Alignments for a candidate for kdgD in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for kdgD in Pseudomonas putida KT2440

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate PP_3599 PP_3599 5-dehydro-4-deoxyglucarate dehydratase

Query= reanno::Putida:PP_3599
         (303 letters)



>FitnessBrowser__Putida:PP_3599
          Length = 303

 Score =  600 bits (1546), Expect = e-176
 Identities = 303/303 (100%), Positives = 303/303 (100%)

Query: 1   MNPQELKSILSHGLLSFPVTDFNAQGDFNPAGYIKRLEWLAPYGASALFAAGGTGEFFSL 60
           MNPQELKSILSHGLLSFPVTDFNAQGDFNPAGYIKRLEWLAPYGASALFAAGGTGEFFSL
Sbjct: 1   MNPQELKSILSHGLLSFPVTDFNAQGDFNPAGYIKRLEWLAPYGASALFAAGGTGEFFSL 60

Query: 61  AASEYSQVIKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120
           AASEYSQVIKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ
Sbjct: 61  AASEYSQVIKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120

Query: 121 DGVAAHVEAVCKSVNIGVVVYNRNVCRLNADLLEKLAERCPNLIGYKDGLGDIELMVSIR 180
           DGVAAHVEAVCKSVNIGVVVYNRNVCRLNADLLEKLAERCPNLIGYKDGLGDIELMVSIR
Sbjct: 121 DGVAAHVEAVCKSVNIGVVVYNRNVCRLNADLLEKLAERCPNLIGYKDGLGDIELMVSIR 180

Query: 181 RRLGERFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFVPKTAMDFYNAIARDDHATVAK 240
           RRLGERFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFVPKTAMDFYNAIARDDHATVAK
Sbjct: 181 RRLGERFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFVPKTAMDFYNAIARDDHATVAK 240

Query: 241 LIDDFFLPYLDIRNRKAGYAVSIVKAGARIAGYDAGPVRTPLTDLTAEEYEMLAALMDKM 300
           LIDDFFLPYLDIRNRKAGYAVSIVKAGARIAGYDAGPVRTPLTDLTAEEYEMLAALMDKM
Sbjct: 241 LIDDFFLPYLDIRNRKAGYAVSIVKAGARIAGYDAGPVRTPLTDLTAEEYEMLAALMDKM 300

Query: 301 GPQ 303
           GPQ
Sbjct: 301 GPQ 303


Lambda     K      H
   0.320    0.136    0.396 

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: 505
Number of extensions: 7
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: 303
Length of database: 303
Length adjustment: 27
Effective length of query: 276
Effective length of database: 276
Effective search space:    76176
Effective search space used:    76176
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: 48 (23.1 bits)

Align candidate PP_3599 PP_3599 (5-dehydro-4-deoxyglucarate dehydratase)
to HMM TIGR03249 (kdgD: 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))

# 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/TIGR03249.hmm
# target sequence database:        /tmp/gapView.1008.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03249  [M=299]
Accession:   TIGR03249
Description: KdgD: 5-dehydro-4-deoxyglucarate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   3.2e-137  442.5   0.0   3.6e-137  442.4   0.0    1.0  1  lcl|FitnessBrowser__Putida:PP_3599  PP_3599 5-dehydro-4-deoxyglucara


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Putida:PP_3599  PP_3599 5-dehydro-4-deoxyglucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.4   0.0  3.6e-137  3.6e-137       1     298 [.       3     300 ..       3     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 442.4 bits;  conditional E-value: 3.6e-137
                           TIGR03249   1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqvvevaveaak 75 
                                         pqelk  +++GllsfPvt+f+a+g++++a + +++e+l++++++alf+agGtGeffsl  +e++qv++ av++++
  lcl|FitnessBrowser__Putida:PP_3599   3 PQELKSILSHGLLSFPVTDFNAQGDFNPAGYIKRLEWLAPYGASALFAAGGTGEFFSLAASEYSQVIKTAVDTCA 77 
                                         89************************************************************************* PP

                           TIGR03249  76 gkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesvdlgvivyqrdnavleadt 150
                                           vP+lagvGg++++aie+a++ae+ Ga+GllllP+yl+ea+q+G+aa+v+av++sv++gv+vy+r+ + l+ad 
  lcl|FitnessBrowser__Putida:PP_3599  78 TSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQDGVAAHVEAVCKSVNIGVVVYNRNVCRLNADL 152
                                         *************************************************************************** PP

                           TIGR03249 151 lerlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevtalaylalGvtsyssaifnfiPkiarkfy 225
                                         le+laer+pnl+G+kdG+Gdie +++i+++lG+r+ ylgGlPtaev+a+ay+alGv +yssa+fnf+Pk+a++fy
  lcl|FitnessBrowser__Putida:PP_3599 153 LEKLAERCPNLIGYKDGLGDIELMVSIRRRLGERFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFVPKTAMDFY 227
                                         *************************************************************************** PP

                           TIGR03249 226 ealrkgdeatvkeilkevilPiveirnrkkGyavslikaGlevvGrdvgpvraPlvdlekeelaeleellkka 298
                                         +a++++d+atv +++++++lP++ irnrk+Gyavs++kaG+++ G d+gpvr+Pl+dl+ ee++ l++l++k+
  lcl|FitnessBrowser__Putida:PP_3599 228 NAIARDDHATVAKLIDDFFLPYLDIRNRKAGYAVSIVKAGARIAGYDAGPVRTPLTDLTAEEYEMLAALMDKM 300
                                         *********************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (303 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 7.10
//
[ok]

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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