GapMind for catabolism of small carbon sources

 

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

Align Sorbitol dehydrogenase; SDH; EC 1.1.1.-; Glucitol dehydrogenase; L-iditol 2-dehydrogenase; EC 1.1.1.14; Polyol dehydrogenase; Xylitol dehydrogenase; EC 1.1.1.9 (uncharacterized)
to candidate 353143 BT3617 sorbitol dehydrogenase (NCBI ptt file)

Query= curated2:Q9Z9U1
         (343 letters)



>FitnessBrowser__Btheta:353143
          Length = 338

 Score =  179 bits (454), Expect = 9e-50
 Identities = 109/322 (33%), Positives = 177/322 (54%), Gaps = 12/322 (3%)

Query: 16  VQEKPEPTPGKHQVKIKVKYTGVCGSDIHTYEGHYP-VAAPVTLGHEFSGEIVELGEGV- 73
           V E  +PT G  +V +++KY G CGSD++T+ G  P V  PV  GHE    I E+G  V 
Sbjct: 14  VVELEKPTVGAGEVLVRIKYVGFCGSDLNTFLGRNPMVKLPVIPGHEVGAVIEEIGPDVP 73

Query: 74  TGFNVGDRVTSETTYSICGKCSYCTSGDYNLCSHRKGLGNQQDGSFAKYVIARQESLHHL 133
            GF  G  VT    Y+ CGKC+ C +G  N C H + LG Q++G   +Y +     +  +
Sbjct: 74  AGFEKGMNVTLNP-YTNCGKCASCRNGRVNACEHNETLGVQRNGVMCEYAVLPWTKI--I 130

Query: 134 PAG-VDDRSAAMTEPLACTHHAIAKTSINKGDLVVVTGPGPIGLLAAQVAKSHGGTVIIT 192
           PAG +  R  A+ EP++   HA+++  +   + V+V G G IG+ A   A   G TVI  
Sbjct: 131 PAGNISSRDCALIEPMSVGFHAVSRAQVIDNEYVMVIGCGMIGIGAIVRAALRGATVIAV 190

Query: 193 GLSNDQVRLKKAKEVGIDYAIDTQEVDIKELVSELTDGYGADVVLECSGAVPAAKQGIDL 252
            L ++++ L  AK VG  YA++++  ++ E + E+T G+GADVV+E  G+       +D 
Sbjct: 191 DLDDEKLVL--AKRVGASYAVNSKTENVHERIQEITAGFGADVVIEAVGSPVTYVMAVDE 248

Query: 253 LRKKGQYAQVGLFAQPEIQFNFEKIIQKEISVVGSRSQKPADWEPALSLLNEKKVNAKTL 312
           +   G+   +G +A+ E+ F  +  +QKE+ + GSR+  PAD+   ++ + E K   + L
Sbjct: 249 VGFTGRVVCIG-YAKKEVAFQTKYFVQKELDIRGSRNALPADFRAVINYMKEGKCPVEEL 307

Query: 313 VTHEYTISEWDKAYHAIKSGEA 334
           ++    I++ + A  A+K   A
Sbjct: 308 IS---KIAKPEDALEAMKEWAA 326


Lambda     K      H
   0.315    0.133    0.388 

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: 313
Number of extensions: 22
Number of successful extensions: 6
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: 343
Length of database: 338
Length adjustment: 28
Effective length of query: 315
Effective length of database: 310
Effective search space:    97650
Effective search space used:    97650
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: 42 (22.0 bits)
S2: 49 (23.5 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