GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgA in Streptacidiphilus oryzae TH49

Align 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16; EC 4.1.2.55) (characterized)
to candidate WP_037582103.1 BS73_RS31540 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase

Query= metacyc::MONOMER-4906
         (205 letters)



>NCBI__GCF_000744815.1:WP_037582103.1
          Length = 204

 Score =  134 bits (336), Expect = 2e-36
 Identities = 69/193 (35%), Positives = 114/193 (59%), Gaps = 7/193 (3%)

Query: 11  KIVAVLRANSVEEAKEKALAVFEGGVHLIEITFTVPDADTVIKELSFLK-EKGAIIGAGT 69
           +++ V+RA  + +A     A+ EGG+  +E+TFT PD    ++  + +  E G  IGAGT
Sbjct: 8   RVLTVVRAPRIPDAAALCRALAEGGIRTVELTFTTPDLTGHLRAAAAVAAETGCRIGAGT 67

Query: 70  VTSVEQCRKAVESGAEFIVSPHLDEEISQFCKEKGVFYMPGVMTPTELVKAMKLGHTILK 129
           V +      AV++GAEF+V+P L  E++   +E+GV  + G  TPTE++ A+ LG   +K
Sbjct: 68  VLTAGDAAAAVDAGAEFLVTPGLRPEVAAVGRERGVPVVMGAFTPTEVLTALDLGAAAVK 127

Query: 130 LFPGEVVGPQFVKAMKGPFPNVKFVPTGGVNLDNVCEWFKAGVLAVGVGS------ALVK 183
           +FP   +GP++ K ++GP P+V+ +P+GGVN  N  E+   G +AV  G+      A+  
Sbjct: 128 IFPAHALGPRYFKDLRGPLPDVRLLPSGGVNAGNAGEFLAQGAIAVSAGTDAVPPQAVAS 187

Query: 184 GTPDEVREKAKAF 196
           G   E+  +A+ F
Sbjct: 188 GDWPEITRRAREF 200


Lambda     K      H
   0.318    0.136    0.393 

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: 116
Number of extensions: 4
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: 205
Length of database: 204
Length adjustment: 21
Effective length of query: 184
Effective length of database: 183
Effective search space:    33672
Effective search space used:    33672
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 (21.7 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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