GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Weissella oryzae SG25

Align glucokinase subunit (EC 2.7.1.1) (characterized)
to candidate WP_027699343.1 TT13_RS07125 ROK family protein

Query= metacyc::MONOMER-6081
         (323 letters)



>NCBI__GCF_000691805.2:WP_027699343.1
          Length = 405

 Score = 68.2 bits (165), Expect = 3e-16
 Identities = 55/177 (31%), Positives = 86/177 (48%), Gaps = 11/177 (6%)

Query: 5   LLGIDLGGTSIKFGILTLDGQVQEKWAIETNILEDGKHIVPDIVSSIKHR-LELYNL-TK 62
           L+  D+G   +++    L G++     I+     D +    D+  ++  R L L +L T 
Sbjct: 85  LMTFDIGRNHLRYLAARLTGEILSHDQIDV----DAEMSYEDLKRTMLERVLRLGDLGTI 140

Query: 63  EDFVGIGMGSPGAVDRNLKTVTGAFNLNWAATQEVGTIIEAELGIPFAIDNDANVAALGE 122
              VGI +G  G V+ N    T  FN  +    ++   +E  L +P  ++N+AN+AA   
Sbjct: 141 NGLVGISIGIHGVVNDNRVAYT-PFN-RFLLEHDLAHELEVALDVPVFLENEANLAAYYL 198

Query: 123 RWVGAGNNNP---DVVFVTLGTGVGGGIIADGNLIHGVAGAGGEIGHIIVEPDTGFE 176
           R     N  P   D   V +  GVG GII +G L+ G+ GA GEIG +IV  D G++
Sbjct: 199 RDFHENNFEPMREDFAVVNVHNGVGAGIIQNGQLVRGIKGAAGEIGRMIVFDDHGWQ 255


Lambda     K      H
   0.316    0.137    0.394 

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: 257
Number of extensions: 14
Number of successful extensions: 1
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: 323
Length of database: 405
Length adjustment: 29
Effective length of query: 294
Effective length of database: 376
Effective search space:   110544
Effective search space used:   110544
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 (21.6 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