GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Bacteroides thetaiotaomicron VPI-5482

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__Btheta:351439
          Length = 259

 Score =  116 bits (291), Expect = 4e-31
 Identities = 74/263 (28%), Positives = 122/263 (46%), Gaps = 19/263 (7%)

Query: 3   KKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYV 62
           K+F  KV ++TGA G IG AT  R+  EG  + + D+++E  +K  A + + G + R   
Sbjct: 2   KRFENKVVVITGAAGGIGEATTRRIVSEGGKVVIADLSQERADKLAAELTQAGADVRPIY 61

Query: 63  CDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAP--VQDYPSDDFARVLTINVTGA 120
              T  ++    VD  ++++G+ID L NN G         ++    D F  V  +N+   
Sbjct: 62  FSATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCCT 121

Query: 121 FHVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNI 180
            ++ + V   M T   G IVN AS++G+    N   YG SK  +I LT+  A  +   NI
Sbjct: 122 MYLSQQVIPIMTTHGGGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKNI 181

Query: 181 RVNAISPG-YMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239
           R NA++PG  + P  +     E                V    +G       G+  ++  
Sbjct: 182 RCNAVAPGLVLTPAALDNLNEE----------------VRNIFLGQCATPYLGEPEDVAA 225

Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262
            +AFL  +D+ ++TG  + + GG
Sbjct: 226 TIAFLASNDARYITGQTIVVDGG 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: 158
Number of extensions: 7
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: 259
Length adjustment: 25
Effective length of query: 237
Effective length of database: 234
Effective search space:    55458
Effective search space used:    55458
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 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