GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Synechococcus elongatus PCC 7942

Align KHG/KDPG aldolase; EC 4.1.3.16; EC 4.1.2.14 (characterized)
to candidate Synpcc7942_0017 Synpcc7942_0017 keto-hydroxyglutarate-aldolase/keto-deoxy- phosphogluconate aldolase

Query= SwissProt::P50846
         (196 letters)



>FitnessBrowser__SynE:Synpcc7942_0017
          Length = 187

 Score =  116 bits (291), Expect = 2e-31
 Identities = 68/175 (38%), Positives = 102/175 (58%), Gaps = 2/175 (1%)

Query: 10  LKEAKLIAVIRSKDKQEACQQIESLLDKGIRAVEVTYTTPGASDIIESFRNR-EDILIGA 68
           L++A+++AV+RS D  +     E+ + +G+R +EVT+T+   ++++   R++  D   GA
Sbjct: 9   LQQARIVAVLRSPDLTQGFAMAETAIARGLRWLEVTWTSDRPAELLSQLRDKYPDCCWGA 68

Query: 69  GTVISAQQAGEAAKAGAQFIVSPGFSADLAEHLSFVKTHYIPGVLTPSEIMEALTFGFTT 128
           G+++S     EA  AGAQF VSP  S  L E        ++PG LTP+EIM A   G   
Sbjct: 69  GSLLSLTDLEEAIAAGAQFGVSPILSLPLLERAQARDLPFLPGALTPTEIMTAHAAGAAV 128

Query: 129 LKLFPSGVFGIP-FMKNLAGPFPQVTFIPTGGIHPSEVPDWLRAGAGAVGVGSQL 182
           +KLFP+   G P ++++L  P         GGIHP  V  +L AGA AVG+GSQL
Sbjct: 129 VKLFPASSAGGPAYVRSLQQPLNHPKLFACGGIHPDAVQSYLDAGAIAVGLGSQL 183


Lambda     K      H
   0.318    0.135    0.386 

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: 108
Number of extensions: 8
Number of successful extensions: 3
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: 196
Length of database: 187
Length adjustment: 20
Effective length of query: 176
Effective length of database: 167
Effective search space:    29392
Effective search space used:    29392
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: 44 (21.6 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