Alignments for a candidate for garL in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for garL in Burkholderia phytofirmans PsJN

Align 5-keto-4-deoxy-D-glucarate aldolase; KDGluc aldolase; KDGlucA; 2-dehydro-3-deoxy-D-glucarate aldolase; 2-keto-3-deoxy-D-glucarate aldolase; 5-dehydro-4-deoxy-D-glucarate aldolase; Alpha-keto-beta-deoxy-D-glucarate aldolase; EC 4.1.2.20 (characterized)
to candidate BPHYT_RS24135 BPHYT_RS24135 alpha-dehydro-beta-deoxy-D-glucarate aldolase

Query= SwissProt::P23522
         (256 letters)



>FitnessBrowser__BFirm:BPHYT_RS24135
          Length = 266

 Score =  319 bits (817), Expect = 4e-92
 Identities = 152/248 (61%), Positives = 191/248 (77%)

Query: 7   PNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALK 66
           PN F+ A+   +  IGCW++L++PI TE+LG+ GFDW++LD EHAPND+ T IPQLMALK
Sbjct: 11  PNSFRRAVCGGETLIGCWASLASPIVTELLGIVGFDWMLLDAEHAPNDVLTLIPQLMALK 70

Query: 67  GSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS 126
            SASAPVVR P N+ V IKRLLD GF NFL+PFVE+ ++A  AVA+TRYPP+GIRGVSVS
Sbjct: 71  DSASAPVVRPPANDSVFIKRLLDSGFSNFLVPFVESADDAARAVAATRYPPQGIRGVSVS 130

Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186
           HR N + TV DYF+ +N N+ ++VQIES++ VD +D I A +GVD +FVGPSDLAAA G 
Sbjct: 131 HRGNHYATVPDYFSVANDNVCVIVQIESRKAVDAIDEILAVDGVDAVFVGPSDLAAAYGQ 190

Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFRSA 246
           LGNA+H DVQ AI H+F RA A GKPSGILAPV+ADA RY+  G   VAV +D+G+ + A
Sbjct: 191 LGNANHSDVQAAIAHVFERAQAAGKPSGILAPVQADAERYISMGCRVVAVCADMGLLKGA 250

Query: 247 TQKLADTF 254
            Q +   F
Sbjct: 251 AQTVQKHF 258


Lambda     K      H
   0.318    0.134    0.392 

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: 212
Number of extensions: 7
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: 256
Length of database: 266
Length adjustment: 25
Effective length of query: 231
Effective length of database: 241
Effective search space:    55671
Effective search space used:    55671
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate BPHYT_RS24135 BPHYT_RS24135 (alpha-dehydro-beta-deoxy-D-glucarate aldolase)
to HMM TIGR03239 (garL: 2-dehydro-3-deoxyglucarate aldolase (EC 4.1.2.20))

# 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/TIGR03239.hmm
# target sequence database:        /tmp/gapView.10179.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03239  [M=249]
Accession:   TIGR03239
Description: GarL: 2-dehydro-3-deoxyglucarate aldolase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   9.1e-128  411.0   0.8   1.1e-127  410.8   0.8    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS24135  BPHYT_RS24135 alpha-dehydro-beta


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS24135  BPHYT_RS24135 alpha-dehydro-beta-deoxy-D-glucarate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.8   0.8  1.1e-127  1.1e-127       1     248 [.      12     259 ..      12     260 .. 0.99

  Alignments for each domain:
  == domain 1  score: 410.8 bits;  conditional E-value: 1.1e-127
                                TIGR03239   1 nrfrqkllarktliglwsalgnpitaevlglagfdwllldgehapndvltlipqlmalkdsasapvvrvp 70 
                                              n fr+++  ++tlig+w++l++pi +e+lg+ gfdw+lld+ehapndvltlipqlmalkdsasapvvr+p
  lcl|FitnessBrowser__BFirm:BPHYT_RS24135  12 NSFRRAVCGGETLIGCWASLASPIVTELLGIVGFDWMLLDAEHAPNDVLTLIPQLMALKDSASAPVVRPP 81 
                                              78******************************************************************** PP

                                TIGR03239  71 lnepviikrlldigfynllipfvesaeeaeravaatryppegirgvsvaqrsnrygtvadyfkkindnit 140
                                              +n+ v ikrlld gf n+l+pfvesa++a+ravaatrypp+girgvsv++r n+y+tv+dyf + ndn++
  lcl|FitnessBrowser__BFirm:BPHYT_RS24135  82 ANDSVFIKRLLDSGFSNFLVPFVESADDAARAVAATRYPPQGIRGVSVSHRGNHYATVPDYFSVANDNVC 151
                                              ********************************************************************** PP

                                TIGR03239 141 vlvqiesrkgvdavdeiaavdgvdgvfvgpsdlaaalgylgnpnhpdvqkairhifdraaahgkavgila 210
                                              v+vqiesrk vda+dei avdgvd+vfvgpsdlaaa+g lgn+nh dvq+ai h+f+ra+a+gk++gila
  lcl|FitnessBrowser__BFirm:BPHYT_RS24135 152 VIVQIESRKAVDAIDEILAVDGVDAVFVGPSDLAAAYGQLGNANHSDVQAAIAHVFERAQAAGKPSGILA 221
                                              ********************************************************************** PP

                                TIGR03239 211 pveadarrylelgatfvavgsdlgvfrsatkalsekfk 248
                                              pv+ada ry+ +g + vav +d+g+++ a+++++++f 
  lcl|FitnessBrowser__BFirm:BPHYT_RS24135 222 PVQADAERYISMGCRVVAVCADMGLLKGAAQTVQKHFM 259
                                              *********************************99985 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (249 nodes)
Target sequences:                          1  (266 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: 5.12
//
[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