GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Escherichia coli BW25113

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate 17191 b3117 threonine dehydratase (NCBI)

Query= BRENDA::O59791
         (323 letters)



>FitnessBrowser__Keio:17191
          Length = 329

 Score =  228 bits (582), Expect = 1e-64
 Identities = 123/308 (39%), Positives = 184/308 (59%), Gaps = 2/308 (0%)

Query: 11  DDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNE 70
           DD+  A +R+     KT +  S+  ++    E+F K EN Q+ G+FK RGA N LS L +
Sbjct: 12  DDIIEAKQRLAGRIYKTGMPRSNYFSERCKGEIFLKFENMQRTGSFKIRGAFNKLSSLTD 71

Query: 71  AQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYK 130
           A+++ GV+  S+GNHAQ ++LS  +LGI  K++MP  AP++KVAAT  Y  +V+++    
Sbjct: 72  AEKRKGVVACSAGNHAQGVSLSCAMLGIDGKVVMPKGAPKSKVAATCDYSAEVVLHGDNF 131

Query: 131 DDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGGLLSG 190
           +D      EI E EG   IPPYD P V+AGQGT   E+ E++  +D + V +GGGGL++G
Sbjct: 132 NDTIAKVSEIVEMEGRIFIPPYDDPKVIAGQGTIGLEIMEDLYDVDNVIVPIGGGGLIAG 191

Query: 191 SALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLGNYTFSII 250
            A+A +   P   V GV+ E  +    SF  G I    T  T+ADG      GN T+ I+
Sbjct: 192 IAVAIKSINPTIRVIGVQSENVHGMAASFHSGEITTHRTTGTLADGCDVSRPGNLTYEIV 251

Query: 251 KEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMK--EKLKNKRIGIIIS 308
           +E VDDI+ VS++E+ + +     R K+V E  G L+ AA  + K  + ++N++   IIS
Sbjct: 252 RELVDDIVLVSEDEIRNSMIALIQRNKVVTEGAGALACAALLSGKLDQYIQNRKTVSIIS 311

Query: 309 GGNVDIER 316
           GGN+D+ R
Sbjct: 312 GGNIDLSR 319


Lambda     K      H
   0.318    0.135    0.384 

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: 243
Number of extensions: 9
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: 323
Length of database: 329
Length adjustment: 28
Effective length of query: 295
Effective length of database: 301
Effective search space:    88795
Effective search space used:    88795
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: 48 (23.1 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