GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_4061 Ga0059261_4061
           Transcriptional regulator/sugar kinase
          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.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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