFLLNNEKSGF--SAEFAKKHGAAISSMGWR 83 
                                      79***********.9**************9...************************9..9***************** PP

                        TIGR01263  80 vedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkekledvgle 157
                                      ved++ afe av+rga+++ +++    k++ ++ai giGd+++++++++g +++i+ +++   e   + e ++++g++
  lcl|FitnessBrowser__PV4:5209702  84 VEDAKFAFEGAVARGAKPAGDEV----KDLPYPAIYGIGDSLIYFIDTFGADNNIYATDFVDLE---NPEIVQEKGFI 154
                                      ******************99998....58*****************************996555...4677889**** PP

                        TIGR01263 158 aiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyleeye 235
                                      ++DH+++nv++g++e++++fy++i+gf+e+++fdik++++aL S++l+s++g++++p+ne+ ++++++QI+eyl+ey+
  lcl|FitnessBrowser__PV4:5209702 155 EVDHLTNNVYKGTMEHWSNFYKDIFGFTEVRYFDIKGSQTALISYALRSPDGSFCIPINEG-KGDDRNQIDEYLREYD 231
                                      ************************************************************5.99************** PP

                        TIGR01263 236 GaGvQHlAlntedivktveelrargveflkipetYYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvv 313
                                      G+GvQHlA++++div+++++++ ++++ l+i  +YYd++ +++++ v+ed e++k+++iLvD+de+G+LLQiFtk+++
  lcl|FitnessBrowser__PV4:5209702 232 GPGVQHLAFRSRDIVASLDAMEGSSIQTLDIIPEYYDTIFDKLPQ-VTEDRERIKHHQILVDGDEDGYLLQIFTKNLF 308
                                      ******************************999***********7.******************************** PP

                        TIGR01263 314 drgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                        g++F+EiIqRk++ GFGegNfkaLfe+iEr+q++rgvl
  lcl|FitnessBrowser__PV4:5209702 309 --GPIFIEIIQRKNNLGFGEGNFKALFESIERDQVRRGVL 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.23
//
[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