GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Sphingomonas koreensis DSMZ 15582

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate Ga0059261_1900 Ga0059261_1900 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)

Query= BRENDA::Q8GR61
         (262 letters)



>FitnessBrowser__Korea:Ga0059261_1900
          Length = 250

 Score =  129 bits (325), Expect = 5e-35
 Identities = 94/262 (35%), Positives = 132/262 (50%), Gaps = 20/262 (7%)

Query: 4   KFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEA-SVREKGVEARSYV 62
           +F  KV +VTG G +IG + +LRLA EG  + +   + EA  KA   ++   G  A    
Sbjct: 2   RFKDKVAIVTGGGRDIGKSISLRLAAEGAKVVINYRSDEAAAKATLDAIEAAGGTALLAR 61

Query: 63  CDVTSEEAVIGTVDSVVRDFG-KIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAF 121
            DVT  + V+  V +    FG K+D L N AG   A   + +     F  V+ +N+  AF
Sbjct: 62  ADVTKADEVVALVKAATDAFGGKVDILVNCAGGMVARKTLAEMDEAFFDTVMDLNLKSAF 121

Query: 122 HVLKAVSRQMITQNYGRIVNTASMAGVKGP-PNMAAYGTSKGAIIALTETAALDLAPYNI 180
            V KAV   +  ++   IVN AS AG  G  P  + Y  SKGA++ LT + A +L P  I
Sbjct: 122 LVTKAVLPHL--ESGAAIVNIASQAGRDGGGPGASIYAASKGALMTLTRSWAKELGPQGI 179

Query: 181 RVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGV 240
           RVNA++PG +G  F                FS      A  + G+ P+RR G  +E+   
Sbjct: 180 RVNALNPGLIGTSF-------------HDIFSKPEGRAA--VAGNTPLRREGHPDEVAAA 224

Query: 241 VAFLLGDDSSFMTGVNLPIAGG 262
           VAFL   D+SF+TG N+ I GG
Sbjct: 225 VAFLASGDASFLTGTNVDINGG 246


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: 168
Number of extensions: 8
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: 250
Length adjustment: 24
Effective length of query: 238
Effective length of database: 226
Effective search space:    53788
Effective search space used:    53788
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