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.32173.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: 7.10
//
[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:

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