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

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.5536.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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 6.88
//
[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