GapMind for catabolism of small carbon sources

 

Alignments for a candidate for eda in Streptacidiphilus oryzae TH49

Align 2-dehydro-3-deoxy-phosphogluconate aldolase (EC 4.1.2.14) (characterized)
to candidate WP_037582103.1 BS73_RS31540 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase

Query= BRENDA::D4GV57
         (219 letters)



>NCBI__GCF_000744815.1:WP_037582103.1
          Length = 204

 Score =  140 bits (354), Expect = 1e-38
 Identities = 77/201 (38%), Positives = 108/201 (53%)

Query: 10  MQRLADSGVVAVMRGADADTIIDVADALHEGGVTAYEITADNPDAMDLIREVSASFSDNE 69
           M  LA   V+ V+R         +  AL EGG+   E+T   PD    +R  +A  ++  
Sbjct: 1   MDVLAADRVLTVVRAPRIPDAAALCRALAEGGIRTVELTFTTPDLTGHLRAAAAVAAETG 60

Query: 70  AIVGAGTALDAPTANAAIQAGAEFVVGPNFDEGVVETCNRYGTLVAPGIMTPTEATDAYS 129
             +GAGT L A  A AA+ AGAEF+V P     V       G  V  G  TPTE   A  
Sbjct: 61  CRIGAGTVLTAGDAAAAVDAGAEFLVTPGLRPEVAAVGRERGVPVVMGAFTPTEVLTALD 120

Query: 130 AGADLVKVFPASSLGPGHLKSMKGPLPQIPMMPTGGVGLDNAADYIEAGAVVVGAGGALM 189
            GA  VK+FPA +LGP + K ++GPLP + ++P+GGV   NA +++  GA+ V AG   +
Sbjct: 121 LGAAAVKIFPAHALGPRYFKDLRGPLPDVRLLPSGGVNAGNAGEFLAQGAIAVSAGTDAV 180

Query: 190 DDEAIENGDFEAITETAREFS 210
             +A+ +GD+  IT  AREF+
Sbjct: 181 PPQAVASGDWPEITRRAREFT 201


Lambda     K      H
   0.314    0.133    0.374 

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: 125
Number of extensions: 5
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: 219
Length of database: 204
Length adjustment: 21
Effective length of query: 198
Effective length of database: 183
Effective search space:    36234
Effective search space used:    36234
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Sep 24 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