GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Salinicoccus carnicancri Crm

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_017548855.1 C792_RS0107525 ROK family glucokinase

Query= BRENDA::Q8R8N4
         (312 letters)



>NCBI__GCF_000330705.1:WP_017548855.1
          Length = 319

 Score =  172 bits (437), Expect = 7e-48
 Identities = 112/312 (35%), Positives = 162/312 (51%), Gaps = 6/312 (1%)

Query: 3   IGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVKDV 62
           +  D+GGT+  +G+ +E+  +I     PT        I  D+ +      + +G  V++ 
Sbjct: 5   LAADIGGTSCKLGVFDEELNLIEKWEIPTDISEEGSHILADVLDSFRSKEEILGFKVEEC 64

Query: 63  KSMGIGVPGVADNEKGIVIRAVNL-FWTKVPLAKEIRKYIDLPIYMENDANVAALAEATF 121
              G+G+PG  D EKGI+   +NL    K  +A    +       ++NDANVAAL E + 
Sbjct: 65  LGTGLGMPGPVDFEKGILNGCINLNIKGKRSIATIFSELSGSAAIVDNDANVAALGEQSK 124

Query: 122 GAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNG-IRCNCGKIGCF 180
           GAG G    V ITLGTGVG G I +G++  G      EIGH+ +  +G  +CNCGK GC 
Sbjct: 125 GAGHGHSEVVMITLGTGVGGGVISEGRLIHGTGGSGGEIGHITVDFDGRFQCNCGKKGCL 184

Query: 181 ETYASATALIR-EGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEY 239
           ET ASAT ++   G  +     + LI     G +   T+K ++DAA   D  A  + EE 
Sbjct: 185 ETVASATGMVNLAGYHSDDHENSVLIAAIKEGTL---TSKAIVDAAMTGDPLAEFVVEEA 241

Query: 240 VKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAEL 299
            +YLAV + +I  + +P   + GGGV+ AG +L   +KK     I        +I  AEL
Sbjct: 242 ARYLAVAMSSISVITNPGYFVFGGGVSRAGRYLTDKIKKYYDSLIFPPAADDVEIVMAEL 301

Query: 300 GNDAGIIGAAIL 311
           GNDAG+ GAA L
Sbjct: 302 GNDAGMYGAARL 313


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: 315
Number of extensions: 20
Number of successful extensions: 4
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 Sep 24 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