Alignments for a candidate for mhpE in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for mhpE in Pseudomonas benzenivorans DSM 8628

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate WP_090446860.1 BLS63_RS17015 4-hydroxy-2-oxovalerate aldolase

Query= metacyc::MONOMER-3404
         (345 letters)



>NCBI__GCF_900100495.1:WP_090446860.1
          Length = 346

 Score =  617 bits (1591), Expect = 0.0
 Identities = 306/337 (90%), Positives = 321/337 (95%)

Query: 1   MTFNPGKKLYISDVTLRDGSHAIRHQYSIQNVQDIARALDKARVDSIEVTHGDGLQGSSF 60
           MT +PGKKLYISDVTLRDGSHAIRHQYS+QNVQDIARALD+ARVDSIEV HGDGLQGSSF
Sbjct: 1   MTLDPGKKLYISDVTLRDGSHAIRHQYSLQNVQDIARALDQARVDSIEVAHGDGLQGSSF 60

Query: 61  NYGFGAHSDLEWIEAAADVIQHARVTVLLVPGIGTVHDLKAAYDAGARSVRVATHCTEAD 120
           NYGF AH+DLEWIEAAADVI+HA++  LL+PGIGTVHDLKAAYDAGAR VRVATHCTEAD
Sbjct: 61  NYGFAAHTDLEWIEAAADVIKHAKIATLLLPGIGTVHDLKAAYDAGARVVRVATHCTEAD 120

Query: 121 VSRQHIEYARELGMDTVGFLMMSHMIPAEQLAAQGKLMETYGAQCIYMADSGGAMNMNDI 180
           +S+QHIEYAR LGMDTVGFLMMSHMIPAEQLA Q KLME+YGA CIYMADSGGAMNM DI
Sbjct: 121 MSKQHIEYARSLGMDTVGFLMMSHMIPAEQLAEQAKLMESYGATCIYMADSGGAMNMQDI 180

Query: 181 RDRMRAFKAVLNPQTQTGMHAHHNLSLGVANSIIAVEEGCDRIDASLAGMGAGAGNAPLE 240
           R+RMRAFKA+L P+TQTGMHAHHNLSLGVANSI AVEEGCDRIDASLAGMGAGAGNAPLE
Sbjct: 181 RERMRAFKALLKPETQTGMHAHHNLSLGVANSITAVEEGCDRIDASLAGMGAGAGNAPLE 240

Query: 241 VFIAAAERLGWNHGTDLYTLMDAADDIVRPLQDRPVRVDRETLGLGYAGVYSSFLRHAEV 300
           VFIAAAERLGWNHGTDLY LMDAADDIVRPLQDRPVRVDRETL LGYAGVYSSFLRHAEV
Sbjct: 241 VFIAAAERLGWNHGTDLYRLMDAADDIVRPLQDRPVRVDRETLALGYAGVYSSFLRHAEV 300

Query: 301 AAAKYGLKTLDILVELGRRRMVGGQEDMIVDVALDLL 337
           AAAKYGLK LDILVELG+RRMVGGQEDMIVDVALDLL
Sbjct: 301 AAAKYGLKPLDILVELGKRRMVGGQEDMIVDVALDLL 337


Lambda     K      H
   0.320    0.135    0.389 

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: 522
Number of extensions: 18
Number of successful extensions: 1
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: 345
Length of database: 346
Length adjustment: 29
Effective length of query: 316
Effective length of database: 317
Effective search space:   100172
Effective search space used:   100172
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_090446860.1 BLS63_RS17015 (4-hydroxy-2-oxovalerate aldolase)
to HMM TIGR03217 (dmpG: 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))

# 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/TIGR03217.hmm
# target sequence database:        /tmp/gapView.31516.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03217  [M=334]
Accession:   TIGR03217
Description: 4OH_2_O_val_ald: 4-hydroxy-2-oxovalerate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
     2e-184  598.3   8.0   2.3e-184  598.1   8.0    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090446860.1  BLS63_RS17015 4-hydroxy-2-oxoval


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090446860.1  BLS63_RS17015 4-hydroxy-2-oxovalerate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  598.1   8.0  2.3e-184  2.3e-184       1     333 [.       7     339 ..       7     340 .. 0.99

  Alignments for each domain:
  == domain 1  score: 598.1 bits;  conditional E-value: 2.3e-184
                                 TIGR03217   1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggsslnyGfsaasdleliea 69 
                                               kkl+i+dvtLrdGsha+rhq++ ++v++ia+aLd+a+vd+ievahGdGL+gss+nyGf+a++dle+iea
  lcl|NCBI__GCF_900100495.1:WP_090446860.1   7 KKLYISDVTLRDGSHAIRHQYSLQNVQDIARALDQARVDSIEVAHGDGLQGSSFNYGFAAHTDLEWIEA 75 
                                               689****************************************************************** PP

                                 TIGR03217  70 aaeavkkakvavlllPGigtveelkaaadaGvkvvrvathcteadvseqhielarelgletvgfLmmsh 138
                                               aa+++k+ak+a+lllPGigtv++lkaa+daG++vvrvathctead+s+qhie+ar lg++tvgfLmmsh
  lcl|NCBI__GCF_900100495.1:WP_090446860.1  76 AADVIKHAKIATLLLPGIGTVHDLKAAYDAGARVVRVATHCTEADMSKQHIEYARSLGMDTVGFLMMSH 144
                                               ********************************************************************* PP

                                 TIGR03217 139 maspeklaeqakllesyGadvvyvvdsaGallpedvkdrvkalkealkpetevGlhahenlslavansi 207
                                               m+++e+laeqakl+esyGa+++y++ds+Ga++++d+++r++a+k+ lkpet++G+hah+nlsl+vansi
  lcl|NCBI__GCF_900100495.1:WP_090446860.1 145 MIPAEQLAEQAKLMESYGATCIYMADSGGAMNMQDIRERMRAFKALLKPETQTGMHAHHNLSLGVANSI 213
                                               ********************************************************************* PP

                                 TIGR03217 208 vaveeGatridaslaglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdrea 276
                                               +aveeG++ridaslag+GagaGnaplev++a+++rlG+++g+dl++l+daa+d+vrPl+drpvrvdre+
  lcl|NCBI__GCF_900100495.1:WP_090446860.1 214 TAVEEGCDRIDASLAGMGAGAGNAPLEVFIAAAERLGWNHGTDLYRLMDAADDIVRPLQDRPVRVDRET 282
                                               ********************************************************************* PP

                                 TIGR03217 277 ltlGyaGvyssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldlake 333
                                               l+lGyaGvyssflrhae aa+kyg+++ dilvelG+r++vgGqedmivdvaldl+k+
  lcl|NCBI__GCF_900100495.1:WP_090446860.1 283 LALGYAGVYSSFLRHAEVAAAKYGLKPLDILVELGKRRMVGGQEDMIVDVALDLLKQ 339
                                               ******************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (346 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 10.03
//
[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