GapMind for catabolism of small carbon sources

 

Alignments for a candidate for garL in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_3931 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase (EC 4.1.2.n4)

Query= SwissProt::P23522
         (256 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3931
          Length = 266

 Score =  224 bits (572), Expect = 1e-63
 Identities = 110/238 (46%), Positives = 152/238 (63%), Gaps = 1/238 (0%)

Query: 8   NKFKAALAAKQVQIGCWSALSNPISTEVLGLAGFDWLVLDGEHAPNDISTFIPQLMALKG 67
           N FKAAL +   Q G W+  +   + E++   G+DW+++DGEHAPN +   + QL A+  
Sbjct: 6   NAFKAALNSSGTQYGIWAGFATGYAAEIVATTGYDWMLIDGEHAPNTVPGVLAQLQAVAP 65

Query: 68  SASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETKEEAELAVASTRYPPEGIRGVSVS- 126
            ++APVVR    +  +IK+LLDIG    +IP VET  +A+  V + RYPP GIRGV    
Sbjct: 66  YSTAPVVRAVNGDANLIKQLLDIGAQTLMIPMVETAAQAQALVRAMRYPPHGIRGVGGGL 125

Query: 127 HRANMFGTVADYFAQSNKNITILVQIESQQGVDNVDAIAATEGVDGIFVGPSDLAAALGH 186
            RA  +  V DY   +++ + ++VQ+ES+ GV+NV AIAA EGVD +F+GP+DL+  LGH
Sbjct: 126 TRATRWDDVPDYLNTAHEQLCLIVQVESRTGVENVAAIAAVEGVDAVFIGPADLSIGLGH 185

Query: 187 LGNASHPDVQKAIQHIFNRASAHGKPSGILAPVEADARRYLEWGATFVAVGSDLGVFR 244
            GN  HP+VQ+ IQ+  N   A GK  GILAP E DARRY  WG  F+AV  D+ + R
Sbjct: 186 AGNPGHPEVQERIQYAVNATLAAGKACGILAPNEEDARRYQRWGCQFIAVAIDISLLR 243


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: 192
Number of extensions: 3
Number of successful extensions: 2
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)

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