GapMind for catabolism of small carbon sources

 

Alignments for a candidate for scrK in Salinicoccus carnicancri Crm

Align fructokinase (EC 2.7.1.4) (characterized)
to candidate WP_017549879.1 C792_RS0112925 sugar kinase

Query= BRENDA::Q6VWJ5
         (386 letters)



>NCBI__GCF_000330705.1:WP_017549879.1
          Length = 315

 Score =  118 bits (295), Expect = 3e-31
 Identities = 82/269 (30%), Positives = 133/269 (49%), Gaps = 8/269 (2%)

Query: 68  VVCFGEMLIDFVPTTSGLSLAEAPAFKKAPGGAPANVAVGISRLGGSSAFIGKVGEDEFG 127
           V+  GE ++  V    G  +  A +FK    GA  N  +G+SRLG  ++++  +GEDE G
Sbjct: 3   VIGIGESMVALVNEPKGY-IRHADSFKPYVAGAEMNTLIGLSRLGHGTSWVSALGEDELG 61

Query: 128 YMLAEILKENNVNSDGMRFDPGARTALAFVTLRKDGEREFMFYRNPSADMLLQEDELDLE 187
            ++   ++  NV++  +      RT + F  +  DG  +  +YR  SA   +   ++D++
Sbjct: 62  ELILHKVRAENVDASHVTHKD-KRTGVFFKQILPDGSVDVTYYREDSAASNMDIRDIDMD 120

Query: 188 LIRKAKVFHYGSISL-ITEPCKSAHIAAAKAAKDAGVILSYDPNLRLPLWPSAESAREGI 246
            IR+AKV +   I+L ++   K     A + A D  V + +DPN+RL +W SA+ ARE I
Sbjct: 121 AIRRAKVLYLTGITLSLSSSAKEMLFEAVRIAGD-DVTVVFDPNIRLKMW-SAKEARETI 178

Query: 247 LSIWNTADIIKISEEEISFLTQGEDPYDDNVVRKLYHPNLKLLLVTEGPEGCRYYTKDFS 306
           L      D +    +E+  L     P  +  ++         +++  G EG  Y      
Sbjct: 179 LEFLPHVDCLIAGRDEVDILMGAMRP--EEALKSFRELGCSKVVLKLGKEGAVYDFDGIG 236

Query: 307 GRVKGIK-VDAVDTTGAGDAFVAGILSQL 334
           G VK  K  + +D  GAGDAF AGI+S L
Sbjct: 237 GSVKNPKQFEEIDPVGAGDAFAAGIISGL 265


Lambda     K      H
   0.317    0.134    0.382 

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: 244
Number of extensions: 11
Number of successful extensions: 3
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: 386
Length of database: 315
Length adjustment: 29
Effective length of query: 357
Effective length of database: 286
Effective search space:   102102
Effective search space used:   102102
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: 49 (23.5 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