GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Lactobacillus silagei IWT126

Align N-acetyl-D-glucosamine kinase; EC 2.7.1.59; GlcNAc kinase (uncharacterized)
to candidate WP_089137286.1 CES79_RS11525 ROK family protein

Query= curated2:Q9KRV2
         (302 letters)



>NCBI__GCF_002217945.1:WP_089137286.1
          Length = 300

 Score = 94.0 bits (232), Expect = 4e-24
 Identities = 72/265 (27%), Positives = 124/265 (46%), Gaps = 23/265 (8%)

Query: 6   DVGGTKIEFGAFNEQLERVATERVATPTDDYAKLVETIAGLVHKYDAQFGVEGTVGLGIP 65
           D+GGT +++G +N+QLE   + +  TP   +A++ + +  L  +      + G V + +P
Sbjct: 14  DIGGTSVKYGYWNQQLENSGSFK--TPKT-WAEMHDKLLSLPSQITQP--IRG-VAISLP 67

Query: 66  GMEDADNGCVL-TVNVPAAKGKPLRADLETKLGRAVKVENDANCFALSEAWDDELKEAAS 124
           G  D   G +  T  VP   G  +R +L       V ++NDANC  L+E W    K+ +S
Sbjct: 68  GSVDIKKGQISGTTAVPYLNGFAIRKELSDDFQLPVTIQNDANCAGLAETWIGNAKDVSS 127

Query: 125 VMGLILGTGFGGGLVYEGKVFSGRNHVAGEIGHMRLPIDAWFHLGEKAPLLGCGCGNKGC 184
           V  LI+GTG GG ++ +G++ +G +H  GE G+  L        G+   L   G      
Sbjct: 128 VALLIIGTGIGGSIIQDGQLLTGHDHFMGEFGYSILN-------GQNKTLSDLG------ 174

Query: 185 MDNYLSGRGFELLYEHYYGEKKKAIDIITAQKEGESKAVEHVERFMELLAICFANIFTAN 244
                  + +  + E        A  I    K+G+  A   +   +  L++   N+ T+ 
Sbjct: 175 -SPVQMAKKYTRISESL--APVDAPQIFEKAKQGDKLAQNCINDMVHWLSLEVYNLITSF 231

Query: 245 DPHVVVLGGGLSNYDLIYEEMPKRV 269
           +P  +++GGG+S  D   E +  RV
Sbjct: 232 NPDRLLIGGGISIRDDFLEMIRNRV 256


Lambda     K      H
   0.319    0.140    0.422 

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: 201
Number of extensions: 8
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 302
Length of database: 300
Length adjustment: 27
Effective length of query: 275
Effective length of database: 273
Effective search space:    75075
Effective search space used:    75075
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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