GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Phaeobacter inhibens BS107

Align 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; 2-oxo-3-deoxygalactonate 6-phosphate aldolase; 6-phospho-2-dehydro-3-deoxygalactonate aldolase; 6-phospho-2-keto-3-deoxygalactonate aldolase; KDPGal; EC 4.1.2.21 (characterized)
to candidate GFF720 PGA1_c07350 2-dehydro-3-deoxy-6-phosphogalactonate aldolase DgoA

Query= SwissProt::Q6BF16
         (205 letters)



>FitnessBrowser__Phaeo:GFF720
          Length = 203

 Score =  171 bits (433), Expect = 8e-48
 Identities = 93/195 (47%), Positives = 123/195 (63%)

Query: 9   LIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTVL 68
           +IAILRG+  +EA A   A+I AG   +E+PLNSP    SI A++D    +A +GAGTVL
Sbjct: 5   IIAILRGLRSEEARAMTDALIAAGITKIEVPLNSPLPYDSIAAMLDQAKGRATVGAGTVL 64

Query: 69  KPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALKIF 128
             + V  L+ MG Q++++P+ + +VIR A   GM   PG  TA+E F+AL AGA  LK F
Sbjct: 65  NTDAVAQLSAMGAQMVISPDCNPDVIRAAKAAGMLSYPGVFTASECFSALRAGADGLKFF 124

Query: 129 PSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVER 188
           P+   G     ALKAVLP+D   +AVGGV P + A W  AG  G G+GS LY+ G++VE 
Sbjct: 125 PAFKLGLDGFSALKAVLPADAETYAVGGVGPADFADWQKAGITGFGIGSSLYKPGRTVED 184

Query: 189 TAQQAAAFVKAYREA 203
            A+ AA  V AY EA
Sbjct: 185 VARLAAETVAAYDEA 199


Lambda     K      H
   0.319    0.134    0.399 

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: 121
Number of extensions: 6
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: 205
Length of database: 203
Length adjustment: 21
Effective length of query: 184
Effective length of database: 182
Effective search space:    33488
Effective search space used:    33488
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 (21.8 bits)
S2: 45 (21.9 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