Alignments for a candidate for HPD in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Herbaspirillum seropedicae SmR1

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate HSERO_RS08335 HSERO_RS08335 4-hydroxyphenylpyruvate dioxygenase

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



>FitnessBrowser__HerbieS:HSERO_RS08335
          Length = 364

 Score =  441 bits (1135), Expect = e-128
 Identities = 228/349 (65%), Positives = 262/349 (75%), Gaps = 5/349 (1%)

Query: 11  NPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQHDINIVLNGSP 70
           NP+GTDGFEFVE+TA +   I ++  L   MGFT  A+HRSK V L++Q  +N +LNG P
Sbjct: 19  NPMGTDGFEFVEYTAADPAAIARVLEL---MGFTAVARHRSKNVTLYRQGQVNFILNGEP 75

Query: 71  TGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELNIPCVEGIGGS 130
             +  AFA+ HG S  AMAFRVK+AAQ        GA+ V +     ELNIP + GIGGS
Sbjct: 76  GSNAAAFAQVHGASVNAMAFRVKDAAQVYKRALELGAEGVEAKLGPMELNIPAIRGIGGS 135

Query: 131 LLYLVDRYGDK-SIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMDVWSGFYERIA 189
           LLYLVDRYG+  SIYDVDF++  G   N   VGL  IDHLTHNVMRG MD WS FY R+ 
Sbjct: 136 LLYLVDRYGENGSIYDVDFQFFPGVERNPKGVGLTYIDHLTHNVMRGAMDTWSSFYTRLF 195

Query: 190 NFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREYHGEGIQHIAL 249
           NFREI+YFDIEGK+TGL SRAMT+PCGKIRIPINESADDKSQIEEFI++Y+GEGIQHIAL
Sbjct: 196 NFREIKYFDIEGKVTGLRSRAMTSPCGKIRIPINESADDKSQIEEFIKQYNGEGIQHIAL 255

Query: 250 STDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNILIDGAP-GDDG 308
            TDDIY TVR LR  GV    T  TYY+ V+ R+ GHGE  D LREL ILIDGAP    G
Sbjct: 256 GTDDIYQTVRALRERGVPLQDTISTYYDLVERRIPGHGEDLDALRELKILIDGAPTAGQG 315

Query: 309 ILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVI 357
           +LLQIFT  +IGP+F+EIIQRKGN GFGEGNFKALFESIE DQ+RRGVI
Sbjct: 316 LLLQIFTQNLIGPVFYEIIQRKGNDGFGEGNFKALFESIELDQMRRGVI 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: 519
Number of extensions: 22
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: 361
Length of database: 364
Length adjustment: 29
Effective length of query: 332
Effective length of database: 335
Effective search space:   111220
Effective search space used:   111220
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 HSERO_RS08335 HSERO_RS08335 (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.23292.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.1e-131  424.0   0.0   3.5e-131  423.8   0.0    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS08335  HSERO_RS08335 4-hydroxyphenylpyr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS08335  HSERO_RS08335 4-hydroxyphenylpyruvate dioxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  423.8   0.0  3.5e-131  3.5e-131       2     352 ..      25     363 ..      24     364 .] 0.98

  Alignments for each domain:
  == domain 1  score: 423.8 bits;  conditional E-value: 3.5e-131
                                  TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakH 69 
                                                gf+fve++++d+  a +++ e +Gf+ava+   +r+k++t++rqg+++++l+ e+ s+  aaaf++ H
  lcl|FitnessBrowser__HerbieS:HSERO_RS08335  25 GFEFVEYTAADPA-AIARVLELMGFTAVAR---HRSKNVTLYRQGQVNFILNGEPGSN--AAAFAQVH 86 
                                                8************.999999*********8...*************************..******** PP

                                  TIGR01263  70 GdgvkdvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpg 137
                                                G +v+++af+v+d+++++++a+e gae v+a+     +e++++ai+giG+++l+lv+r+ge+gsi+++
  lcl|FitnessBrowser__HerbieS:HSERO_RS08335  87 GASVNAMAFRVKDAAQVYKRALELGAEGVEAKLG--PMELNIPAIRGIGGSLLYLVDRYGENGSIYDV 152
                                                *******************************996..99****************************** PP

                                  TIGR01263 138 feevsekaalkekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvla 205
                                                ++++     +++++++vgl++iDH+++nv rg ++++++fy ++++f+eik+fdi++++++L+S++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS08335 153 DFQFFPG--VERNPKGVGLTYIDHLTHNVMRGAMDTWSSFYTRLFNFREIKYFDIEGKVTGLRSRAMT 218
                                                ***9997..566679***************************************************** PP

                                  TIGR01263 206 saegkvklplnepaskkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdn 273
                                                s++gk+++p+ne  s ++ksQIee++++y+G+G+QH+Al t+di++tv++lr+rgv + ++ +tYYd 
  lcl|FitnessBrowser__HerbieS:HSERO_RS08335 219 SPCGKIRIPINE--SADDKSQIEEFIKQYNGEGIQHIALGTDDIYQTVRALRERGVPLQDTISTYYDL 284
                                                ************..89**************************************************** PP

                                  TIGR01263 274 lkervkklvkedleelkelkiLvDrd...eeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfka 338
                                                +++r++  + edl+ l+elkiL+D++    +GlLLQiFt++++  g++F+EiIqRkg++GFGegNfka
  lcl|FitnessBrowser__HerbieS:HSERO_RS08335 285 VERRIPG-HGEDLDALRELKILIDGAptaGQGLLLQIFTQNLI--GPVFYEIIQRKGNDGFGEGNFKA 349
                                                ******7.*****************9988899***********..*********************** PP

                                  TIGR01263 339 LfeaiEreqekrgv 352
                                                Lfe+iE +q +rgv
  lcl|FitnessBrowser__HerbieS:HSERO_RS08335 350 LFESIELDQMRRGV 363
                                                ************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (364 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: 10.23
//
[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