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_017547482.1 C792_RS0100525 SDR family oxidoreductase

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_000330705.1:WP_017547482.1
          Length = 257

 Score =  167 bits (422), Expect = 3e-46
 Identities = 95/263 (36%), Positives = 141/263 (53%), Gaps = 10/263 (3%)

Query: 1   MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60
           MS +F G+V ++TG  G IG  TAL+  +EG  + ++D+N E+L  A   +  +G E  +
Sbjct: 1   MSNRFEGQVVIITGGSGGIGKQTALQFLQEGAKVTIVDINEESLTSAREELSRQG-EVLA 59

Query: 61  YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120
              DV+ E  V   + + V  FGK+D LFNNAG  G    + D   D+F  V  +N+ G 
Sbjct: 60  VQADVSDEADVENYIRATVEKFGKVDVLFNNAGIIGKVGSLVDQEYDNFKAVTGVNMNGV 119

Query: 121 FHVLKAVSRQMITQNY-GRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179
           F  LK   +QMI Q   G I+NT S+   +G P  +AY  +K A++ LT+TAA++ A +N
Sbjct: 120 FLGLKHAIKQMIKQGTPGSIINTGSVDSFRGSPEQSAYSATKHAVVGLTKTAAVEAAGHN 179

Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239
           IRVN+I P  +           + A V       +   V ++    +P+ RY D ++I  
Sbjct: 180 IRVNSIHPAPV--------DTPMMAHVEESRDKKNSASVREKFTSGIPLNRYADSSDIAD 231

Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262
           +V FL  DDS F+TG    I GG
Sbjct: 232 LVLFLASDDSKFVTGSQYSIDGG 254


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: 183
Number of extensions: 14
Number of successful extensions: 4
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: 257
Length adjustment: 24
Effective length of query: 238
Effective length of database: 233
Effective search space:    55454
Effective search space used:    55454
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