GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Pseudomonas simiae WCS417

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate GFF826 PS417_04195 5-dehydro-4-deoxyglucarate dehydratase

Query= reanno::WCS417:GFF826
         (303 letters)



>FitnessBrowser__WCS417:GFF826
          Length = 303

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

Query: 1   MNPQELKSILSHGLLSFPVTDFNAQGDFHQAGYIKRLEWLAPYGATALFAAGGTGEFFSL 60
           MNPQELKSILSHGLLSFPVTDFNAQGDFHQAGYIKRLEWLAPYGATALFAAGGTGEFFSL
Sbjct: 1   MNPQELKSILSHGLLSFPVTDFNAQGDFHQAGYIKRLEWLAPYGATALFAAGGTGEFFSL 60

Query: 61  AASEYSQVVKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120
           AASEYSQVVKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ
Sbjct: 61  AASEYSQVVKTAVDTCATSVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQ 120

Query: 121 DGVAAHVEAVCKSVKIGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR 180
           DGVAAHVEAVCKSVKIGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR
Sbjct: 121 DGVAAHVEAVCKSVKIGVVVYNRNVCRLTAPLLERLAERCPNLIGYKDGLGDIELMVSIR 180

Query: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAKDDHATVSK 240
           RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAKDDHATVSK
Sbjct: 181 RRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAIAKDDHATVSK 240

Query: 241 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIVGYDAGPVRTPLTDLLPEEYEALAALIDKQ 300
           IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIVGYDAGPVRTPLTDLLPEEYEALAALIDKQ
Sbjct: 241 IIDDFFLPYLDIRNRKAGYAVSIVKAGAKIVGYDAGPVRTPLTDLLPEEYEALAALIDKQ 300

Query: 301 GAQ 303
           GAQ
Sbjct: 301 GAQ 303


Lambda     K      H
   0.320    0.137    0.399 

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: 456
Number of extensions: 9
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 GFF826 PS417_04195 (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.24734.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                          -----------
   2.4e-137  442.9   0.0   2.7e-137  442.8   0.0    1.0  1  lcl|FitnessBrowser__WCS417:GFF826  PS417_04195 5-dehydro-4-deoxyglu


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF826  PS417_04195 5-dehydro-4-deoxyglucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  442.8   0.0  2.7e-137  2.7e-137       1     298 [.       3     300 ..       3     301 .. 0.99

  Alignments for each domain:
  == domain 1  score: 442.8 bits;  conditional E-value: 2.7e-137
                          TIGR03249   1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqvvevaveaakg 76 
                                        pqelk  +++GllsfPvt+f+a+g++++a + +++e+l+++++ alf+agGtGeffsl  +e++qvv+ av++++ 
  lcl|FitnessBrowser__WCS417:GFF826   3 PQELKSILSHGLLSFPVTDFNAQGDFHQAGYIKRLEWLAPYGATALFAAGGTGEFFSLAASEYSQVVKTAVDTCAT 78 
                                        89************************************************************************** PP

                          TIGR03249  77 kvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesvdlgvivyqrdnavleadtle 152
                                         vP+lagvGg++++aie+a++ae+ Ga+GllllP+yl+ea+q+G+aa+v+av++sv++gv+vy+r+ + l+a+ le
  lcl|FitnessBrowser__WCS417:GFF826  79 SVPILAGVGGSTRQAIEYAQEAERLGAKGLLLLPHYLTEASQDGVAAHVEAVCKSVKIGVVVYNRNVCRLTAPLLE 154
                                        **************************************************************************** PP

                          TIGR03249 153 rlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevtalaylalGvtsyssaifnfiPkiarkfyeal 228
                                        rlaer+pnl+G+kdG+Gdie +++i+++lGdr+ ylgGlPtaev+a+ay+alGv +yssa+fnfiPk+a++fy+a+
  lcl|FitnessBrowser__WCS417:GFF826 155 RLAERCPNLIGYKDGLGDIELMVSIRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYHAI 230
                                        **************************************************************************** PP

                          TIGR03249 229 rkgdeatvkeilkevilPiveirnrkkGyavslikaGlevvGrdvgpvraPlvdlekeelaeleellkka 298
                                        +k+d+atv++i+++++lP++ irnrk+Gyavs++kaG+++vG d+gpvr+Pl+dl  ee++ l++l++k+
  lcl|FitnessBrowser__WCS417:GFF826 231 AKDDHATVSKIIDDFFLPYLDIRNRKAGYAVSIVKAGAKIVGYDAGPVRTPLTDLLPEEYEALAALIDKQ 300
                                        ******************************************************************9985 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 6.58
//
[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