GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Nocardiopsis gilva YIM 90087

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate WP_017620227.1 CDO52_RS05395 ROK family glucokinase

Query= BRENDA::B1VZT1
         (313 letters)



>NCBI__GCF_002263495.1:WP_017620227.1
          Length = 344

 Score =  323 bits (828), Expect = 4e-93
 Identities = 159/313 (50%), Positives = 220/313 (70%), Gaps = 3/313 (0%)

Query: 2   GLTIGVDIGGTKIAAGVVDEEGRILSTFKVATPPTAEG---IVDAICAAVAGASEGHDVE 58
           GLT+G+DIGG+K+AAGVV+  GR+L+  +  TP  ++    + D I + +      + V 
Sbjct: 13  GLTVGIDIGGSKVAAGVVNPSGRVLARRRTETPDKSKSPKVVEDTIVSVIEELRREYPVH 72

Query: 59  AVGIGAAGYVDDKRATVLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEYRFGA 118
           AVG+GAAG+VD++RA+VLFAP++ WR EPL++ + QR+ LPVVVENDANA+AW E R GA
Sbjct: 73  AVGVGAAGFVDEQRASVLFAPHLAWRKEPLREALTQRLELPVVVENDANASAWAEVRVGA 132

Query: 119 GQGHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHIRVVPDGLLCGCGSQGCWEQY 178
           G+G DD++ + LGTG+GG II+  KL RGR+G+A EFGH+ VVP G  C CG++GCWEQY
Sbjct: 133 GRGVDDILVVNLGTGIGGAIILDGKLHRGRYGIAGEFGHMTVVPGGHRCECGNRGCWEQY 192

Query: 179 ASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFRELAR 238
           ASG A+ R A++ A A    A  L+    G    I G  +S+ AR+GD  +V+   +   
Sbjct: 193 ASGNAVTRDARELAAADSPVARGLIQAVGGDPALITGPLVSDLAREGDRASVELLEDAGG 252

Query: 239 WAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQVLAAQLG 298
           W G GLA+LA+ FDP  FI+GGGVSD G+L+L P R +FRR L G  +RP A+++ A+LG
Sbjct: 253 WLGIGLANLAAAFDPELFIIGGGVSDCGDLLLGPARTAFRRQLTGRGYRPEARIVRAELG 312

Query: 299 GKAGLVGAADLAR 311
            +AGL+GA+ LAR
Sbjct: 313 NEAGLIGASLLAR 325


Lambda     K      H
   0.319    0.140    0.427 

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: 392
Number of extensions: 16
Number of successful extensions: 2
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: 313
Length of database: 344
Length adjustment: 28
Effective length of query: 285
Effective length of database: 316
Effective search space:    90060
Effective search space used:    90060
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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