GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Desulfacinum hydrothermale DSM 13146

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_084057691.1 B9A12_RS09725 ROK family protein

Query= BRENDA::Q8RDE9
         (315 letters)



>NCBI__GCF_900176285.1:WP_084057691.1
          Length = 325

 Score =  185 bits (470), Expect = 1e-51
 Identities = 95/314 (30%), Positives = 166/314 (52%), Gaps = 3/314 (0%)

Query: 3   KFLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEM 62
           K + GVD+GGT +   ++D  G ++   K  + +++GP+ +  R+ +    +L D GL  
Sbjct: 4   KCVIGVDIGGTHMRCALMDRKGTVLAFRKDRSRSDEGPEALTRRLVQQCRDLLADGGLSN 63

Query: 63  SNLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIGE 122
           + L  +G+G  G L+   G ++  PNLP  +  P+   + + L + V +ENDAN   +GE
Sbjct: 64  ARLGAVGLGVAGKLDTASGTILFSPNLPSLAGFPLAVRVQEALQVPVAMENDANVFGLGE 123

Query: 123 HLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSN-AAEIGHHTINFDGPRCNCGNY 181
              G  R V N++ +T+ TG+GG     G+L+ G+    + EIGH  ++  GP C CG  
Sbjct: 124 AWLGKARNVSNWIGVTLGTGVGGCFFANGRLWQGDRLGFSGEIGHMIVDPQGPECACGQK 183

Query: 182 GCFEAYASGTAIARFAREGIEKGIKTK--IKELAGEGEVKAEHVFEAAKLGDEFAKELVE 239
           GC EA+AS TA+ +  R+  ++ +     ++E     ++ A  ++ AA+ GD  A+ L  
Sbjct: 184 GCLEAHASATALVQGVRQAQKEAVPLSDLLQEALRRDQLTAHTIYRAARGGDPVARRLFA 243

Query: 240 KEAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVKA 299
           +  + L V ++N+  F       IGGGVSA WD     M++  ++     + +   V + 
Sbjct: 244 RMGWALAVALSNLFTFLGISTAVIGGGVSASWDQFAPAMLDYFQQVPSMLDPQSIHVHRT 303

Query: 300 QLGENIGVLGAAAL 313
           +L +   + GAA+L
Sbjct: 304 ELEDRASIYGAASL 317


Lambda     K      H
   0.316    0.138    0.398 

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: 246
Number of extensions: 14
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: 315
Length of database: 325
Length adjustment: 28
Effective length of query: 287
Effective length of database: 297
Effective search space:    85239
Effective search space used:    85239
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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