GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Skermanella stibiiresistens SB22

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_037458219.1 N825_RS25105 SDR family oxidoreductase

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_000576635.1:WP_037458219.1
          Length = 249

 Score =  150 bits (379), Expect = 2e-41
 Identities = 90/259 (34%), Positives = 133/259 (51%), Gaps = 19/259 (7%)

Query: 4   KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSYVC 63
           ++ G+  ++TG    IG   A RL  EG ++ L D+N +++ KA A + +K +  +  V 
Sbjct: 6   RYKGRRAVITGGASGIGFGVASRLVAEGASVCLWDVNPDSIAKATAELGDKAMGVQVNVA 65

Query: 64  DVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHV 123
           D  + E         V   G ID L   AG  G    + DYP D + +V+ INV G FH 
Sbjct: 66  DWDTVERA---ASETVAKLGGIDVLVACAGITGPNTTLWDYPVDSWRQVMDINVNGIFHC 122

Query: 124 LKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVN 183
            +AV   M++  YGRIVN AS+AG +G PN +AY TSK A+I LT++   +LA  NI VN
Sbjct: 123 NRAVVPHMMSGGYGRIVNIASVAGKEGNPNASAYSTSKAAVIGLTKSLGKELAKTNITVN 182

Query: 184 AISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAF 243
           A++P                A V +  F    +     M+  +PM R+G + EI  +V +
Sbjct: 183 AVTP----------------AAVKTAIFDQMTQQHIDFMLSKIPMGRFGLVEEITSLVCW 226

Query: 244 LLGDDSSFMTGVNLPIAGG 262
           +  D+ SF TG     +GG
Sbjct: 227 IASDECSFTTGSVFDASGG 245


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: 167
Number of extensions: 10
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: 249
Length adjustment: 24
Effective length of query: 238
Effective length of database: 225
Effective search space:    53550
Effective search space used:    53550
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 24 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