GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gyaR in Sinorhizobium meliloti 1021

Align glyoxylate reductase (EC 1.1.1.26); 4-hydroxybutyrate dehydrogenase (EC 1.1.1.61); glyoxylate reductase (NADP+) (EC 1.1.1.79) (characterized)
to candidate SM_b20679 SM_b20679 tartronate semialdehyde reductase

Query= BRENDA::Q9LSV0
         (289 letters)



>FitnessBrowser__Smeli:SM_b20679
          Length = 294

 Score =  145 bits (366), Expect = 1e-39
 Identities = 86/283 (30%), Positives = 143/283 (50%)

Query: 3   VGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIA 62
           +GF+GLGIMG  M+ +L   G ++      +    ELVE+G  + E+P  + +     I 
Sbjct: 4   IGFIGLGIMGTPMARHLQDAGHEIITSKFVIPPRQELVENGLEIVETPKALAETVDTIIL 63

Query: 63  MLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSG 122
           ML D      V+F + GV   + EGK  IDMS++    + +  + +   G  +++ PVSG
Sbjct: 64  MLPDTPEVKDVLFGENGVYYGLGEGKLVIDMSSISPIETKEFAKKVRETGAEYIDAPVSG 123

Query: 123 SKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMN 182
            +  A++  L I+A G  + FE ++P F ++GK    +G  G+G   K+   +I+   + 
Sbjct: 124 GEVGAKNASLSIMAGGKPSSFERALPLFKLMGKNITLVGDCGDGQVTKVANQIIVALTIE 183

Query: 183 AFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMRL 242
           A SE LV A K+G     + + L  G  ++ + +  G  M K ++ P F +   QKD+ L
Sbjct: 184 AVSEALVFASKAGADPARVREALMGGFASSRILEVHGDRMIKRTFEPGFRISLHQKDLNL 243

Query: 243 ALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVK 285
           AL       +S+P  AA  E F    + G   LD S ++ A++
Sbjct: 244 ALQGAKSLGISLPNTAATQELFNNCAANGDSGLDHSGLVRALE 286


Lambda     K      H
   0.317    0.134    0.379 

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: 205
Number of extensions: 7
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: 289
Length of database: 294
Length adjustment: 26
Effective length of query: 263
Effective length of database: 268
Effective search space:    70484
Effective search space used:    70484
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 (21.6 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