Alignments for a candidate for mhpE in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for mhpE in Pseudomonas fluorescens GW456-L13

Align 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39) (characterized)
to candidate PfGW456L13_2506 4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39)

Query= BRENDA::P51017
         (346 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506
          Length = 344

 Score =  589 bits (1518), Expect = e-173
 Identities = 292/339 (86%), Positives = 321/339 (94%)

Query: 1   MNLHGKSVILHDMSLRDGMHAKRHQISLEQMVAVATGLDQAGMPLIEITHGDGLGGRSIN 60
           MNL GKSV LHDMSLRDGMHAK+HQIS+EQMV+VATGLD AG+PLIEITHGDGLGG S+N
Sbjct: 1   MNLQGKSVRLHDMSLRDGMHAKQHQISIEQMVSVATGLDAAGVPLIEITHGDGLGGASLN 60

Query: 61  YGFPAHSDEEYLRAVIPQLKQAKVSALLLPGIGTVDHLKMALDCGVSTIRVATHCTEADV 120
           YGFPAHSDEEY  AVIP++KQAKVSALLLPGIGT+DHLKMA + GVSTIRVATHCTEADV
Sbjct: 61  YGFPAHSDEEYFSAVIPKMKQAKVSALLLPGIGTLDHLKMAHEHGVSTIRVATHCTEADV 120

Query: 121 SEQHIGMARKLGVDTVGFLMMAHMISAEKVLEQAKLMESYGANCIYCTDSAGYMLPDEVS 180
           S QHIGM+ K+G+DTVGFLMMAHM+S EK+LEQA+LMESYGANCIYCTDSAGYMLPDEV+
Sbjct: 121 SGQHIGMSAKMGLDTVGFLMMAHMVSPEKLLEQARLMESYGANCIYCTDSAGYMLPDEVT 180

Query: 181 EKIGLLRAELNPATEVGFHGHHNMGMAIANSLAAIEAGAARIDGSVAGLGAGAGNTPLEV 240
           +KIG LRA LN  TEVGFHGHHNMGMAIANSLAAIEAGAARIDGSVAGLGAGAGNTPLEV
Sbjct: 181 QKIGALRAGLNAGTEVGFHGHHNMGMAIANSLAAIEAGAARIDGSVAGLGAGAGNTPLEV 240

Query: 241 FVAVCKRMGVETGIDLYKIMDVAEDLVVPMMDQPIRVDRDALTLGYAGVYSSFLLFAQRA 300
           FVAV +RMGV +G+DLYKIMDVAEDLVVPMMDQPIR+DRDALTLGYAGVYSSFLLFA+RA
Sbjct: 241 FVAVLERMGVNSGVDLYKIMDVAEDLVVPMMDQPIRLDRDALTLGYAGVYSSFLLFAKRA 300

Query: 301 EKKYGVSARDILVELGRRGTVGGQEDMIEDLALDMARAR 339
           E+KYG++AR++LVELGRRGTVGGQEDMIEDLAL ++RAR
Sbjct: 301 EQKYGIAARELLVELGRRGTVGGQEDMIEDLALTLSRAR 339


Lambda     K      H
   0.320    0.135    0.386 

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: 538
Number of extensions: 17
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: 346
Length of database: 344
Length adjustment: 29
Effective length of query: 317
Effective length of database: 315
Effective search space:    99855
Effective search space used:    99855
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 PfGW456L13_2506 (4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39))
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.725.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                               -----------
   5.2e-170  550.9   8.3   5.9e-170  550.7   8.3    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506  4-hydroxy-2-oxovalerate aldolase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506  4-hydroxy-2-oxovalerate aldolase (EC 4.1.3.39)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  550.7   8.3  5.9e-170  5.9e-170       1     333 [.       6     338 ..       6     339 .. 0.99

  Alignments for each domain:
  == domain 1  score: 550.7 bits;  conditional E-value: 5.9e-170
                                               TIGR03217   1 kkltitdvtLrdGshavrhqftaeevraiaaaLdeagvdaievahGdGLggssln 55 
                                                             k+++++d++LrdG+ha++hq+++e+++++a++Ld+agv+ ie++hGdGLgg+sln
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506   6 KSVRLHDMSLRDGMHAKQHQISIEQMVSVATGLDAAGVPLIEITHGDGLGGASLN 60 
                                                             5799*************************************************** PP

                                               TIGR03217  56 yGfsaasdlelieaaaeavkkakvavlllPGigtveelkaaadaGvkvvrvathc 110
                                                             yGf+a+sd+e+ +a++ ++k+akv++lllPGigt+++lk+a++ Gv+++rvathc
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506  61 YGFPAHSDEEYFSAVIPKMKQAKVSALLLPGIGTLDHLKMAHEHGVSTIRVATHC 115
                                                             ******************************************************* PP

                                               TIGR03217 111 teadvseqhielarelgletvgfLmmshmaspeklaeqakllesyGadvvyvvds 165
                                                             teadvs qhi+++ ++gl+tvgfLmm+hm+spekl eqa+l+esyGa+++y++ds
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506 116 TEADVSGQHIGMSAKMGLDTVGFLMMAHMVSPEKLLEQARLMESYGANCIYCTDS 170
                                                             ******************************************************* PP

                                               TIGR03217 166 aGallpedvkdrvkalkealkpetevGlhahenlslavansivaveeGatridas 220
                                                             aG++lp++v++++ al++ l+  tevG+h+h+n+++a+ans++a+e+Ga+rid+s
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506 171 AGYMLPDEVTQKIGALRAGLNAGTEVGFHGHHNMGMAIANSLAAIEAGAARIDGS 225
                                                             ******************************************************* PP

                                               TIGR03217 221 laglGagaGnaplevlvavldrlGletgvdlfklldaaedvvrPlldrpvrvdre 275
                                                             +aglGagaGn+plev+vavl+r+G++ gvdl+k++d+aed+v+P++d+p+r+dr+
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506 226 VAGLGAGAGNTPLEVFVAVLERMGVNSGVDLYKIMDVAEDLVVPMMDQPIRLDRD 280
                                                             ******************************************************* PP

                                               TIGR03217 276 altlGyaGvyssflrhaeraaekygvdardilvelGrrklvgGqedmivdvaldl 330
                                                             altlGyaGvyssfl++a+ra++kyg+ ar++lvelGrr +vgGqedmi d+al+l
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506 281 ALTLGYAGVYSSFLLFAKRAEQKYGIAARELLVELGRRGTVGGQEDMIEDLALTL 335
                                                             ******************************************************* PP

                                               TIGR03217 331 ake 333
                                                             +++
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2506 336 SRA 338
                                                             986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (334 nodes)
Target sequences:                          1  (344 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: 00:00:00.00
# Mc/sec: 11.77
//
[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