GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xdhA in Phyllobacterium leguminum ORS 1419

Align D-xylulose reductase (EC 1.1.1.9) (characterized)
to candidate WP_110751435.1 C7477_RS09440 L-iditol 2-dehydrogenase

Query= BRENDA::Q8GR61
         (262 letters)



>NCBI__GCF_003217235.1:WP_110751435.1
          Length = 258

 Score =  132 bits (331), Expect = 9e-36
 Identities = 89/263 (33%), Positives = 136/263 (51%), Gaps = 10/263 (3%)

Query: 1   MSKKFNGKVCLVTGAGGNIGLATALRLAEEGTAIALLDMNREALEKAEASVREKGVEARS 60
           MS +  GK   +TGA   IG A A   A EG  +AL D++   L++A+ S  + G  A +
Sbjct: 1   MSGRLEGKSAFITGAARGIGFAFAEAFAREGATVALADID---LDRAQESAAKIGERAYA 57

Query: 61  YVCDVTSEEAVIGTVDSVVRDFGKIDFLFNNAGYQGAFAPVQDYPSDDFARVLTINVTGA 120
              DVT   ++   V   V   G ID L NNA      AP+ +   + F R+  +NV G 
Sbjct: 58  VQIDVTDIASIERAVAEAVAKTGGIDILVNNAALFD-MAPMVEITRESFERLYAVNVHGV 116

Query: 121 FHVLKAVSRQMITQNYG-RIVNTASMAGVKGPPNMAAYGTSKGAIIALTETAALDLAPYN 179
              ++AV+R MI +  G +I+N AS AG +G   +A Y ++K A+I+LT++A LDL  + 
Sbjct: 117 LFTMQAVARAMIARGRGGKIINMASQAGRRGEALVAVYCSTKAAVISLTQSAGLDLIRHG 176

Query: 180 IRVNAISPGYMGPGFMWERQVELQAKVGSQYFSTDPKVVAQQMIGSVPMRRYGDINEIPG 239
           I VNAI+PG +  G  W     L AK  ++      ++V +    +VP  R G   ++ G
Sbjct: 177 INVNAIAPGVV-DGEHWAGVDALFAKHENRPLGEKKRLVGE----AVPFGRMGRPEDLTG 231

Query: 240 VVAFLLGDDSSFMTGVNLPIAGG 262
           +  FL G +S ++      + GG
Sbjct: 232 MAIFLAGPESDYVVAQTYNVDGG 254


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: 158
Number of extensions: 16
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: 258
Length adjustment: 24
Effective length of query: 238
Effective length of database: 234
Effective search space:    55692
Effective search space used:    55692
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