GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Pedobacter sp. GW460-11-11-14-LB5

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate CA265_RS08355 CA265_RS08355 short-chain dehydrogenase

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__Pedo557:CA265_RS08355
          Length = 254

 Score =  119 bits (299), Expect = 5e-32
 Identities = 79/255 (30%), Positives = 126/255 (49%), Gaps = 13/255 (5%)

Query: 8   KVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVCDVTS 67
           K  +VTG G  IG A A  LA++G  + ++++  E  +     ++  G  A SY CDV+ 
Sbjct: 7   KKAVVTGGGSGIGKAIATILAKQGAEVHIIELGTEHAQDTLDEIKTNGGVAFSYGCDVSD 66

Query: 68  EEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLKAV 127
            +AV     +V  + G I+ L NNAG              DF RV+ +NV G ++ L A 
Sbjct: 67  HQAVA----AVFNEIGNINILINNAGI-AHIGKADTTDEADFDRVMRVNVKGVYNCLHAA 121

Query: 128 SRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAISP 187
             Q+     G I+N AS+A + G P+   Y  +KGA+ A+T + A D    NIR N+ISP
Sbjct: 122 IPQIRLSGGGVIINMASIAALIGLPDRFVYSAAKGAVKAITMSVAKDYIGENIRCNSISP 181

Query: 188 GYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLLGD 247
             +   F       +   +   Y    P++  +++  + P+ R     E+  +  +L  D
Sbjct: 182 ARVHTPF-------VDGFLQKNYPDNIPEMF-EKLSKTQPIGRMAKPEEVGALALYLCSD 233

Query: 248 DSSFMTGVNLPIAGG 262
           ++SF+TG + PI GG
Sbjct: 234 EASFITGCDYPIDGG 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: 175
Number of extensions: 6
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: 254
Length adjustment: 24
Effective length of query: 238
Effective length of database: 230
Effective search space:    54740
Effective search space used:    54740
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