GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Sinorhizobium meliloti 1021

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 SMc00882 SMc00882 2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Query= SwissProt::Q6BF16
         (205 letters)



>FitnessBrowser__Smeli:SMc00882
          Length = 212

 Score =  170 bits (431), Expect = 2e-47
 Identities = 96/193 (49%), Positives = 118/193 (61%)

Query: 8   PLIAILRGITPDEALAHVGAVIDAGFDAVEIPLNSPQWEQSIPAIVDAYGDKALIGAGTV 67
           PLIAILRG+ P+EA   VGA+I+ GF A+EIPLNSP   +SI   V       LIGAGTV
Sbjct: 12  PLIAILRGLKPEEAEGVVGALIETGFTAIEIPLNSPDPFRSIETAVKMAPAGCLIGAGTV 71

Query: 68  LKPEQVDALARMGCQLIVTPNIHSEVIRRAVGYGMTVCPGCATATEAFTALEAGAQALKI 127
           L   QV+ LA +G +L+V+PN+   VIR A   GM   PG  T TEA  A  AGA  LK 
Sbjct: 72  LTTAQVERLADVGGRLMVSPNVEPAVIRLAATKGMVTMPGVFTPTEALAAAAAGASGLKF 131

Query: 128 FPSSAFGPQYIKALKAVLPSDIAVFAVGGVTPENLAQWIDAGCAGAGLGSDLYRAGQSVE 187
           FP+S  GP  I A++AVLP D+ + AVGGV+  N A +   G    GLGS LY+ G S  
Sbjct: 132 FPASVLGPSGITAIRAVLPGDLEIAAVGGVSEVNFADYAAIGIRSFGLGSSLYKPGMSAG 191

Query: 188 RTAQQAAAFVKAY 200
              Q+A A + AY
Sbjct: 192 DVRQRAIATLAAY 204


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: 139
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: 205
Length of database: 212
Length adjustment: 21
Effective length of query: 184
Effective length of database: 191
Effective search space:    35144
Effective search space used:    35144
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