GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mannokinase in Desulfacinum hydrothermale DSM 13146

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_084057691.1 B9A12_RS09725 ROK family protein

Query= metacyc::MONOMER-19002
         (326 letters)



>NCBI__GCF_900176285.1:WP_084057691.1
          Length = 325

 Score =  160 bits (406), Expect = 3e-44
 Identities = 107/330 (32%), Positives = 175/330 (53%), Gaps = 14/330 (4%)

Query: 5   MEKPYVVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEV---CKNLLPLII 61
           M+   V+G+DIGGT+    ++D +GT++A    +++     E     +   C++LL    
Sbjct: 1   MKDKCVIGVDIGGTHMRCALMDRKGTVLAFRKDRSRSDEGPEALTRRLVQQCRDLL---- 56

Query: 62  ANGGVD--KIKGIGIG-APNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDA 118
           A+GG+   ++  +G+G A   +  +GTI F+PNLP     PLA   +E L +P A+ NDA
Sbjct: 57  ADGGLSNARLGAVGLGVAGKLDTASGTILFSPNLPSLAGFPLAVRVQEALQVPVAMENDA 116

Query: 119 NAAAVGEMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHD-GFAGELGHVIVRRDGR 177
           N   +GE   G AR + ++I +TLGTGVG     NG++  G   GF+GE+GH+IV   G 
Sbjct: 117 NVFGLGEAWLGKARNVSNWIGVTLGTGVGGCFFANGRLWQGDRLGFSGEIGHMIVDPQGP 176

Query: 178 ICGCGRKGCLETYCSATGVARTAREFLAARTDAS--LLRNIPAESIVSKDVYDAAVQGDK 235
            C CG+KGCLE + SAT + +  R+        S  L   +  + + +  +Y AA  GD 
Sbjct: 177 ECACGQKGCLEAHASATALVQGVRQAQKEAVPLSDLLQEALRRDQLTAHTIYRAARGGDP 236

Query: 236 LAQEIFEFTGNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKG 295
           +A+ +F   G  L  AL++   F      ++ GG++ S D     ++   +     +   
Sbjct: 237 VARRLFARMGWALAVALSNLFTFLGISTAVIGGGVSASWDQFAPAMLDYFQQVPSMLDPQ 296

Query: 296 KAKLLVSELKDSDAAVLGASALAWELKDLR 325
              +  +EL+D  A++ GA++LAW+  D R
Sbjct: 297 SIHVHRTELEDR-ASIYGAASLAWQTVDRR 325


Lambda     K      H
   0.318    0.138    0.399 

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: 281
Number of extensions: 14
Number of successful extensions: 5
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: 326
Length of database: 325
Length adjustment: 28
Effective length of query: 298
Effective length of database: 297
Effective search space:    88506
Effective search space used:    88506
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