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.2483071.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 17.42
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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:

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:

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:

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:

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