GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgD in Paraburkholderia bryophila 376MFSha3.1

Align 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) (characterized)
to candidate H281DRAFT_05319 H281DRAFT_05319 5-dehydro-4-deoxyglucarate dehydratase

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



>FitnessBrowser__Burk376:H281DRAFT_05319
          Length = 305

 Score =  594 bits (1532), Expect = e-175
 Identities = 296/305 (97%), Positives = 303/305 (99%)

Query: 1   MTTPQELKQIVSEGLLSFPVTDFDEQGDFRADTYAERLEWLAPYGASALFVAGGTGEFFS 60
           MTTPQELKQIVS+GLLSFPVTDFDE+GDFRADTYAERLEWLAPYGASALFVAGGTGEFFS
Sbjct: 1   MTTPQELKQIVSQGLLSFPVTDFDEKGDFRADTYAERLEWLAPYGASALFVAGGTGEFFS 60

Query: 61  LTHNDYSNVVKTATEVCKGKVPILAGAGGPTRVAIAYAQEAERHGANGILLMPHYLTEAC 120
           LTH+DYSNVV+TATEVCKGKVPILAGAGGPTRVAIAYA+EAERHGANGILLMPHYLTEAC
Sbjct: 61  LTHDDYSNVVRTATEVCKGKVPILAGAGGPTRVAIAYAKEAERHGANGILLMPHYLTEAC 120

Query: 121 QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVS 180
           QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMV+
Sbjct: 121 QEGIAAHAEEVCKSVPNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVT 180

Query: 181 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV 240
           IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV
Sbjct: 181 IRRRLGDRFSYLGGLPTAEVYAAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATV 240

Query: 241 GKLIDEFFLPYLAIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMGKLDALIK 300
           GKLIDEFFLPYL IRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEM +LDALIK
Sbjct: 241 GKLIDEFFLPYLKIRNRRAGYAVSIVKAGAKLVGHSAGPVRAPLTDLTEEEMAQLDALIK 300

Query: 301 TLGPQ 305
           TLGPQ
Sbjct: 301 TLGPQ 305


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: 496
Number of extensions: 17
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: 305
Length of database: 305
Length adjustment: 27
Effective length of query: 278
Effective length of database: 278
Effective search space:    77284
Effective search space used:    77284
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 H281DRAFT_05319 H281DRAFT_05319 (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.3917694.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.7e-139  449.3   0.0   3.1e-139  449.1   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05319  H281DRAFT_05319 5-dehydro-4-deox


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05319  H281DRAFT_05319 5-dehydro-4-deoxyglucarate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  449.1   0.0  3.1e-139  3.1e-139       1     297 [.       4     301 ..       4     303 .. 0.99

  Alignments for each domain:
  == domain 1  score: 449.1 bits;  conditional E-value: 3.1e-139
                                    TIGR03249   1 pqelkkkigsGllsfPvtpfdadgsldeaalrenieflldedlealfvagGtGeffsltkaeveqv 66 
                                                  pqelk+ +++GllsfPvt+fd++g+++ ++++e++e+l++++++alfvagGtGeffslt+ ++++v
  lcl|FitnessBrowser__Burk376:H281DRAFT_05319   4 PQELKQIVSQGLLSFPVTDFDEKGDFRADTYAERLEWLAPYGASALFVAGGTGEFFSLTHDDYSNV 69 
                                                  89**************************************************************** PP

                                    TIGR03249  67 vevaveaakgkvPvlagvGgnlsvaieiaraaekkGadGllllPpylieaeqeGlaayvkaviesv 132
                                                  v+ a+e++kgkvP+lag+Gg ++vai +a++ae++Ga+G+ll+P+yl+ea qeG+aa+ ++v++sv
  lcl|FitnessBrowser__Burk376:H281DRAFT_05319  70 VRTATEVCKGKVPILAGAGGPTRVAIAYAKEAERHGANGILLMPHYLTEACQEGIAAHAEEVCKSV 135
                                                  *****************************************************************9 PP

                                    TIGR03249 133 .dlgvivyqrdnavleadtlerlaerlpnlvGfkdGiGdiekvieitqklGdrllylgGlPtaevt 197
                                                   ++gvi+y+r+n++l+ad+le laer+pnl+GfkdG+G+ie++++i+++lGdr+ ylgGlPtaev+
  lcl|FitnessBrowser__Burk376:H281DRAFT_05319 136 pNMGVIIYNRANSKLNADMLEGLAERCPNLIGFKDGVGEIENMVTIRRRLGDRFSYLGGLPTAEVY 201
                                                  68**************************************************************** PP

                                    TIGR03249 198 alaylalGvtsyssaifnfiPkiarkfyealrkgdeatvkeilkevilPiveirnrkkGyavslik 263
                                                  a+ay+alGv +yssa+fnfiPk+a++fy+a++ +d+atv ++++e++lP+++irnr++Gyavs++k
  lcl|FitnessBrowser__Burk376:H281DRAFT_05319 202 AAAYKALGVPVYSSAVFNFIPKTAMDFYRAIAADDHATVGKLIDEFFLPYLKIRNRRAGYAVSIVK 267
                                                  ****************************************************************** PP

                                    TIGR03249 264 aGlevvGrdvgpvraPlvdlekeelaeleellkk 297
                                                  aG+++vG+++gpvraPl+dl++ee+a+l++l+k 
  lcl|FitnessBrowser__Burk376:H281DRAFT_05319 268 AGAKLVGHSAGPVRAPLTDLTEEEMAQLDALIKT 301
                                                  ********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (305 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: 13.86
//
[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