Alignments for a candidate for HPD in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Phaeobacter inhibens BS107

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate GFF747 PGA1_c07610 4-hydroxyphenylpyruvate dioxygenase Hpd

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



>FitnessBrowser__Phaeo:GFF747
          Length = 366

 Score =  348 bits (893), Expect = e-100
 Identities = 177/354 (50%), Positives = 245/354 (69%), Gaps = 9/354 (2%)

Query: 6   ENPMGLMGFEFIEFASPTPNTLEPIFEIMGFTKVATHRSKD-VHLYRQGAINLILNNEPH 64
           ENP G  GFEF+EFA P P  L  +F  MG+  VA H+SK  + L++QG I  +LN E  
Sbjct: 16  ENPAGTDGFEFVEFAHPDPQELRDLFARMGYELVARHKSKPGIELWQQGDITYVLNAEKG 75

Query: 65  SVASYFAAEHGPSVCGMAFRVKDSQKAYKRALELGAQPIHIETGPMELNLPAIKGIGGAP 124
           S A  F A+HGP    M +RV D+QKA++ A+  GA+    E     +++PAIKGIGG+ 
Sbjct: 76  SFAERFVADHGPCAPSMGWRVVDAQKAFEHAVSKGAEAY--EGDDKTMDVPAIKGIGGSL 133

Query: 125 LYLIDRFGEGSSIYDIDFVFIEGVDRNPVGAGLKIIDHLTHNVYRGRMAYWAGFYEKLFN 184
           +Y ID++ + +S Y+ +F ++      P G G   +DHLTHNV++G M  W  FY +LFN
Sbjct: 134 IYFIDQYYD-TSPYNTEFEWL--TQSKPRGVGFYYLDHLTHNVFKGNMDKWFRFYGELFN 190

Query: 185 FREIRYFDIKGEYTGLTSKAMTAPDGMIRIPLNEESSKGAGQIEEFLMQFNGEGIQHVAF 244
           F+EIR+FDI+G++TGL S+A+T+P G IRIP+NE+  +  GQI  +L ++NGEGIQH+A 
Sbjct: 191 FKEIRFFDIEGKFTGLLSRALTSPCGRIRIPINEDRGE-TGQIVSYLKKYNGEGIQHIAV 249

Query: 245 LTDDLVKTWDHLKSIGMRFMTAPPDTYYEMLEGRLPNHGEPVDELQSRGILLDGAS--EQ 302
            ++D+    D +   G++FM APP +YYEM   R+  H EP+D +Q  GIL+DG    + 
Sbjct: 250 GSEDIYGATDEISDRGIKFMPAPPASYYEMSHDRVIGHEEPLDRMQKHGILIDGEGVVDG 309

Query: 303 GDKRLLLQIFSETLMGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLA 356
           G+ ++LLQIFS+T++GP+FFEFIQRKGDDGFGEGNFKALFESIER+Q+  G LA
Sbjct: 310 GETKILLQIFSKTVIGPIFFEFIQRKGDDGFGEGNFKALFESIEREQIANGELA 363


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: 508
Number of extensions: 33
Number of successful extensions: 6
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: 366
Length adjustment: 29
Effective length of query: 329
Effective length of database: 337
Effective search space:   110873
Effective search space used:   110873
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 GFF747 PGA1_c07610 (4-hydroxyphenylpyruvate dioxygenase Hpd)
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.12990.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   5.8e-116  373.8   0.0   6.6e-116  373.6   0.0    1.0  1  lcl|FitnessBrowser__Phaeo:GFF747  PGA1_c07610 4-hydroxyphenylpyruv


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Phaeo:GFF747  PGA1_c07610 4-hydroxyphenylpyruvate dioxygenase Hpd
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  373.6   0.0  6.6e-116  6.6e-116       2     352 ..      23     361 ..      22     362 .. 0.95

  Alignments for each domain:
  == domain 1  score: 373.6 bits;  conditional E-value: 6.6e-116
                         TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkdvaf 78 
                                       gf+fvefa++d++  ++ l+ ++G+e+va+   +++  + +++qg+it+vl+ae+ s   a++f+a+HG+++ ++++
  lcl|FitnessBrowser__Phaeo:GFF747  23 GFEFVEFAHPDPQ-ELRDLFARMGYELVAR--HKSKPGIELWQQGDITYVLNAEKGSF--AERFVADHGPCAPSMGW 94 
                                       8***********9.99*************8..66677899****************99..***************** PP

                         TIGR01263  79 evedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkekledvg 155
                                       +v d+++afe+av++gaea++  +    k+++++aikgiG++++++++++ ++ s +++++e+ ++    +k+ +vg
  lcl|FitnessBrowser__Phaeo:GFF747  95 RVVDAQKAFEHAVSKGAEAYEGDD----KTMDVPAIKGIGGSLIYFIDQYYDT-SPYNTEFEWLTQ----SKPRGVG 162
                                       *******************87764....79******************97666.677777878875....45689** PP

                         TIGR01263 156 leaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkksQIeeyle 232
                                       ++++DH+++nv +g+++k+  fy ++++fkei+ fdi++++++L S++l+s++g++++p+ne  +  +++QI  yl+
  lcl|FitnessBrowser__Phaeo:GFF747 163 FYYLDHLTHNVFKGNMDKWFRFYGELFNFKEIRFFDIEGKFTGLLSRALTSPCGRIRIPINE--DRGETGQIVSYLK 237
                                       **************************************************************..8899********* PP

                         TIGR01263 233 eyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd...eeG... 302
                                       +y+G+G+QH+A+ +edi+ +++e+++rg++f++ +p +YY++ ++rv   ++e+l+++++++iL+D++   + G   
  lcl|FitnessBrowser__Phaeo:GFF747 238 KYNGEGIQHIAVGSEDIYGATDEISDRGIKFMPaPPASYYEMSHDRVIG-HEEPLDRMQKHGILIDGEgvvDGGetk 313
                                       *********************************999************7.******************997666888 PP

                         TIGR01263 303 lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgv 352
                                       +LLQiF+k+v+  g++FfE+IqRkg++GFGegNfkaLfe+iEreq+  g+
  lcl|FitnessBrowser__Phaeo:GFF747 314 ILLQIFSKTVI--GPIFFEFIQRKGDDGFGEGNFKALFESIEREQIANGE 361
                                       ***********..********************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (366 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: 12.20
//
[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