GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Sphingomonas indica Dd16

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_085218348.1 B9N75_RS08190 3-hydroxybutyrate dehydrogenase

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_900177405.1:WP_085218348.1
          Length = 261

 Score =  130 bits (328), Expect = 2e-35
 Identities = 82/259 (31%), Positives = 133/259 (51%), Gaps = 9/259 (3%)

Query: 7   GKVCLVTGAGGNIGLATALRLAEEGTAIALLDM-NREALEKAEASVREKGVEARSYV-CD 64
           GK  L+TG+   IGLA A  LA  G  I L    +R+A+ K +  +         Y   D
Sbjct: 5   GKAALITGSTSGIGLAYAKTLAGAGAHIMLNGFGDRDAIAKIQREIEGLSGARTDYSDAD 64

Query: 65  VTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAFHVL 124
           +T+  A+   +       G +D L NNAG Q   APV ++P D +  ++ +N++ AFH +
Sbjct: 65  LTNPAAIEAMIGQAKSSLGGVDILINNAGMQHV-APVDEFPIDKWNAIIALNLSAAFHAI 123

Query: 125 KAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIRVNA 184
           +     M  + +GRI++TAS   +   PN +AY  +K  I  LT+T AL++A + I VN 
Sbjct: 124 RLAVPHMKEKKWGRIISTASAHSLVASPNKSAYVAAKHGIAGLTKTVALEVATHGITVNC 183

Query: 185 ISPGYMGPGFMWERQVELQ-AKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVVAF 243
           ISPGY     +W + VE Q          T  +V+   ++ + P +++    ++  +  +
Sbjct: 184 ISPGY-----VWTQLVEDQIPDTMKSRGLTREQVMNDVLLAAQPTKQFVTPEQVASLALY 238

Query: 244 LLGDDSSFMTGVNLPIAGG 262
           L  DD++ +TG NL + GG
Sbjct: 239 LCSDDAAAITGANLSMDGG 257


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: 139
Number of extensions: 6
Number of successful extensions: 5
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: 261
Length adjustment: 25
Effective length of query: 237
Effective length of database: 236
Effective search space:    55932
Effective search space used:    55932
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