GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Nocardiopsis gilva YIM 90087

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_017620227.1 CDO52_RS05395 ROK family glucokinase

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



>NCBI__GCF_002263495.1:WP_017620227.1
          Length = 344

 Score =  166 bits (419), Expect = 1e-45
 Identities = 106/314 (33%), Positives = 167/314 (53%), Gaps = 11/314 (3%)

Query: 11  VGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLIIANGGVDKIK 70
           VGIDIGG+    G+V+  G ++A    +T   P   +    V   ++ +I        + 
Sbjct: 16  VGIDIGGSKVAAGVVNPSGRVLARRRTET---PDKSKSPKVVEDTIVSVIEELRREYPVH 72

Query: 71  GIGIGAPNG-NYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAVGEMTYG 129
            +G+GA    +    ++ FAP+L W+   PL     +RL +P  + NDANA+A  E+  G
Sbjct: 73  AVGVGAAGFVDEQRASVLFAPHLAWRKE-PLREALTQRLELPVVVENDANASAWAEVRVG 131

Query: 130 AARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRICGCGRKGCLET 189
           A RG+ D +++ LGTG+G  I+++G++  G  G AGE GH+ V   G  C CG +GC E 
Sbjct: 132 AGRGVDDILVVNLGTGIGGAIILDGKLHRGRYGIAGEFGHMTVVPGGHRCECGNRGCWEQ 191

Query: 190 YCSATGVARTAREFLAARTDAS--LLRNIPAES--IVSKDVYDAAVQGDKLAQEIFEFTG 245
           Y S   V R ARE  AA +  +  L++ +  +   I    V D A +GD+ + E+ E  G
Sbjct: 192 YASGNAVTRDARELAAADSPVARGLIQAVGGDPALITGPLVSDLAREGDRASVELLEDAG 251

Query: 246 NILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNI-YKGKAKLLVSEL 304
             LG  LA+  A   PE  I+ GG++  GD ++ P   A    L    Y+ +A+++ +EL
Sbjct: 252 GWLGIGLANLAAAFDPELFIIGGGVSDCGDLLLGPARTAFRRQLTGRGYRPEARIVRAEL 311

Query: 305 KDSDAAVLGASALA 318
             ++A ++GAS LA
Sbjct: 312 -GNEAGLIGASLLA 324


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: 309
Number of extensions: 13
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: 326
Length of database: 344
Length adjustment: 28
Effective length of query: 298
Effective length of database: 316
Effective search space:    94168
Effective search space used:    94168
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