GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Limnohabitans curvus MWH-C5

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_108358580.1 B9Z44_RS13785 3-oxoacyl-ACP reductase FabG

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_003063475.1:WP_108358580.1
          Length = 255

 Score =  164 bits (415), Expect = 2e-45
 Identities = 91/261 (34%), Positives = 144/261 (55%), Gaps = 17/261 (6%)

Query: 2   SKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARSY 61
           +++  GKV L+TGA   IGLATAL+ A EG  + + D+ + A+++A    +  G +A  +
Sbjct: 9   AQRLQGKVSLITGAAQGIGLATALKFAREGAIVIVCDVKQAAVDEAVKQCQALGAQALGF 68

Query: 62  VCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGAF 121
           V DVT  + V  TV +V+  FG+ID L NNAG     A +Q    + F RV+ +N+ G F
Sbjct: 69  VVDVTQRDMVDATVKAVLDKFGRIDVLVNNAGIT-QDARLQKMTLEQFDRVIDVNLRGVF 127

Query: 122 HVLKAVSRQMITQNYGRIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYNIR 181
           H  +AV+  M+ Q  G I+N +S+ G+ G      Y  +K  +I  T+T + +L P  IR
Sbjct: 128 HCAQAVTEAMVAQGSGVILNASSVVGIYGNFGQTNYAATKFGVIGFTKTWSRELGPKGIR 187

Query: 182 VNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPGVV 241
           VNA++PG+                + +   ST P+ V  +M   VP++R G   +I  V 
Sbjct: 188 VNAVAPGF----------------IQTPILSTIPEKVIHEMTDRVPLKRLGQPEDIANVY 231

Query: 242 AFLLGDDSSFMTGVNLPIAGG 262
           AFL  D+++++ G  + +AGG
Sbjct: 232 AFLASDEAAYINGTVIEVAGG 252


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: 161
Number of extensions: 5
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: 255
Length adjustment: 24
Effective length of query: 238
Effective length of database: 231
Effective search space:    54978
Effective search space used:    54978
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