GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Gracilibacillus halophilus YIM-C55.5

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_003464513.1 J416_RS03055 ROK family transcriptional regulator

Query= BRENDA::Q8RDE9
         (315 letters)



>NCBI__GCF_000359605.1:WP_003464513.1
          Length = 392

 Score =  155 bits (393), Expect = 1e-42
 Identities = 98/312 (31%), Positives = 156/312 (50%), Gaps = 16/312 (5%)

Query: 4   FLCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEMS 63
           F   +DLG   I   + D  GNI  + +I  +     D + +++   I ++ +       
Sbjct: 82  FTISIDLGVKHILGVLTDLRGNI-HAEEIIAIDNTAFDFISQQLMNCIDRLKQQAPTSEY 140

Query: 64  NLKGIGIGSPGPLNAKKGIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAAIGEH 123
            + GIG+G PG +    G ++  PNL  W  V + + L     + + +EN+ANA A GE 
Sbjct: 141 GIVGIGVGVPGVVTTD-GHILLAPNLG-WKRVSLQQKLYDHYQVPILIENEANAGAYGEK 198

Query: 124 LFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTINFDGPRCNCGNYGC 183
           +FG G+  +  VYI+ S GIG G++++G+LY G    + E+GH TI  DG  C CGN GC
Sbjct: 199 VFGIGQATNQLVYISASIGIGVGLLLDGQLYKGLRGFSGELGHMTIEKDGAACRCGNNGC 258

Query: 184 FEAYASGTAIARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKLGDEFAKELVEKEAF 243
           +E YAS  A+       +EK       E A  G V    + E A  G++ A  L ++   
Sbjct: 259 WELYASEKAL-------LEKA------EQASLGTVTLTDLVEKANQGEDIAIRLFKELGD 305

Query: 244 YLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPNAEVCEVVKAQLGE 303
           YLGVG+ N +  +NP ++ +G  +    D +   M + + K  +  N    ++  AQLG+
Sbjct: 306 YLGVGVTNTIHIFNPEQVVLGNSLIQAADFILPAMKKRIEKNTIGFNKNDVKLNVAQLGQ 365

Query: 304 NIGVLGAAALLL 315
              +LG AA  +
Sbjct: 366 YSTLLGIAAFTI 377


Lambda     K      H
   0.316    0.138    0.398 

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: 315
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: 315
Length of database: 392
Length adjustment: 29
Effective length of query: 286
Effective length of database: 363
Effective search space:   103818
Effective search space used:   103818
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