Alignments for a candidate for HPD in Methylosarcina fibrata AML-C10

GapMind for catabolism of small carbon sources

Alignments for a candidate for HPD in Methylosarcina fibrata AML-C10

Align 4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (characterized)
to candidate WP_020564183.1 A3OW_RS0114560 4-hydroxyphenylpyruvate dioxygenase

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



>NCBI__GCF_000372865.1:WP_020564183.1
          Length = 354

 Score =  422 bits (1085), Expect = e-123
 Identities = 221/360 (61%), Positives = 257/360 (71%), Gaps = 9/360 (2%)

Query: 1   MNAVNKIEQHNPIGTDGFEFVEFTAPNAEGIEQLRTLFTQMGFTETAKHRSKEVWLFQQH 60
           MNA+  I   NP+GTDGFEFVE+TAP+   +E+L   F  MGF   A+HRSK+V L++Q 
Sbjct: 1   MNAM--INASNPVGTDGFEFVEYTAPDTRELEKL---FVSMGFAAVARHRSKDVVLYRQG 55

Query: 61  DINIVLNGSPTGHVHAFAEKHGPSACAMAFRVKNAAQAAAYVESQGAKLVGSHANFGELN 120
            IN ++N  P     AFA  HGPS CA A RVKNAA+        GA+    +    ELN
Sbjct: 56  RINFIINHEPASFAQAFARVHGPSICAFAIRVKNAAECFKRALELGAEPHRGNVGPMELN 115

Query: 121 IPCVEGIGGSLLYLVDRYGDK-SIYDVDFEYIEGRTPNDNAVGLMCIDHLTHNVMRGQMD 179
           IP + GIG SL+YLVDRYG++ SIYDVDF  + G        GL  IDHLTHNV  G MD
Sbjct: 116 IPAIRGIGRSLIYLVDRYGEEHSIYDVDFVPLPGADLKPEGAGLTEIDHLTHNVYHGDMD 175

Query: 180 VWSGFYERIANFREIRYFDIEGKLTGLFSRAMTAPCGKIRIPINESADDKSQIEEFIREY 239
            W+ FY R+ NF EIRYFDI GK+TGL SRAMT+PCGKIRIPINE  D KSQI+E++  Y
Sbjct: 176 RWAEFYRRLFNFHEIRYFDIHGKMTGLKSRAMTSPCGKIRIPINEPTDAKSQIQEYLAAY 235

Query: 240 HGEGIQHIALSTDDIYATVRQLRANGVDFMTTPDTYYEKVDTRVAGHGEPTDVLRELNIL 299
           HGEGIQHIAL+TDDIY  V QLRANGV FM  PD YYE +D R+  H EP   LR+  IL
Sbjct: 236 HGEGIQHIALATDDIYGAVEQLRANGVRFMDVPDAYYETIDVRLPRHREPVARLRQDGIL 295

Query: 300 IDGA--PGDDGILLQIFTNTVIGPIFFEIIQRKGNQGFGEGNFKALFESIEEDQLRRGVI 357
           IDG   PG  G+LLQIFTNTVIGPIFFEIIQRKGN+GFGEGNF+ALFE+IE DQ+RRGVI
Sbjct: 296 IDGTHEPG-GGLLLQIFTNTVIGPIFFEIIQRKGNEGFGEGNFQALFEAIERDQIRRGVI 354


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: 501
Number of extensions: 20
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: 354
Length adjustment: 29
Effective length of query: 332
Effective length of database: 325
Effective search space:   107900
Effective search space used:   107900
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_020564183.1 A3OW_RS0114560 (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.3793343.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.1e-130  420.3   0.0   4.6e-130  420.2   0.0    1.0  1  NCBI__GCF_000372865.1:WP_020564183.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000372865.1:WP_020564183.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.2   0.0  4.6e-130  4.6e-130       2     352 ..      15     353 ..      14     354 .] 0.96

  Alignments for each domain:
  == domain 1  score: 420.2 bits;  conditional E-value: 4.6e-130
                             TIGR01263   2 gfdfvefavgdakqaakalveklGfeavaketgsrekastvlrqgeitlvltaelsssseaaaflakHGdgvk 74 
                                           gf+fve++++d++  +++l+ ++Gf+ava+   +r+k+++++rqg+i++++++e++s   a+af++ HG++++
  NCBI__GCF_000372865.1:WP_020564183.1  15 GFEFVEYTAPDTR-ELEKLFVSMGFAAVAR---HRSKDVVLYRQGRINFIINHEPASF--AQAFARVHGPSIC 81 
                                           8***********9.8999999********8...**********************999..************* PP

                             TIGR01263  75 dvafevedveaafeaavergaeavsapeeedekevklaaikgiGdvvltlveregekgsilpgfeevsekaal 147
                                           + a++v++++++f++a+e gae+ + ++    +e++++ai+giG ++++lv+r+ge++si+++++     a  
  NCBI__GCF_000372865.1:WP_020564183.1  82 AFAIRVKNAAECFKRALELGAEPHRGNVG--PMELNIPAIRGIGRSLIYLVDRYGEEHSIYDVDFVPLPGA-- 150
                                           ***********************999996..99******************************99777765.. PP

                             TIGR01263 148 kekledvgleaiDHvvgnvergelekvaefyekilgfkeiksfdikteasaLkSkvlasaegkvklplnepas 220
                                           + k+e++gl++iDH+++nv++g+++++aefy+++++f+ei++fdi++++++LkS++++s++gk+++p+nep  
  NCBI__GCF_000372865.1:WP_020564183.1 151 DLKPEGAGLTEIDHLTHNVYHGDMDRWAEFYRRLFNFHEIRYFDIHGKMTGLKSRAMTSPCGKIRIPINEP-- 221
                                           45559*****************************************************************8.. PP

                             TIGR01263 221 kkkksQIeeyleeyeGaGvQHlAlntedivktveelrargveflkipetYYdnlkervkklvkedleelkelk 293
                                           ++ ksQI+eyl++y+G+G+QH+Al t+di+ +ve+lra+gv+f+++p++YY++++ r+++ ++e++ +l++ +
  NCBI__GCF_000372865.1:WP_020564183.1 222 TDAKSQIQEYLAAYHGEGIQHIALATDDIYGAVEQLRANGVRFMDVPDAYYETIDVRLPR-HREPVARLRQDG 293
                                           899********************************************************7.************ PP

                             TIGR01263 294 iLvDrd...eeGlLLQiFtkpvvdrgtlFfEiIqRkgakGFGegNfkaLfeaiEreqekrgv 352
                                           iL+D+      GlLLQiFt++v+  g++FfEiIqRkg++GFGegNf+aLfeaiEr+q++rgv
  NCBI__GCF_000372865.1:WP_020564183.1 294 ILIDGThepGGGLLLQIFTNTVI--GPIFFEIIQRKGNEGFGEGNFQALFEAIERDQIRRGV 353
                                           *****9744456***********..***********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (353 nodes)
Target sequences:                          1  (354 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: 00:00:00.00
# Mc/sec: 27.15
//
[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