Alignments for a candidate for HPD in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Burkholderia phytofirmans PsJN

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate BPHYT_RS18295 BPHYT_RS18295 4-hydroxyphenylpyruvate dioxygenase

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



>FitnessBrowser__BFirm:BPHYT_RS18295
          Length = 365

 Score =  421 bits (1082), Expect = e-122
 Identities = 214/361 (59%), 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 EP 
Sbjct: 6   WENPLGTDGFEFIEYTAPDPKALGKLFEQMGFTAVARHRHKDVTLYRQGEINFIVNGEPD 65

Query: 65  SVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAP 124
           S A  F   HGPS+C +AFRV+D+ KAYK ALE GA     +TGPMELN+PAIKGIG + 
Sbjct: 66  SFAQRFTRLHGPSICAIAFRVQDAAKAYKEALEKGAWGFDNKTGPMELNIPAIKGIGDSL 125

Query: 125 LYLIDRF-----GEGSSI-----YDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAY 174
           +Y +DR+      E +SI     YD+DF  I G + NPVG GL  IDHLTHNV+RGRM  
Sbjct: 126 IYFVDRWRGKNGAEPNSIGNIDIYDVDFEPIAGANPNPVGHGLTYIDHLTHNVHRGRMQE 185

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

Query: 235 NGEGIQHVAFLTDDLVKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVDELQSRGI 294
           +GEGIQH+A  ++D+ +T D L+   +  +    DTYYE+++ R+PNHGEP+DEL+ R I
Sbjct: 246 HGEGIQHIALGSNDIYRTVDGLRGSNISLLDT-IDTYYELVDRRVPNHGEPLDELRKRKI 304

Query: 295 LLDGASEQGDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGV 354
           L+DGA E     LLLQIF+E  +GP+FFE IQRKG+ GFGEGNFKALFESIE DQ+RRGV
Sbjct: 305 LIDGAPED----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: 544
Number of extensions: 28
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 BPHYT_RS18295 BPHYT_RS18295 (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.15785.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   2.2e-123  398.2   0.0   2.6e-123  397.9   0.0    1.1  1  lcl|FitnessBrowser__BFirm:BPHYT_RS18295  BPHYT_RS18295 4-hydroxyphenylpyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS18295  BPHYT_RS18295 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  397.9   0.0  2.6e-123  2.6e-123       2     352 ..      14     360 ..      13     361 .. 0.93

  Alignments for each domain:
  == domain 1  score: 397.9 bits;  conditional E-value: 2.6e-123
                                TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGd 71 
                                              gf+f+e++++d+k a+ +l+e++Gf+ava+   +r+k++t++rqgei+++++ e+ s   a++f + HG+
  lcl|FitnessBrowser__BFirm:BPHYT_RS18295  14 GFEFIEYTAPDPK-ALGKLFEQMGFTAVAR---HRHKDVTLYRQGEINFIVNGEPDSF--AQRFTRLHGP 77 
                                              8************.***************8...*********************9999..********** PP

                                TIGR01263  72 gvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekg......... 132
                                              +++++af+v+d+++a+++a+e+ga  +++++    +e++++aikgiGd+++++v+r + k+         
  lcl|FitnessBrowser__BFirm:BPHYT_RS18295  78 SICAIAFRVQDAAKAYKEALEKGAWGFDNKTG--PMELNIPAIKGIGDSLIYFVDRWRGKNgaepnsign 145
                                              ***************************99986..99*******************977444122222222 PP

                                TIGR01263 133 .silpgfeevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkS 201
                                               +i+++++  +  a ++ ++ + gl++iDH+++nv+rg+++++aefye++++f+e+++fdi+++++++kS
  lcl|FitnessBrowser__BFirm:BPHYT_RS18295 146 iDIYDVDF--EPIAGANPNPVGHGLTYIDHLTHNVHRGRMQEWAEFYERLFNFREVRYFDIEGKVTGVKS 213
                                              22445544..45555677789************************************************* PP

                                TIGR01263 202 kvlasaegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYY 271
                                              k+++s++gk+++p+ne + ++  +QI+eyl++y+G+G+QH+Al ++di++tv+ lr + + +l++ +tYY
  lcl|FitnessBrowser__BFirm:BPHYT_RS18295 214 KAMTSPCGKIRIPINE-EGSETAGQIQEYLDAYHGEGIQHIALGSNDIYRTVDGLRGSNISLLDTIDTYY 282
                                              ****************.7889************************************************* PP

                                TIGR01263 272 dnlkervkklvkedleelkelkiLvDrdeeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfe 341
                                              + +++rv++ + e+l+el+++kiL+D++ e lLLQiFt++ +  g++FfEiIqRkg++GFGegNfkaLfe
  lcl|FitnessBrowser__BFirm:BPHYT_RS18295 283 ELVDRRVPN-HGEPLDELRKRKILIDGAPEDLLLQIFTENQI--GPIFFEIIQRKGNQGFGEGNFKALFE 349
                                              ********7.********************************..************************** PP

                                TIGR01263 342 aiEreqekrgv 352
                                              +iE +q++rgv
  lcl|FitnessBrowser__BFirm:BPHYT_RS18295 350 SIELDQIRRGV 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 7.71
//
[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