Alignments for a candidate for kdgD in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for kdgD in Cupriavidus basilensis 4G11

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate RR42_RS29080 RR42_RS29080 5-dehydro-4-deoxyglucarate dehydratase

Query= reanno::BFirm:BPHYT_RS24155
         (305 letters)



>FitnessBrowser__Cup4G11:RR42_RS29080
          Length = 304

 Score =  518 bits (1335), Expect = e-152
 Identities = 257/305 (84%), Positives = 279/305 (91%), Gaps = 1/305 (0%)

Query: 1   MTTPQELKQIVSEGLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFS 60
           MTTPQELKQIVSEGLLSFPVTDFD QG+FR +TY ERLEWLAPYGA+ALF AGGTGEFFS
Sbjct: 1   MTTPQELKQIVSEGLLSFPVTDFDAQGNFRPETYVERLEWLAPYGATALFAAGGTGEFFS 60

Query: 61  LTHNDYSNVVKTATEVCKGKVPILAGAGGPTRVAIAYAQEAERHGANGILLMPHYLTEAC 120
           LT +DY+NV++TA E C GKVPILAGAGGPTR+AIAYA+EA+R GA GILL+PHYLTEAC
Sbjct: 61  LTPDDYTNVIRTAVETCAGKVPILAGAGGPTRMAIAYAKEAQRLGAKGILLLPHYLTEAC 120

Query: 121 QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVS 180
           Q+GIA H EEVCKSV ++GVI+YNR NS++NADMLE LA+RCPNLIGFKDGVGEIE MV 
Sbjct: 121 QDGIANHIEEVCKSV-HIGVIVYNRGNSRINADMLERLADRCPNLIGFKDGVGEIEGMVR 179

Query: 181 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV 240
           IRR+LGDR SYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHAT 
Sbjct: 180 IRRKLGDRLSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATT 239

Query: 241 GKLIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMGKLDALIK 300
            +LIDEFFLPYL IRNRRAGYAVSIVKAGAKLVGH AGPVRAPLTDL E+E+  LDALIK
Sbjct: 240 NRLIDEFFLPYLDIRNRRAGYAVSIVKAGAKLVGHDAGPVRAPLTDLDEQELAMLDALIK 299

Query: 301 TLGPQ 305
            LGPQ
Sbjct: 300 KLGPQ 304


Lambda     K      H
   0.319    0.136    0.398 

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: 429
Number of extensions: 15
Number of successful extensions: 2
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: 305
Length of database: 304
Length adjustment: 27
Effective length of query: 278
Effective length of database: 277
Effective search space:    77006
Effective search space used:    77006
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 (21.7 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS29080 RR42_RS29080 (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.7373.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.1e-139  450.6   0.0   1.3e-139  450.4   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS29080  RR42_RS29080 5-dehydro-4-deoxygl


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS29080  RR42_RS29080 5-dehydro-4-deoxyglucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  450.4   0.0  1.3e-139  1.3e-139       1     298 [.       4     301 ..       4     302 .. 1.00

  Alignments for each domain:
  == domain 1  score: 450.4 bits;  conditional E-value: 1.3e-139
                                 TIGR03249   1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqvvev 69 
                                               pqelk+ +++GllsfPvt+fda+g+++++++ e++e+l+++++ alf+agGtGeffslt+ ++ +v++ 
  lcl|FitnessBrowser__Cup4G11:RR42_RS29080   4 PQELKQIVSEGLLSFPVTDFDAQGNFRPETYVERLEWLAPYGATALFAAGGTGEFFSLTPDDYTNVIRT 72 
                                               89******************************************************************* PP

                                 TIGR03249  70 aveaakgkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesvdlgviv 138
                                               ave+++gkvP+lag+Gg +++ai +a++a++ Ga+G+lllP+yl+ea q+G+a+++++v++sv++gviv
  lcl|FitnessBrowser__Cup4G11:RR42_RS29080  73 AVETCAGKVPILAGAGGPTRMAIAYAKEAQRLGAKGILLLPHYLTEACQDGIANHIEEVCKSVHIGVIV 141
                                               ********************************************************************* PP

                                 TIGR03249 139 yqrdnavleadtlerlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevtalaylalGvt 207
                                               y+r n+ ++ad+lerla+r+pnl+GfkdG+G+ie +++i++klGdrl ylgGlPtaev+a+ay+alGv 
  lcl|FitnessBrowser__Cup4G11:RR42_RS29080 142 YNRGNSRINADMLERLADRCPNLIGFKDGVGEIEGMVRIRRKLGDRLSYLGGLPTAEVYAAAYKALGVP 210
                                               ********************************************************************* PP

                                 TIGR03249 208 syssaifnfiPkiarkfyealrkgdeatvkeilkevilPiveirnrkkGyavslikaGlevvGrdvgpv 276
                                               +yssa+fnfiPk+a++fy+a++ +d+at +++++e++lP++ irnr++Gyavs++kaG+++vG+d+gpv
  lcl|FitnessBrowser__Cup4G11:RR42_RS29080 211 VYSSAVFNFIPKTAMDFYRAIAADDHATTNRLIDEFFLPYLDIRNRRAGYAVSIVKAGAKLVGHDAGPV 279
                                               ********************************************************************* PP

                                 TIGR03249 277 raPlvdlekeelaeleellkka 298
                                               raPl+dl+++ela l++l+kk+
  lcl|FitnessBrowser__Cup4G11:RR42_RS29080 280 RAPLTDLDEQELAMLDALIKKL 301
                                               ********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (304 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: 00:00:00.01
# Mc/sec: 8.93
//
[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