GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Nostoc punctiforme PCC 73102 ATCC 29133; PCC 73102

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_012407138.1 NPUN_RS01685 ROK family protein

Query= BRENDA::Q8R8N4
         (312 letters)



>NCBI__GCF_000020025.1:WP_012407138.1
          Length = 319

 Score =  143 bits (360), Expect = 6e-39
 Identities = 104/323 (32%), Positives = 166/323 (51%), Gaps = 23/323 (7%)

Query: 3   IGVDLGGTNIAVGLVEEDGKIIATGSRP-TKPERGYEAIARDIAELSFELLQRMGISV-K 60
           + +D GGT +A  LV         GSR   + ER    +  + A    E+++ +  S+ +
Sbjct: 5   LALDFGGTKLAAALVN-------VGSRKWLRYERRLSPVGAN-ASTDLEIMRSLIYSLLE 56

Query: 61  DVKSMGIGVP--GVADNEKGIVIRAVNLF-WTKVPLAKEIRKYIDLPIYMENDANVAALA 117
           D K   IGV   G  D   G V  + ++  W  +PL   + +   + + ++NDANVAAL 
Sbjct: 57  DAKPAAIGVSFGGPVDASTGTVRLSHHVAGWENIPLKGLLEEEFGVSVGVDNDANVAALG 116

Query: 118 EATFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKI 177
           E  FGAG+G  S   IT+ TGVG G+IL+G+ + GA   A EIGH+V+  +G  C CGK 
Sbjct: 117 EHRFGAGQGYDSLFYITVSTGVGGGWILNGQPWRGAGGMAGEIGHIVVDPSGPVCLCGKR 176

Query: 178 GCFETYASATALIREGKKAAKRNP--------NTLILKFANGDIEGITAKNVIDAAKQYD 229
           GC E  AS   + +  ++  +  P          ++   A  D+  +T + V +AA   D
Sbjct: 177 GCVERLASGPYMAQNVREILENEPQRRGGFRDGEILRGLAGDDLTLLTGQLVSEAAAAGD 236

Query: 230 EEALKIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKEL 289
           + A ++  +    L VGI N+ NL +P+  +LGGGV  AG+   + + ++VA      E+
Sbjct: 237 DLAKEVLHKAAWALGVGIGNVANLMNPQRFVLGGGVTKAGEDFWR-VVRQVARETALPEV 295

Query: 290 PYADIRKAELGNDAGIIGAAILS 312
            + +I  A LG+DA + G   ++
Sbjct: 296 DF-EIVPAVLGDDAPLWGGVAIA 317


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: 335
Number of extensions: 22
Number of successful extensions: 2
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: 312
Length of database: 319
Length adjustment: 27
Effective length of query: 285
Effective length of database: 292
Effective search space:    83220
Effective search space used:    83220
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 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