GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Sphingomonas koreensis DSMZ 15582

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 Ga0059261_1625 Ga0059261_1625 2-keto-3-deoxy-6-phosphogluconate aldolase

Query= SwissProt::Q6BF16
         (205 letters)



>FitnessBrowser__Korea:Ga0059261_1625
          Length = 208

 Score =  180 bits (457), Expect = 1e-50
 Identities = 95/192 (49%), Positives = 123/192 (64%)

Query: 8   PLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTV 67
           PLIAILRG+ P E  A   A+ DAGF  +E+PLNSP   +SI  +    GD+A++G GTV
Sbjct: 15  PLIAILRGVKPGEVEAIGDALADAGFTLIEVPLNSPDPFESITRLARRLGDRAMVGGGTV 74

Query: 68  LKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALKI 127
           L+  +V A+A    +LIV+PN    VI     +G+   PG AT TEAF AL+AGA ALK+
Sbjct: 75  LREAEVTAVAESAGRLIVSPNASPAVIAATAAHGLISLPGIATPTEAFAALDAGATALKL 134

Query: 128 FPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVE 187
           FP+ A  P  +KA++AVLP    V  VGG+TP+ +  W DAG +G GLGS LYR G S  
Sbjct: 135 FPAEAASPVALKAMRAVLPVATRVLPVGGITPDTIQPWRDAGASGFGLGSALYRPGFSAA 194

Query: 188 RTAQQAAAFVKA 199
               +AAAFV+A
Sbjct: 195 EVGARAAAFVRA 206


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: 164
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: 205
Length of database: 208
Length adjustment: 21
Effective length of query: 184
Effective length of database: 187
Effective search space:    34408
Effective search space used:    34408
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