Alignments for a candidate for garL in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for garL in Klebsiella michiganensis M5al

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 BWI76_RS24830 BWI76_RS24830 5-keto-4-deoxy-D-glucarate aldolase

Query= SwissProt::P23522
         (256 letters)



>FitnessBrowser__Koxy:BWI76_RS24830
          Length = 256

 Score =  476 bits (1225), Expect = e-139
 Identities = 239/256 (93%), Positives = 247/256 (96%)

Query: 1   MNNDVFPNKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIP 60
           MNND+FPNKFKAALAA QVQIGCWSAL++PISTEVLGLAGFDWLVLDGEHAPNDISTFIP
Sbjct: 1   MNNDIFPNKFKAALAAHQVQIGCWSALASPISTEVLGLAGFDWLVLDGEHAPNDISTFIP 60

Query: 61  QLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGI 120
           QLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVET+E+A  AVASTRYPPEGI
Sbjct: 61  QLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETEEQAVNAVASTRYPPEGI 120

Query: 121 RGVSVSHRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDL 180
           RGVSVSHRANMFGTV DYFAQSNKNITILVQIESQQGVDNVDAIAAT GVDGIFVGPSDL
Sbjct: 121 RGVSVSHRANMFGTVPDYFAQSNKNITILVQIESQQGVDNVDAIAATPGVDGIFVGPSDL 180

Query: 181 AAALGHLGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDL 240
           AAALGHLGNASHP+VQ+AIQHIF  A  HGKPSGILAPVEADARRYLEWGATFVAVGSDL
Sbjct: 181 AAALGHLGNASHPEVQEAIQHIFASAKKHGKPSGILAPVEADARRYLEWGATFVAVGSDL 240

Query: 241 GVFRSATQKLADTFKK 256
           GVFRSATQKLAD+FKK
Sbjct: 241 GVFRSATQKLADSFKK 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: 330
Number of extensions: 4
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 BWI76_RS24830 BWI76_RS24830 (5-keto-4-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.26260.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                               -----------
   4.1e-149  481.0   0.1   4.6e-149  480.8   0.1    1.0  1  lcl|FitnessBrowser__Koxy:BWI76_RS24830  BWI76_RS24830 5-keto-4-deoxy-D-g


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS24830  BWI76_RS24830 5-keto-4-deoxy-D-glucarate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.8   0.1  4.6e-149  4.6e-149       1     249 []       8     256 .]       8     256 .] 1.00

  Alignments for each domain:
  == domain 1  score: 480.8 bits;  conditional E-value: 4.6e-149
                               TIGR03239   1 nrfrqkllarktliglwsalgnpitaevlglagfdwllldgehapndvltlipqlmalkdsasapvvrvpl 71 
                                             n+f+++l+a++++ig+wsal++pi++evlglagfdwl+ldgehapnd++t+ipqlmalk+sasapvvrvp+
  lcl|FitnessBrowser__Koxy:BWI76_RS24830   8 NKFKAALAAHQVQIGCWSALASPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKGSASAPVVRVPT 78 
                                             8********************************************************************** PP

                               TIGR03239  72 nepviikrlldigfynllipfvesaeeaeravaatryppegirgvsvaqrsnrygtvadyfkkindnitvl 142
                                             nepviikrlldigfyn+lipfve++e+a +ava+tryppegirgvsv++r+n++gtv+dyf+++n+nit+l
  lcl|FitnessBrowser__Koxy:BWI76_RS24830  79 NEPVIIKRLLDIGFYNFLIPFVETEEQAVNAVASTRYPPEGIRGVSVSHRANMFGTVPDYFAQSNKNITIL 149
                                             *********************************************************************** PP

                               TIGR03239 143 vqiesrkgvdavdeiaavdgvdgvfvgpsdlaaalgylgnpnhpdvqkairhifdraaahgkavgilapve 213
                                             vqies++gvd+vd+iaa++gvdg+fvgpsdlaaalg+lgn++hp+vq+ai+hif++a++hgk++gilapve
  lcl|FitnessBrowser__Koxy:BWI76_RS24830 150 VQIESQQGVDNVDAIAATPGVDGIFVGPSDLAAALGHLGNASHPEVQEAIQHIFASAKKHGKPSGILAPVE 220
                                             *********************************************************************** PP

                               TIGR03239 214 adarrylelgatfvavgsdlgvfrsatkalsekfkk 249
                                             adarryle+gatfvavgsdlgvfrsat++l++ fkk
  lcl|FitnessBrowser__Koxy:BWI76_RS24830 221 ADARRYLEWGATFVAVGSDLGVFRSATQKLADSFKK 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 6.94
//
[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