Alignments for a candidate for kdgD in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for kdgD in Acidovorax sp. GW101-3H11

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate Ac3H11_2339 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)

Query= BRENDA::B7WZA5
         (303 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2339
          Length = 303

 Score =  536 bits (1382), Expect = e-157
 Identities = 264/303 (87%), Positives = 278/303 (91%)

Query: 1   MTPQDLKDVMSSGLLSFPVTDFDAQGNFNAKGYAARLEWLAPYGASALFAAGGTGEYFSL 60
           MTPQDLK +M SGLLSFP+TDFD QGNF  K Y  RLEWLAPYGASALFAAGGTGEYFSL
Sbjct: 1   MTPQDLKTIMGSGLLSFPITDFDEQGNFRPKTYIERLEWLAPYGASALFAAGGTGEYFSL 60

Query: 61  YGEEYGQIIKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ 120
            G EY ++IKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ
Sbjct: 61  SGPEYSEVIKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQ 120

Query: 121 EGLIAHVEQVCKSVKFGVIVYNRDRTRFTPESLAILAERCPNLVGFKDGMGNIETMSSIF 180
           EGLI HV QVC SVKFGVIVYNRDRT+ T ESLAILAERCPNL+GFKDG+GNIETMSSI+
Sbjct: 121 EGLIEHVAQVCNSVKFGVIVYNRDRTKLTAESLAILAERCPNLIGFKDGVGNIETMSSIY 180

Query: 181 MKMGDRFAYLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPRTAMAFYEAVRTDDMATQHK 240
           MKMGDRF+YLGGLPTAEVYAAAYKALGTPVYSSAVFNFIP+TAM FY+AV  DD+ATQHK
Sbjct: 181 MKMGDRFSYLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPKTAMDFYKAVAADDIATQHK 240

Query: 241 LLKEFFMPYLKIRNRVEGYGVSIIKAGAKLVGHDAGPVRAPLTDLKPAEMEELKVLIDKL 300
           LLKEFFMPYL IRNRVEGYGVSIIKAGAK+VGHD GPVRAPLTDLKP E+EEL  LI KL
Sbjct: 241 LLKEFFMPYLAIRNRVEGYGVSIIKAGAKIVGHDGGPVRAPLTDLKPHEVEELAALIKKL 300

Query: 301 GPQ 303
           GPQ
Sbjct: 301 GPQ 303


Lambda     K      H
   0.320    0.138    0.405 

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: 447
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 Ac3H11_2339 (5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41))
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.30264.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                        -----------
     7e-134  431.6   0.0   7.8e-134  431.4   0.0    1.0  1  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2339  5-dehydro-4-deoxyglucarate dehyd


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2339  5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  431.4   0.0  7.8e-134  7.8e-134       1     298 [.       3     300 ..       3     301 .. 1.00

  Alignments for each domain:
  == domain 1  score: 431.4 bits;  conditional E-value: 7.8e-134
                                        TIGR03249   1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkae 62 
                                                      pq+lk+ +gsGllsfP+t+fd++g+++++++ e++e+l++++++alf+agGtGe+fsl+  e
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2339   3 PQDLKTIMGSGLLSFPITDFDEQGNFRPKTYIERLEWLAPYGASALFAAGGTGEYFSLSGPE 64 
                                                      89************************************************************ PP

                                        TIGR03249  63 veqvvevaveaakgkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaay 124
                                                      +++v++ av++++gkvP++ag+Gg +++ai  a++ae+ Ga+G+lllP+yl+ea qeGl+++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2339  65 YSEVIKTAVDTCRGKVPIIAGAGGPTRTAIAHAQEAERLGAHGILLLPHYLTEAGQEGLIEH 126
                                                      ************************************************************** PP

                                        TIGR03249 125 vkaviesvdlgvivyqrdnavleadtlerlaerlpnlvGfkdGiGdiekvieitqklGdrll 186
                                                      v +v++sv++gvivy+rd ++l+a++l+ laer+pnl+GfkdG+G+ie++ +i+ k+Gdr+ 
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2339 127 VAQVCNSVKFGVIVYNRDRTKLTAESLAILAERCPNLIGFKDGVGNIETMSSIYMKMGDRFS 188
                                                      ************************************************************** PP

                                        TIGR03249 187 ylgGlPtaevtalaylalGvtsyssaifnfiPkiarkfyealrkgdeatvkeilkevilPiv 248
                                                      ylgGlPtaev+a+ay+alG  +yssa+fnfiPk+a++fy+a++ +d at +++lke+++P++
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2339 189 YLGGLPTAEVYAAAYKALGTPVYSSAVFNFIPKTAMDFYKAVAADDIATQHKLLKEFFMPYL 250
                                                      ************************************************************** PP

                                        TIGR03249 249 eirnrkkGyavslikaGlevvGrdvgpvraPlvdlekeelaeleellkka 298
                                                      +irnr +Gy vs+ikaG+++vG+d gpvraPl+dl+ +e++el++l+kk+
  lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2339 251 AIRNRVEGYGVSIIKAGAKIVGHDGGPVRAPLTDLKPHEVEELAALIKKL 300
                                                      ************************************************96 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 11.06
//
[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