GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Lactobacillus silagei IWT126

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_054653999.1 CES79_RS01675 ROK family protein

Query= BRENDA::Q8R8N4
         (312 letters)



>NCBI__GCF_002217945.1:WP_054653999.1
          Length = 320

 Score =  196 bits (497), Expect = 8e-55
 Identities = 111/311 (35%), Positives = 172/311 (55%), Gaps = 1/311 (0%)

Query: 1   MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60
           M +G+DLGGTNI +GL+  D  +      PT+ E   + +  ++     +LL        
Sbjct: 4   MYLGIDLGGTNIKIGLLNADLTVQMKLKVPTESETNSQTVMANMIAGIKQLLAETQTDTS 63

Query: 61  DVKSMGIGVPGVADNEKGIVIRAVNL-FWTKVPLAKEIRKYIDLPIYMENDANVAALAEA 119
            +K++GIGVPG  D +KG+ I + N   W  VP+ + I     LP Y++ND  V    E 
Sbjct: 64  QIKAVGIGVPGQMDIKKGLSIFSPNFTHWENVPVVQLIEAQFHLPTYIDNDVRVNLYGEW 123

Query: 120 TFGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVIGDNGIRCNCGKIGC 179
             GAGRG ++ + +TLGTG+G+  I DG++  G  + A E+GH+ +  +G  C CG  GC
Sbjct: 124 QLGAGRGKQNVLMVTLGTGLGAAIITDGQMMYGKSNSAGELGHLNMYRHGRPCACGSSGC 183

Query: 180 FETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALKIFEEY 239
              Y SA  +++  ++       ++I ++ + D   ITAK V +A  Q D+ A  + +E 
Sbjct: 184 LGRYVSARGMVKTVQEHLAAGETSVITEWTHNDQAQITAKMVSEAYDQQDQLAQTVMQET 243

Query: 240 VKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPYADIRKAEL 299
            + L  G+ + INL++PE II+GGG+A AGD LL P +  +A + L       DI  A+L
Sbjct: 244 GEILGYGLASAINLYNPERIIIGGGMAAAGDRLLTPARAVIAGHALKVAREVCDIVPAQL 303

Query: 300 GNDAGIIGAAI 310
           G  AG+IGA +
Sbjct: 304 GAWAGMIGAGV 314


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: 279
Number of extensions: 12
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: 320
Length adjustment: 27
Effective length of query: 285
Effective length of database: 293
Effective search space:    83505
Effective search space used:    83505
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.

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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