GapMind for catabolism of small carbon sources

 

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

Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate 352759 BT3232 gluconate 5-dehydrogenase (NCBI ptt file)

Query= uniprot:A0A4R8NY47
         (263 letters)



>FitnessBrowser__Btheta:352759
          Length = 267

 Score =  123 bits (308), Expect = 5e-33
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 6/252 (2%)

Query: 16  SLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPRFFPC 75
           SL GK  ++TG   GIG A+  A+  QGA VCF DI  E  +  +A+  +  +    + C
Sbjct: 8   SLKGKVALVTGASYGIGFAIASAYAEQGATVCFNDINQELVDKGMAAYAEKGIKAHGYVC 67

Query: 76  NLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFFCA 135
           ++ +  A++A    IE  +G +DIL+NNA    R    ++  A +   + ++L   F  +
Sbjct: 68  DVTDEPAVQAMVATIEKEVGTIDILVNNAGIIRRVPMHEMEAADFRRVIDIDLNAPFIVS 127

Query: 136 QAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRVNA 195
           +AVLP M +++ G I+N  S+   LG   ++ Y  AK G++ +T  +  ++G   ++ N 
Sbjct: 128 KAVLPAMMKKRAGKIINICSMMSELGRETVSAYAAAKGGLKMLTRNICSEYGEYNIQCNG 187

Query: 196 IIPGAIRTPRQTLLWHTPEEEAK------ILAAQCLPVRVDPHDVAALALFLSSDSGAKC 249
           I PG I TP+   L     + ++      I A       +DP ++   A+FL+S++    
Sbjct: 188 IGPGYIATPQTAPLREKQADGSRHPFDSFICAKTPAGRWLDPEELTGPAVFLASEASNAV 247

Query: 250 TGREYYVDAGWL 261
            G   YVD G L
Sbjct: 248 NGHVLYVDGGIL 259


Lambda     K      H
   0.322    0.137    0.417 

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: 173
Number of extensions: 10
Number of successful extensions: 2
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: 263
Length of database: 267
Length adjustment: 25
Effective length of query: 238
Effective length of database: 242
Effective search space:    57596
Effective search space used:    57596
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