GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Saccharomonospora marina XMU15

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_009153825.1 SACMADRAFT_RS10680 ROK family protein

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



>NCBI__GCF_000244955.1:WP_009153825.1
          Length = 317

 Score =  165 bits (417), Expect = 2e-45
 Identities = 105/315 (33%), Positives = 170/315 (53%), Gaps = 12/315 (3%)

Query: 11  VGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLIIANGGVDKIK 70
           +G+D+GGT+   G+VD +G ++ +  V T   P+ E   ++    ++  +     V  + 
Sbjct: 4   IGVDVGGTSVRAGVVDEQGALLDTARVGT---PSDELALEDAVAGVIDELRNRHEVGAV- 59

Query: 71  GIGIGAPNGNYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAVGEMTYGA 130
           G+ + A   +    ++ FAP+LPW+G  P+A    +R+G+P  L +DANAAAV E  +GA
Sbjct: 60  GLAVAAFVRSDRR-SVMFAPHLPWRGA-PVADRVSKRVGLPVTLEHDANAAAVAEHRFGA 117

Query: 131 ARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRICGCGRKGCLETY 190
           ARG +   ++ +GTG+G+G++++G++  G  G A ELGH+ V   GR C CG+ GC E Y
Sbjct: 118 ARGARVAALVAIGTGIGAGLLLDGRLFRGAHGVAPELGHLCVVPGGRACPCGKHGCWERY 177

Query: 191 CSATGVARTAREFLAARTDASLLRNIPAE----SIVSKDVYDAAVQGDKLAQEIFEFTGN 246
           CS T +A TA E LA     S +          SI  + V  AA  GD +AQ        
Sbjct: 178 CSGTALAATAVELLARHPGRSTVLAWETAGDPGSITGRRVAGAARDGDPIAQRAMAELAR 237

Query: 247 ILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNI-YKGKAKLLVSELK 305
            LGE LA       PE +++ GG+++S    +    +     +    ++  A++  S+L 
Sbjct: 238 WLGEGLALVADVYDPEVVVIAGGVSESAPLFLDEAREHYARAVTGAGHRPLARIRTSQLG 297

Query: 306 DSDAAVLGASALAWE 320
           D + A++GA+ALA E
Sbjct: 298 D-ETALVGAAALARE 311


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: 274
Number of extensions: 14
Number of successful extensions: 4
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: 317
Length adjustment: 28
Effective length of query: 298
Effective length of database: 289
Effective search space:    86122
Effective search space used:    86122
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