Alignments for a candidate for HPD in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Sinorhizobium meliloti 1021

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate SMc03211 SMc03211 4-hydroxyphenylpyruvate dioxygenase

Query= reanno::psRCH2:GFF3449
         (361 letters)



>FitnessBrowser__Smeli:SMc03211
          Length = 370

 Score =  367 bits (942), Expect = e-106
 Identities = 190/357 (53%), Positives = 246/357 (68%), Gaps = 11/357 (3%)

Query: 7   IEQHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVL 66
           I   NP GTDGFEFVEF  P  E   +L  LF +MG+T  A+H++K++ +++Q DIN VL
Sbjct: 13  ISAENPAGTDGFEFVEFAHPEPE---KLAELFGRMGYTPIARHKTKDITVWRQGDINYVL 69

Query: 67  NGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEG 126
           N     H   F  +HGP A +MA+RV +A  A  +  ++GA+    +     L++P + G
Sbjct: 70  NAQAGSHAMRFVGEHGPCAPSMAWRVVDAKHAFEHAVAKGAEAYTGNNKC--LDVPAIVG 127

Query: 127 IGGSLLYLVDRYGDK-SIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDVWSGFY 185
           IGGSLLY V+ YG+K S YD +FE++  R P    VG   +DHLTHNV RG MD W  FY
Sbjct: 128 IGGSLLYFVEAYGEKGSAYDAEFEWLGERDPKPPGVGFYYLDHLTHNVYRGNMDKWWAFY 187

Query: 186 ERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQ 245
             + NF++I +FDI+G++TGL SRA+T+PCGKIRIP+NES DD SQIEE++++Y GEGIQ
Sbjct: 188 RELFNFKQIHFFDIDGRITGLVSRAITSPCGKIRIPLNESKDDTSQIEEYLKKYKGEGIQ 247

Query: 246 HIALSTDDIYATVRQLRANGVDFMT-TPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAP 304
           HIA+ T+ IY    +L  NG+ FM   P+TYYE    RV GH EP D +R   ILIDG  
Sbjct: 248 HIAVGTEAIYDATDKLAENGLKFMPGPPETYYEMSHQRVHGHDEPIDRMRTHGILIDGEG 307

Query: 305 GDDG----ILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVI 357
             +G    ILLQIF+ TVIGPIFFE IQRKG++GFGEGNF+ALFESIE DQ+RRGV+
Sbjct: 308 VVNGGMTKILLQIFSRTVIGPIFFEFIQRKGDEGFGEGNFRALFESIEADQIRRGVL 364


Lambda     K      H
   0.320    0.139    0.412 

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: 475
Number of extensions: 20
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: 361
Length of database: 370
Length adjustment: 30
Effective length of query: 331
Effective length of database: 340
Effective search space:   112540
Effective search space used:   112540
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 SMc03211 SMc03211 (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.8931.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-125  404.8   0.0   2.5e-125  404.6   0.0    1.0  1  lcl|FitnessBrowser__Smeli:SMc03211  SMc03211 4-hydroxyphenylpyruvate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Smeli:SMc03211  SMc03211 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.6   0.0  2.5e-125  2.5e-125       2     353 .]      23     364 ..      22     364 .. 0.97

  Alignments for each domain:
  == domain 1  score: 404.6 bits;  conditional E-value: 2.5e-125
                           TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvkdv 76 
                                         gf+fvefa+++++ ++++l+ ++G++ +a+   +++k++tv+rqg+i++vl+a+  s+  a++f+ +HG+++ ++
  lcl|FitnessBrowser__Smeli:SMc03211  23 GFEFVEFAHPEPE-KLAELFGRMGYTPIAR---HKTKDITVWRQGDINYVLNAQAGSH--AMRFVGEHGPCAPSM 91 
                                         8***********9.99999**********8...*************************..*************** PP

                           TIGR01263  77 afevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaalkekl 151
                                         a++v d+++afe+av++gaea++ ++    k ++++ai giG+++l++ve++gekgs +++++e+  +   + k+
  lcl|FitnessBrowser__Smeli:SMc03211  92 AWRVVDAKHAFEHAVAKGAEAYTGNN----KCLDVPAIVGIGGSLLYFVEAYGEKGSAYDAEFEWLGE--RDPKP 160
                                         *********************98886....79**********************************97..67778 PP

                           TIGR01263 152 edvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepaskkkksQ 226
                                         ++vg++++DH+++nv+rg+++k++ fy+++++fk+i+ fdi++++++L+S++++s++gk+++plne  sk+++sQ
  lcl|FitnessBrowser__Smeli:SMc03211 161 PGVGFYYLDHLTHNVYRGNMDKWWAFYRELFNFKQIHFFDIDGRITGLVSRAITSPCGKIRIPLNE--SKDDTSQ 233
                                         9*****************************************************************..9****** PP

                           TIGR01263 227 IeeyleeyeGaGvQHlAlntedivktveelrargveflk.ipetYYdnlkervkklvkedleelkelkiLvDrd. 299
                                         Ieeyl++y+G+G+QH+A+ te i++++++l ++g++f++ +petYY++ ++rv+  ++e+++++++++iL+D++ 
  lcl|FitnessBrowser__Smeli:SMc03211 234 IEEYLKKYKGEGIQHIAVGTEAIYDATDKLAENGLKFMPgPPETYYEMSHQRVHG-HDEPIDRMRTHGILIDGEg 307
                                         ******************************************************7.******************9 PP

                           TIGR01263 300 ..eeG...lLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgvl 353
                                           + G   +LLQiF+++v+  g++FfE+IqRkg++GFGegNf+aLfe+iE +q++rgvl
  lcl|FitnessBrowser__Smeli:SMc03211 308 vvNGGmtkILLQIFSRTVI--GPIFFEFIQRKGDEGFGEGNFRALFESIEADQIRRGVL 364
                                         966669999**********..***********************************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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 12.37
//
[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