GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA5 in Methylocapsa aurea KYG

Align 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized)
to candidate WP_036258924.1 DL86_RS05195 acetoacetyl-CoA reductase

Query= SwissProt::Q1NEI6
         (249 letters)



>NCBI__GCF_000746085.1:WP_036258924.1
          Length = 241

 Score =  145 bits (366), Expect = 7e-40
 Identities = 92/237 (38%), Positives = 132/237 (55%), Gaps = 2/237 (0%)

Query: 11  RCAIVTGGASGLGKQVAARIIAEGGAVALWDLNGDALAATQAEIDATHVVALDVSDHAAV 70
           R A+V+GG+ G+G  ++  + A G  VA      D  AA         V   DVS++   
Sbjct: 3   RVAVVSGGSRGIGAAISKGLHAAGYKVAATYAGNDEAAANFKAETGIPVYKWDVSNYKEC 62

Query: 71  AAAAKDSAAALGKVDILICSAGITGATVPVWEFPVDSFQRVIDINLNGLFYCNREVVPFM 130
           A   K     LG ++ILI +AGIT  T+     P   F  VI+ NLN LF   R V+  M
Sbjct: 63  AEGLKKVGDDLGPIEILINNAGITRDTMFHKMTPEQWFD-VINTNLNSLFNMTRPVIEGM 121

Query: 131 LENGYGRIVNLASVAGKEGNPNASAYSASKAGVIGFTKSLGKELAGKGVIANALTPATFE 190
            E G+GRIVN++S+ G++G    + Y+ASKAG IGFTKSL +E AGKG+  NA+ P    
Sbjct: 122 RERGFGRIVNISSINGQKGQMGQTNYTASKAGDIGFTKSLAQENAGKGITVNAVCPGYIA 181

Query: 191 SPILDQLPQSQVD-YMRSKIPMGRLGLVEESAAMVCFMASEECSFTTASTFDTSGGR 246
           + ++  +P+  ++  +   IP+ RLG  EE A +V F+ +EE  F T ST   +GG+
Sbjct: 182 TDMVKAVPKEVLEKSVLPLIPLRRLGEPEEVARVVVFLVAEESGFITGSTLSVNGGQ 238


Lambda     K      H
   0.318    0.132    0.381 

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: 151
Number of extensions: 4
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: 249
Length of database: 241
Length adjustment: 24
Effective length of query: 225
Effective length of database: 217
Effective search space:    48825
Effective search space used:    48825
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: 46 (22.3 bits)

This GapMind analysis is from Apr 09 2024. 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