GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdh in Lactobacillus shenzhenensis LY-73

Align L-iditol 2-dehydrogenase (EC 1.1.1.14) (characterized)
to candidate WP_022529592.1 L248_RS07685 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= BRENDA::Q1J2J0
         (255 letters)



>NCBI__GCF_000469325.1:WP_022529592.1
          Length = 273

 Score =  134 bits (337), Expect = 2e-36
 Identities = 80/250 (32%), Positives = 125/250 (50%), Gaps = 11/250 (4%)

Query: 14  FRLDGRHALVTGGAQGIGFEIARGLAQAGARVTIADLNPDVGEGAARELDGTFERLNVTD 73
           + L G+ A++TGG  G+G   A  +A+AGA + I     D  +   R ++    ++   D
Sbjct: 25  YSLAGKVAVITGGNTGLGQGYAVAMAEAGADIFIPTFGKDEWDNTRRLIEKRGRKVEFMD 84

Query: 74  AD---------AVADLARRLPDVDVLVNNAGIVRNAPAEDTPDDDWRAVLSVNLDGVFWC 124
            +          VA+   ++  +D+LVNNAG++R  P  ++ D DW  V+++NL  V+  
Sbjct: 85  VNLTEPGITDKVVAEAVEKMGHIDILVNNAGMIRRNPLLESKDKDWDQVIAINLTAVYHM 144

Query: 125 CREFGRTMLARGRGAIVSTASMSGLISNHPQPQAAYNASKAAVIHLTRSLAGEWASRGVR 184
                +    +  G I++  SM         P  +Y ASK  V  LT++ A E  +  V+
Sbjct: 145 SLSAAKVFAKQKHGKIINIGSMLSFQGGKFIP--SYTASKHGVAGLTKAFASEMGAYNVQ 202

Query: 185 VNAVAPGYTATPLTRRGLETPEWRETWLKETPLGRLAEPREIAPAVLYLASDAASFVTGH 244
           VNA+APGY  T  T      P   +  L   P G  A+P E+    ++LASDAAS++ G 
Sbjct: 203 VNAIAPGYIKTANTAPIRRDPARNKEILDRIPAGHWADPSELMGVAVFLASDAASYINGA 262

Query: 245 TLVVDGGYTV 254
            + VDGGY V
Sbjct: 263 IIPVDGGYLV 272


Lambda     K      H
   0.319    0.134    0.408 

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: 170
Number of extensions: 9
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: 255
Length of database: 273
Length adjustment: 25
Effective length of query: 230
Effective length of database: 248
Effective search space:    57040
Effective search space used:    57040
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 (21.8 bits)
S2: 47 (22.7 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