GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gntK in Pedobacter sp. GW460-11-11-14-LB5

Align D-gluconate kinase, thermosensitive (EC 2.7.1.12) (characterized)
to candidate CA265_RS25410 CA265_RS25410 gluconate kinase

Query= ecocyc::GLUCONOKINI-MONOMER
         (187 letters)



>FitnessBrowser__Pedo557:CA265_RS25410
          Length = 168

 Score =  150 bits (380), Expect = 9e-42
 Identities = 77/167 (46%), Positives = 109/167 (65%), Gaps = 1/167 (0%)

Query: 1   MAGESFILMGVSGSGKTLIGSKVAALLSAKFIDGDDLHPAKNIDKMSQGIPLSDEDRLPW 60
           MAG   ILMGVSGSGKT+IG  +A  ++A+FIDGD+LH  +N+DKM+ GIPL+D DRL W
Sbjct: 1   MAG-FIILMGVSGSGKTVIGKALAPKINAEFIDGDNLHSQRNVDKMAAGIPLTDADRLDW 59

Query: 61  LERLNDASYSLYKKNETGFIVCSSLKKQYRDILRKGSPHVHFLWLDGDYETILARMQRRA 120
           L+ +            +  I CS+LKK YR++LR  +P + F++L G +  I  R+ +R+
Sbjct: 60  LQLIAKVGREHVAHGTSCIIACSALKKSYRNLLRNDNPSIRFVYLQGSFGLIHDRIAKRS 119

Query: 121 GHFMPVALLKSQFEALERPQADEQDIVRIDINHDIANVTEQCRQAVL 167
             +MP +LLKSQFE LE P ADE D+V + I+  I  +  +  +A L
Sbjct: 120 HQYMPASLLKSQFETLEEPLADEGDVVTVLIDQSIPEIVNEIVKADL 166


Lambda     K      H
   0.320    0.135    0.396 

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: 98
Number of extensions: 3
Number of successful extensions: 1
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: 187
Length of database: 168
Length adjustment: 19
Effective length of query: 168
Effective length of database: 149
Effective search space:    25032
Effective search space used:    25032
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 44 (21.6 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