GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Acidovorax sp. GW101-3H11

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2257
          Length = 267

 Score =  135 bits (341), Expect = 7e-37
 Identities = 97/257 (37%), Positives = 137/257 (53%), Gaps = 21/257 (8%)

Query: 7   GKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYV-CDV 65
           G+VC+VTG    IG A   R A EG    ++D++     + +A   E G     YV CDV
Sbjct: 20  GRVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDA---RGQALAAELGA---LYVRCDV 73

Query: 66  TSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVLK 125
             +  V   V  V+   G+ID L NNAG   A A   +    DF  VL +N+ G+F V +
Sbjct: 74  GDKAQVDALVAQVLAAHGRIDVLVNNAGIFRA-ADFLEVTEADFDAVLRVNLKGSFLVGQ 132

Query: 126 AVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNAI 185
           AV+R M+T   G IVN +S+ GV   PN+A+Y  SKG +  LT   AL LA  NIRVNA+
Sbjct: 133 AVARAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNAV 192

Query: 186 SPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAFLL 245
           +PG +          EL AK      ++D     ++++   PM+R G  +EI  VVA+L 
Sbjct: 193 APGTIA--------TELAAKA---VLTSDE--AKRKIMSRTPMKRLGQPSEIADVVAWLA 239

Query: 246 GDDSSFMTGVNLPIAGG 262
            D +S++TG  + + GG
Sbjct: 240 SDAASYVTGEIVTVDGG 256


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: 170
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: 262
Length of database: 267
Length adjustment: 25
Effective length of query: 237
Effective length of database: 242
Effective search space:    57354
Effective search space used:    57354
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