GapMind for catabolism of small carbon sources

 

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

Align sorbitol dehydrogenase, D-fructose forming (EC 1.1.1.14) (characterized)
to candidate 351439 BT1911 7-alpha-hydroxysteroid dehydrogenase (NCBI ptt file)

Query= reanno::BFirm:BPHYT_RS16120
         (260 letters)



>FitnessBrowser__Btheta:351439
          Length = 259

 Score =  127 bits (319), Expect = 2e-34
 Identities = 92/258 (35%), Positives = 133/258 (51%), Gaps = 17/258 (6%)

Query: 4   RLQDKVAILTGAASGIGEAVARRYLDEGARCVLVDV--KPADSFGDSLRATYGDRVLTVS 61
           R ++KV ++TGAA GIGEA  RR + EG + V+ D+  + AD     L     D V  + 
Sbjct: 3   RFENKVVVITGAAGGIGEATTRRIVSEGGKVVIADLSQERADKLAAELTQAGAD-VRPIY 61

Query: 62  ADVTRRDDIQRIVASTLERFGQIDILFNNAALFD-MRPILEESWDV--FDRLFAVNVKGM 118
              T     + +V   ++ +GQID+L NN    D  R +  E  D+  FD +F +N+   
Sbjct: 62  FSATELQSCKELVDFAMKEYGQIDVLINNVGGTDPKRDLNIEKLDIDYFDEVFHLNLCCT 121

Query: 119 FFLMQAVAQKMVEQGCGGKIINMSSQAGRRGEALVSHYCATKAAVLSYTQSAALALAPHK 178
            +L Q V   M   G GG I+N++S +G   +A  + Y A+KA V++ T+  A  +    
Sbjct: 122 MYLSQQVIPIMTTHG-GGNIVNVASISGLTADANGTLYGASKAGVINLTKYIATQMGKKN 180

Query: 179 INVNGIAPGVVDTPMWNEVDALFARYENRPLGEKKRLVGEAVPLGRMGVPDDLTGAALFL 238
           I  N +APG+V TP    +D L     N  LG+       A P   +G P+D+     FL
Sbjct: 181 IRCNAVAPGLVLTPA--ALDNLNEEVRNIFLGQC------ATPY--LGEPEDVAATIAFL 230

Query: 239 ASADADYITAQTLNVDGG 256
           AS DA YIT QT+ VDGG
Sbjct: 231 ASNDARYITGQTIVVDGG 248


Lambda     K      H
   0.321    0.135    0.393 

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: 180
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: 260
Length of database: 259
Length adjustment: 24
Effective length of query: 236
Effective length of database: 235
Effective search space:    55460
Effective search space used:    55460
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 (21.9 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