Alignments for a candidate for garL in Escherichia coli BW25113

GapMind for catabolism of small carbon sources

Alignments for a candidate for garL in Escherichia coli BW25113

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 17199 b3126 alpha-dehydro-beta-deoxy-D-glucarate aldolase (NCBI)

Query= SwissProt::P23522
         (256 letters)



>FitnessBrowser__Keio:17199
          Length = 256

 Score =  508 bits (1307), Expect = e-149
 Identities = 256/256 (100%), Positives = 256/256 (100%)

Query: 1   MNNDVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIP 60
           MNNDVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIP
Sbjct: 1   MNNDVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIP 60

Query: 61  QLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGI 120
           QLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGI
Sbjct: 61  QLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGI 120

Query: 121 RGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDL 180
           RGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDL
Sbjct: 121 RGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDL 180

Query: 181 AAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDL 240
           AAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDL
Sbjct: 181 AAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDL 240

Query: 241 GVFRSATQKLADTFKK 256
           GVFRSATQKLADTFKK
Sbjct: 241 GVFRSATQKLADTFKK 256


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: 354
Number of extensions: 5
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: 256
Length adjustment: 24
Effective length of query: 232
Effective length of database: 232
Effective search space:    53824
Effective search space used:    53824
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 17199 b3126 (alpha-dehydro-beta-deoxy-D-glucarate aldolase (NCBI))
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.29799.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   7.3e-152  490.0   0.1   8.1e-152  489.8   0.1    1.0  1  lcl|FitnessBrowser__Keio:17199  b3126 alpha-dehydro-beta-deoxy-D


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:17199  b3126 alpha-dehydro-beta-deoxy-D-glucarate aldolase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  489.8   0.1  8.1e-152  8.1e-152       1     249 []       8     256 .]       8     256 .] 1.00

  Alignments for each domain:
  == domain 1  score: 489.8 bits;  conditional E-value: 8.1e-152
                       TIGR03239   1 nrfrqkllarktliglwsalgnpitaevlglagfdwllldgehapndvltlipqlmalkdsasapvvrvplnepviikr 79 
                                     n+f+++l+a++++ig+wsal+npi++evlglagfdwl+ldgehapnd++t+ipqlmalk+sasapvvrvp+nepviikr
  lcl|FitnessBrowser__Keio:17199   8 NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPTNEPVIIKR 86 
                                     8****************************************************************************** PP

                       TIGR03239  80 lldigfynllipfvesaeeaeravaatryppegirgvsvaqrsnrygtvadyfkkindnitvlvqiesrkgvdavdeia 158
                                     lldigfyn+lipfve++eeae ava+tryppegirgvsv++r+n++gtvadyf+++n+nit+lvqies++gvd+vd+ia
  lcl|FitnessBrowser__Keio:17199  87 LLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIA 165
                                     ******************************************************************************* PP

                       TIGR03239 159 avdgvdgvfvgpsdlaaalgylgnpnhpdvqkairhifdraaahgkavgilapveadarrylelgatfvavgsdlgvfr 237
                                     a++gvdg+fvgpsdlaaalg+lgn++hpdvqkai+hif+ra+ahgk++gilapveadarryle+gatfvavgsdlgvfr
  lcl|FitnessBrowser__Keio:17199 166 ATEGVDGIFVGPSDLAAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFR 244
                                     ******************************************************************************* PP

                       TIGR03239 238 satkalsekfkk 249
                                     sat++l+++fkk
  lcl|FitnessBrowser__Keio:17199 245 SATQKLADTFKK 256
                                     **********96 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (249 nodes)
Target sequences:                          1  (256 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: 6.64
//
[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