GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Salinicoccus carnicancri Crm

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_017547471.1 C792_RS0100470 SDR family oxidoreductase

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_000330705.1:WP_017547471.1
          Length = 252

 Score =  152 bits (383), Expect = 9e-42
 Identities = 88/255 (34%), Positives = 133/255 (52%), Gaps = 10/255 (3%)

Query: 8   KVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVTS 67
           K+ L+TG  G IG A A    + G  + L+D+  ++L  A+ ++    +E    V DVT 
Sbjct: 4   KIVLITGGAGGIGQAIAKEHLDNGNTVVLVDLKEDSLNIAKENLGGNNIEI--IVGDVTD 61

Query: 68  EEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKAV 127
           E  V   VD  V  F ++D  +NNAG  G F P++D   ++F +++ IN TG F  LK V
Sbjct: 62  EGDVKNYVDKTVEKFSRVDIFYNNAGVNGPFKPIKDLDKNEFEKIMAINTTGVFLGLKFV 121

Query: 128 SRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAISP 187
             QM  Q +G +VNTAS A   G   M  Y  SK A+  LT+TAAL++   NIRVNAI+P
Sbjct: 122 LPQMEKQGFGNVVNTASNAAYIGSAGMPGYIASKHAVAGLTKTAALEVGDKNIRVNAIAP 181

Query: 188 GYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLGD 247
             +          ++   + +     +P+   + +   +P  R+G   E+  V  FL  +
Sbjct: 182 AAI--------DTDMLTDIRNNLSPGEPEKSGEALKQGIPFGRFGTPAEVAKVAYFLGSE 233

Query: 248 DSSFMTGVNLPIAGG 262
           D+SF+TG    + GG
Sbjct: 234 DASFVTGSLYNVDGG 248


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: 193
Number of extensions: 13
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: 262
Length of database: 252
Length adjustment: 24
Effective length of query: 238
Effective length of database: 228
Effective search space:    54264
Effective search space used:    54264
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: 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