Alignments for a candidate for HPD in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Stenotrophomonas chelatiphaga DSM 21508

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_057509090.1 ABB28_RS13355 4-hydroxyphenylpyruvate dioxygenase

Query= BRENDA::Q09PG8
         (367 letters)



>NCBI__GCF_001431535.1:WP_057509090.1
          Length = 370

 Score =  525 bits (1352), Expect = e-154
 Identities = 258/370 (69%), Positives = 296/370 (80%), Gaps = 3/370 (0%)

Query: 1   MNASAQAQTSPAVA-PVATFENPMGIDGFEFVEFASP--EPEKLHELFRNLGFVQVARHK 57
           MN + Q  + P +   V TFENPMGIDGFEFVEFA+P    ++LH  FR++GF  V +H 
Sbjct: 1   MNTTVQTASHPNLGMQVTTFENPMGIDGFEFVEFAAPAGRGQELHAYFRSMGFSAVLKHA 60

Query: 58  TRPIYNYRQNDCTFLINEDPDSFAADFARVHGPSACGFAIRVNKLAEWVRVQALKNGAKS 117
           TRPI  YRQ    FL+NEDPDSFAADFA  HGP ACGFAIR  K    V   AL NGA+ 
Sbjct: 61  TRPITVYRQGGVNFLVNEDPDSFAADFAEKHGPCACGFAIRFQKPGAEVYQTALGNGAEP 120

Query: 118 IADKETSKAVAAPVIEGIGGCMLYIVDRYDDKGTIHDPDWEWLPGAQMMPKGFGLTFIDH 177
           +  K  S+AV APVI+GIG CMLY+VDRY D G+I+  D+  + GA   PKGFGLTFIDH
Sbjct: 121 VDFKPDSRAVDAPVIKGIGDCMLYLVDRYGDAGSIYGDDYVAVEGADPAPKGFGLTFIDH 180

Query: 178 LTHNVYFGNMSKWADYYERLFQFREIRYFDIKGAKTGLLSKAMTAPDGMVRIPLNESPDP 237
           LTHN+YFGNM +W+DYYERLF FREIRYFDIKG KTGL+SKAMTAPDG+VRIPLNES DP
Sbjct: 181 LTHNLYFGNMQQWSDYYERLFNFREIRYFDIKGLKTGLVSKAMTAPDGIVRIPLNESSDP 240

Query: 238 KSQINEYLDQYRGEGIQHIACFTDDIYATVEAMRAHGIEFLDTPNAYYAVIDERIPNHGE 297
           KSQINEYLD Y+GEGIQHIACFTDDIYATVEAMR  G++FLDTP+ Y+ VID+R+P HGE
Sbjct: 241 KSQINEYLDAYKGEGIQHIACFTDDIYATVEAMREQGVQFLDTPDTYFDVIDQRVPGHGE 300

Query: 298 DVARMKESRILIDADPETKKKLLLQIFTKNCVGPIFFEIIQRKGNTGFGEGNFQALFESI 357
           DVAR+  ++ILIDADPET ++ LLQIFT NC+GPIFFEIIQRKGN GFGEGNF ALFESI
Sbjct: 301 DVARLARNKILIDADPETHQRKLLQIFTLNCIGPIFFEIIQRKGNEGFGEGNFTALFESI 360

Query: 358 EREQMARGVL 367
           ER+QM RGVL
Sbjct: 361 ERDQMRRGVL 370


Lambda     K      H
   0.321    0.138    0.421 

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: 635
Number of extensions: 30
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: 367
Length of database: 370
Length adjustment: 30
Effective length of query: 337
Effective length of database: 340
Effective search space:   114580
Effective search space used:   114580
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_057509090.1 ABB28_RS13355 (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.16546.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-118  382.0   0.0   2.1e-118  381.8   0.0    1.0  1  lcl|NCBI__GCF_001431535.1:WP_057509090.1  ABB28_RS13355 4-hydroxyphenylpyr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_001431535.1:WP_057509090.1  ABB28_RS13355 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  381.8   0.0  2.1e-118  2.1e-118       2     353 .]      28     370 .]      27     370 .] 0.95

  Alignments for each domain:
  == domain 1  score: 381.8 bits;  conditional E-value: 2.1e-118
                                 TIGR01263   2 gfdfvefavgdak.qaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakH 69 
                                               gf+fvefa++  + q ++a+++++Gf+av k   ++++ +tv+rqg +++++++ + s   aa+f++kH
  lcl|NCBI__GCF_001431535.1:WP_057509090.1  28 GFEFVEFAAPAGRgQELHAYFRSMGFSAVLK---HATRPITVYRQGGVNFLVNEDPDSF--AADFAEKH 91 
                                               89******99876599**************9...********************99999..******** PP

                                 TIGR01263  70 Gdgvkdvafeved.veaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpg 137
                                               G+++++ a++ ++  ++++++a+ +gae+v+ +   d+ +v++++ikgiGd +l+lv+r+g++gsi+  
  lcl|NCBI__GCF_001431535.1:WP_057509090.1  92 GPCACGFAIRFQKpGAEVYQTALGNGAEPVDFKP--DSRAVDAPVIKGIGDCMLYLVDRYGDAGSIYGD 158
                                               **********9872588*************9987..588****************************88 PP

                                 TIGR01263 138 feevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlas 206
                                               +  + e   ++ ++++ gl+ iDH+++n++ g++++++++ye++++f+ei++fdik+  ++L+Sk++++
  lcl|NCBI__GCF_001431535.1:WP_057509090.1 159 DYVAVEG--ADPAPKGFGLTFIDHLTHNLYFGNMQQWSDYYERLFNFREIRYFDIKGLKTGLVSKAMTA 225
                                               7766554..466678****************************************************** PP

                                 TIGR01263 207 aegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdnlk 275
                                               ++g v++plne  s++ ksQI+eyl++y+G+G+QH+A  t+di++tve++r++gv+fl++p+tY+d ++
  lcl|NCBI__GCF_001431535.1:WP_057509090.1 226 PDGIVRIPLNE--SSDPKSQINEYLDAYKGEGIQHIACFTDDIYATVEAMREQGVQFLDTPDTYFDVID 292
                                               ***********..99****************************************************** PP

                                 TIGR01263 276 ervkklvkedleelkelkiLvDrd...eeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfe 341
                                               +rv+  + ed+ +l ++kiL+D d   ++  LLQiFt +++  g++FfEiIqRkg++GFGegNf aLfe
  lcl|NCBI__GCF_001431535.1:WP_057509090.1 293 QRVPG-HGEDVARLARNKILIDADpetHQRKLLQIFTLNCI--GPIFFEIIQRKGNEGFGEGNFTALFE 358
                                               ****7.******************866677***********..************************** PP

                                 TIGR01263 342 aiEreqekrgvl 353
                                               +iEr+q +rgvl
  lcl|NCBI__GCF_001431535.1:WP_057509090.1 359 SIERDQMRRGVL 370
                                               *********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (370 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.91
//
[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