GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Sphingomonas koreensis DSMZ 15582

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate Ga0059261_4061 Ga0059261_4061 Transcriptional regulator/sugar kinase

Query= BRENDA::Q8R8N4
         (312 letters)



>FitnessBrowser__Korea:Ga0059261_4061
          Length = 291

 Score = 84.0 bits (206), Expect = 4e-21
 Identities = 80/315 (25%), Positives = 132/315 (41%), Gaps = 44/315 (13%)

Query: 3   IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62
           + ++ GGT +   LV ++G +       T PE      A + A L+F    R  ++   +
Sbjct: 8   LAIETGGTKLLARLVRDEGVVAEARWPTTSPE------AAEAALLAFA--GRTPLAGVGI 59

Query: 63  KSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEATFG 122
            + G  V   A    G V+      WT   L   + + + +P+ ++ D N AALAEA  G
Sbjct: 60  AAFGPVVVDPAAANYGEVLATPKPGWTGANLRAALEQALGVPVAIDTDVNAAALAEAAAG 119

Query: 123 AGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGCFET 182
           AG+G  S   +T+GTG+G+G   DG+  +GA H  PE+GH+ +                 
Sbjct: 120 AGQGCSSLAYVTVGTGIGAGLARDGRTLTGALH--PEMGHVPV----------------- 160

Query: 183 YASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVID--AAKQYDEEALKIFEEYV 240
                 L  EG      +P      F +G  EG+ A   +      +  E++   F    
Sbjct: 161 ------LRFEG------DPTPSACPFHSGCAEGMAAGPAVQRRLGGKLLEDSPADFAAVA 208

Query: 241 KYLAVGIVNIINLFDPEVIILGGGVANA---GDFLLKPLKKEVAENILFKELPYADIRKA 297
            YL      I+  + P  I++GGGV +    G      ++  +    +   +  AD  ++
Sbjct: 209 DYLGQLFATIVLAWSPHRIVVGGGVMDVPGLGKAATVRMRVALGGYGVGSAVGEADFIRS 268

Query: 298 ELGNDAGIIGAAILS 312
                AG+ GA IL+
Sbjct: 269 AALEHAGLEGALILA 283


Lambda     K      H
   0.318    0.140    0.397 

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: 251
Number of extensions: 20
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 312
Length of database: 291
Length adjustment: 27
Effective length of query: 285
Effective length of database: 264
Effective search space:    75240
Effective search space used:    75240
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: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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