GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gadh3 in Burkholderia phytofirmans PsJN

Align D-gluconate dehydrogenase 21.7 kD subunit (EC 1.1.99.3) (characterized)
to candidate BPHYT_RS30775 BPHYT_RS30775 gluconate 2-dehydrogenase

Query= metacyc::MONOMER-12747
         (251 letters)



>FitnessBrowser__BFirm:BPHYT_RS30775
          Length = 251

 Score =  216 bits (549), Expect = 5e-61
 Identities = 113/243 (46%), Positives = 153/243 (62%), Gaps = 13/243 (5%)

Query: 10  RREFLRKSLTLIPVVT-VASTGLGGSLLAAASETAIAATPATPGKQPAGSGQGYEPGYFT 68
           RR FL KS+ ++PV   +A+    G L A+AS +   ++ A P          Y+P +F 
Sbjct: 18  RRRFLIKSVAVLPVAGGLAACDRPGGLTASASASTADSSNAAP----------YQPKFFK 67

Query: 69  AEEWAFIKAAVERLIPADEMGPGALEAGVPEYIDRQMNTPYAAGALWYMQGPFKADAAPE 128
            +EW+ ++AA++RLIPAD  GPGALE  V  +IDRQM   +   A WYM GPF  DA P 
Sbjct: 68  PDEWSVLQAAIDRLIPADAEGPGALELDVATFIDRQMEGAFGHAAAWYMHGPFHPDATPL 127

Query: 129 MGWQSKLVPKDIYRLGIAATDAWCK-ELKGQTFAAQDSATRDDLLKQLEAGTPQFDAVPA 187
            G+QS + P+D+YR GIAA DA CK    G+ F    +A +D LL  +++G  +F+   A
Sbjct: 128 AGYQSPMSPRDLYRTGIAALDAHCKAHFGGKPFVQLTTAQQDTLLHAMDSGKVKFEQTSA 187

Query: 188 KLFFNLLLQNTKEGFFSDPIHGGNKGLVGWTLIGFPGARADFMDWV-ERNEQYPFPAVSI 246
           + F  LL QNTKEG+FSDPIHGGNK    WT+IGFPGARAD++DWV +  + YP   V+I
Sbjct: 188 RHFIALLWQNTKEGYFSDPIHGGNKHAASWTMIGFPGARADYLDWVAQPGKVYPLGPVTI 247

Query: 247 RGE 249
            G+
Sbjct: 248 EGK 250


Lambda     K      H
   0.317    0.135    0.414 

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: 230
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: 251
Length of database: 251
Length adjustment: 24
Effective length of query: 227
Effective length of database: 227
Effective search space:    51529
Effective search space used:    51529
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 (21.6 bits)
S2: 46 (22.3 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