GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mannokinase in Salinicoccus carnicancri Crm

Align N-acetylglucosamine kinase (EC 2.7.1.59) (characterized)
to candidate WP_017548855.1 C792_RS0107525 ROK family glucokinase

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



>NCBI__GCF_000330705.1:WP_017548855.1
          Length = 319

 Score =  165 bits (417), Expect = 2e-45
 Identities = 100/315 (31%), Positives = 164/315 (52%), Gaps = 12/315 (3%)

Query: 10  VVGIDIGGTNTVFGIVDARGTIIASGAVKTQVYPTVEEYADEVCKNLLPLI-----IANG 64
           ++  DIGGT+   G+ D    +I    + T +     E    +  ++L        I   
Sbjct: 4   ILAADIGGTSCKLGVFDEELNLIEKWEIPTDI----SEEGSHILADVLDSFRSKEEILGF 59

Query: 65  GVDKIKGIGIGAPNG-NYYTGTIEFAPNLPWKGVLPLASMFEERLGIPTALTNDANAAAV 123
            V++  G G+G P   ++  G +    NL  KG   +A++F E  G    + NDAN AA+
Sbjct: 60  KVEECLGTGLGMPGPVDFEKGILNGCINLNIKGKRSIATIFSELSGSAAIVDNDANVAAL 119

Query: 124 GEMTYGAARGMKDFIMITLGTGVGSGIVINGQVVYGHDGFAGELGHVIVRRDGRI-CGCG 182
           GE + GA  G  + +MITLGTGVG G++  G++++G  G  GE+GH+ V  DGR  C CG
Sbjct: 120 GEQSKGAGHGHSEVVMITLGTGVGGGVISEGRLIHGTGGSGGEIGHITVDFDGRFQCNCG 179

Query: 183 RKGCLETYCSATGVARTAREFLAARTDASLLRNIPAESIVSKDVYDAAVQGDKLAQEIFE 242
           +KGCLET  SATG+   A        ++ L+  I   ++ SK + DAA+ GD LA+ + E
Sbjct: 180 KKGCLETVASATGMVNLAGYHSDDHENSVLIAAIKEGTLTSKAIVDAAMTGDPLAEFVVE 239

Query: 243 FTGNILGEALADAIAFSSPEAIILFGGLAKSGDYIMKPIMKAMENNLLNIYKGKAKLLVS 302
                L  A++     ++P   +  GG++++G Y+   I K  ++ +        +++++
Sbjct: 240 EAARYLAVAMSSISVITNPGYFVFGGGVSRAGRYLTDKIKKYYDSLIFPPAADDVEIVMA 299

Query: 303 ELKDSDAAVLGASAL 317
           EL  +DA + GA+ L
Sbjct: 300 EL-GNDAGMYGAARL 313


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: 286
Number of extensions: 16
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: 319
Length adjustment: 28
Effective length of query: 298
Effective length of database: 291
Effective search space:    86718
Effective search space used:    86718
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