GapMind for catabolism of small carbon sources

 

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

Align NADPH-dependent D-xylose reductase; XR; EC 1.1.1.307 (characterized)
to candidate 350911 BT1383 oxidoreductase, aldo/keto reductase (NCBI ptt file)

Query= SwissProt::Q8X195
         (321 letters)



>FitnessBrowser__Btheta:350911
          Length = 278

 Score =  148 bits (373), Expect = 2e-40
 Identities = 101/295 (34%), Positives = 148/295 (50%), Gaps = 43/295 (14%)

Query: 8   LNNGLKMPQIGFGCWKVDNATCAETIYEAIKVGYRLFDGAMDYGNEKEVGEGVNKAIKDG 67
           LNNG++MP +G+G ++V    C   + +AI VGYR  D A  Y NE    EGV  A++  
Sbjct: 6   LNNGVEMPILGYGVYQVTPEECERCVLDAISVGYRSIDTAQAYYNE----EGVGNAVRKC 61

Query: 68  LVKREELFIVSKLWNNFHHPDSVKLAIKKVLSDLNLEYIDLFYMHFPIAQKFVPIEKKYP 127
            V REELFI +K+W +    +  K +I + L  L  +Y+DL  +H P             
Sbjct: 62  GVPREELFITTKVWISNGGYEKAKASIDESLRKLQSDYVDLLLIHQPF------------ 109

Query: 128 PNFYCGDGDKWSFEDVPLLTTWRAMEELVEEGLVKSIGISNFVGALIQDLLRGCKIRPAV 187
            N Y G              T+RAMEE  + G  ++IG+SNF      DL   C+I+PAV
Sbjct: 110 -NDYYG--------------TYRAMEEAYKAGKARAIGVSNFYPDRFIDLAEFCEIKPAV 154

Query: 188 LEIEHHPYLVQPRLIEYAKTEGIHVTAYSSFGPQSFVELDHPKVKDCTTLFKHETITSIA 247
            ++E H +  Q +  E  K    + T   S+GP  F E            F +E + +I 
Sbjct: 155 NQVETHVFNQQVKPQEIMKK---YDTKVMSWGP--FAE-------GRNNFFSNEVLKAIG 202

Query: 248 SAHDVPPAKVLLRWATQRGLAVIPKSNKKERLLGNLKINDFDLTEAELEKIEALD 302
             +    A+V LR+  QR + VIPKS +KER++ N  + DF L+  ++E+I  LD
Sbjct: 203 EQYGKSVAQVALRFLIQRDIIVIPKSTRKERMIENFDVFDFTLSVKDMEEIAGLD 257


Lambda     K      H
   0.320    0.139    0.431 

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: 209
Number of extensions: 9
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: 321
Length of database: 278
Length adjustment: 27
Effective length of query: 294
Effective length of database: 251
Effective search space:    73794
Effective search space used:    73794
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 (21.8 bits)
S2: 48 (23.1 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