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_017617089.1 CDO52_RS11555 ROK family glucokinase

Query= BRENDA::B1VZT1
         (313 letters)



>NCBI__GCF_002263495.1:WP_017617089.1
          Length = 317

 Score =  333 bits (853), Expect = 4e-96
 Identities = 166/317 (52%), Positives = 221/317 (69%), Gaps = 5/317 (1%)

Query: 1   MGLTIGVDIGGTKIAAGVVDEEGRILSTFKVATPPT--AEGIVDAICAAVAGASE---GH 55
           M LTIGVDIGGTK+AAG+VD +GRIL        PT  +E + D I   V    E   GH
Sbjct: 1   MRLTIGVDIGGTKVAAGMVDPDGRILGDVVRYPTPTNDSEALADVIGRVVVELRERHTGH 60

Query: 56  DVEAVGIGAAGYVDDKRATVLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEYR 115
           D+ AVG+G AG+VD+ RA ++ A N+    +P+ +++ +R+ LPVVVENDANAAAW E R
Sbjct: 61  DIAAVGVGIAGFVDEDRARIVLAANLGLSDDPITERIRRRIDLPVVVENDANAAAWAEAR 120

Query: 116 FGAGQGHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHIRVVPDGLLCGCGSQGCW 175
           FGAG+G D V+ +TLGTG+GGGI++  +L+RGR+GVAAE GH R+V  G  CGCG+ GCW
Sbjct: 121 FGAGRGSDHVVLVTLGTGVGGGIVMDGRLQRGRYGVAAEVGHYRMVRHGRRCGCGNNGCW 180

Query: 176 EQYASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFRE 235
           EQYASGRALV  A+  A   P  AA LL L +G +  I G  I++AA +GD  A++ FR 
Sbjct: 181 EQYASGRALVAEAQDLATTDPVRAAYLLKLAEGDISRIRGPEITQAALEGDEGALECFRA 240

Query: 236 LARWAGAGLADLASLFDPSAFIVGGGVSDEGELVLDPIRKSFRRWLIGGEWRPHAQVLAA 295
           +  W G GLADLA++ DP  F+VGGGVS+ G+++L+P R SF++ + G   R  A +  A
Sbjct: 241 VGEWVGLGLADLAAILDPECFVVGGGVSEAGDILLEPARASFKKHVTGRATRRLADIRTA 300

Query: 296 QLGGKAGLVGAADLARQ 312
           +LG +AG+VGAADLAR+
Sbjct: 301 ELGPQAGIVGAADLARR 317


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: 387
Number of extensions: 19
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: 317
Length adjustment: 27
Effective length of query: 286
Effective length of database: 290
Effective search space:    82940
Effective search space used:    82940
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: 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