Alignments for a candidate for HPD in Paraburkholderia sp. CCGE1002

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Paraburkholderia sp. CCGE1002

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_013090780.1 BC1002_RS14680 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_456
         (358 letters)



>NCBI__GCF_000092885.1:WP_013090780.1
          Length = 365

 Score =  417 bits (1072), Expect = e-121
 Identities = 212/361 (58%), Positives = 267/361 (73%), Gaps = 15/361 (4%)

Query: 5   YENPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKDVHLYRQGAINLILNNEPH 64
           +ENP+G  GFEFIE+ +P P  L  +FE MGFT VA HR KDV LYRQG IN I+N E H
Sbjct: 6   WENPVGTDGFEFIEYTAPDPKALGKLFERMGFTAVARHRHKDVTLYRQGDINFIVNAEKH 65

Query: 65  SVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAP 124
           S A  FA  HGPS+C +AFRV+D+ KAY +ALE GA     +TGPMELN+PAIKGIG + 
Sbjct: 66  SFAQRFARLHGPSICAIAFRVQDAAKAYAQALEKGAWGFDNKTGPMELNIPAIKGIGDSL 125

Query: 125 LYLIDRF-GEGSS---------IYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAY 174
           +Y +DR+ G+  +         IYD+DF  I G + NPVG GL  IDHLTHNV+RGRM  
Sbjct: 126 IYFVDRWRGKNGAAPNSIGDIDIYDVDFEPIPGANPNPVGHGLTYIDHLTHNVHRGRMQE 185

Query: 175 WAGFYEKLFNFREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQF 234
           WA FYE+LFNFRE+RYFDI+G+ TG+ SKAMT+P G IRIP+NEE S  AGQI+E+L  +
Sbjct: 186 WAEFYERLFNFREVRYFDIEGKVTGVKSKAMTSPCGKIRIPINEEGSDTAGQIQEYLDAY 245

Query: 235 NGEGIQHVAFLTDDLVKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVDELQSRGI 294
           +GEGIQH+A  T D+ +T D L++  +  +    DTYYE+++ R+PNHGEP++EL+ R I
Sbjct: 246 HGEGIQHIALGTGDIYRTVDGLRASNISLLDT-IDTYYELVDRRVPNHGEPLEELRKRKI 304

Query: 295 LLDGASEQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGV 354
           L+DGA +     LLLQIF+E  +GP+FFE IQRKG+ GFGEGNFKALFESIE DQ+RRGV
Sbjct: 305 LIDGAPDD----LLLQIFTENQIGPIFFEIIQRKGNQGFGEGNFKALFESIELDQIRRGV 360

Query: 355 L 355
           +
Sbjct: 361 V 361


Lambda     K      H
   0.321    0.141    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: 538
Number of extensions: 29
Number of successful extensions: 4
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: 358
Length of database: 365
Length adjustment: 29
Effective length of query: 329
Effective length of database: 336
Effective search space:   110544
Effective search space used:   110544
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 WP_013090780.1 BC1002_RS14680 (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.20911.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.3e-124  402.2   0.0   1.6e-124  402.0   0.0    1.1  1  lcl|NCBI__GCF_000092885.1:WP_013090780.1  BC1002_RS14680 4-hydroxyphenylpy


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000092885.1:WP_013090780.1  BC1002_RS14680 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  402.0   0.0  1.6e-124  1.6e-124       2     352 ..      14     360 ..      13     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 402.0 bits;  conditional E-value: 1.6e-124
                                 TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHG 70 
                                               gf+f+e++++d+k a+ +l+e++Gf+ava+   +r+k++t++rqg+i+++++ae++s   a++f++ HG
  lcl|NCBI__GCF_000092885.1:WP_013090780.1  14 GFEFIEYTAPDPK-ALGKLFERMGFTAVAR---HRHKDVTLYRQGDINFIVNAEKHSF--AQRFARLHG 76 
                                               8************.***************8...***********************99..********* PP

                                 TIGR01263  71 dgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekg....... 132
                                               ++++++af+v+d+++a+++a+e+ga  +++++    +e++++aikgiGd+++++v+r + k+       
  lcl|NCBI__GCF_000092885.1:WP_013090780.1  77 PSICAIAFRVQDAAKAYAQALEKGAWGFDNKTG--PMELNIPAIKGIGDSLIYFVDRWRGKNgaapnsi 143
                                               ****************************99986..99*******************9875551122211 PP

                                 TIGR01263 133 ...silpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasa 198
                                                  +i+++++  +    ++ ++ + gl++iDH+++nv+rg+++++aefye++++f+e+++fdi++++++
  lcl|NCBI__GCF_000092885.1:WP_013090780.1 144 gdiDIYDVDF--EPIPGANPNPVGHGLTYIDHLTHNVHRGRMQEWAEFYERLFNFREVRYFDIEGKVTG 210
                                               1112344444..444456777899********************************************* PP

                                 TIGR01263 199 LkSkvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkip 267
                                               +kSk+++s++gk+++p+ne + ++  +QI+eyl++y+G+G+QH+Al t di++tv+ lra+ + +l++ 
  lcl|NCBI__GCF_000092885.1:WP_013090780.1 211 VKSKAMTSPCGKIRIPINE-EGSDTAGQIQEYLDAYHGEGIQHIALGTGDIYRTVDGLRASNISLLDTI 278
                                               *******************.788********************************************** PP

                                 TIGR01263 268 etYYdnlkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNf 336
                                               +tYY+ +++rv++ + e+leel+++kiL+D++ + lLLQiFt++ +  g++FfEiIqRkg++GFGegNf
  lcl|NCBI__GCF_000092885.1:WP_013090780.1 279 DTYYELVDRRVPN-HGEPLEELRKRKILIDGAPDDLLLQIFTENQI--GPIFFEIIQRKGNQGFGEGNF 344
                                               ************7.********************************..********************* PP

                                 TIGR01263 337 kaLfeaiEreqekrgv 352
                                               kaLfe+iE +q++rgv
  lcl|NCBI__GCF_000092885.1:WP_013090780.1 345 KALFESIELDQIRRGV 360
                                               **************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (365 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: 7.65
//
[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