GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Sphingomonas koreensis DSMZ 15582

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate Ga0059261_4061 Ga0059261_4061 Transcriptional regulator/sugar kinase

Query= BRENDA::B1VZT1
         (313 letters)



>FitnessBrowser__Korea:Ga0059261_4061
          Length = 291

 Score = 87.0 bits (214), Expect = 5e-22
 Identities = 92/321 (28%), Positives = 135/321 (42%), Gaps = 56/321 (17%)

Query: 5   IGVDIGGTKIAAGVVDEEGRILSTFKVATPPTAEGIVDAICAAVAGASEGHDVEAVGIGA 64
           + ++ GGTK+ A +V +EG +       T P A    +A   A AG +    +  VGI A
Sbjct: 8   LAIETGGTKLLARLVRDEGVVAEARWPTTSPEA---AEAALLAFAGRTP---LAGVGIAA 61

Query: 65  AG--YVDDKRAT---VLFAPNIDWRHEPLKDKVEQRVGLPVVVENDANAAAWGEYRFGAG 119
            G   VD   A    VL  P   W    L+  +EQ +G+PV ++ D NAAA  E   GAG
Sbjct: 62  FGPVVVDPAAANYGEVLATPKPGWTGANLRAALEQALGVPVAIDTDVNAAALAEAAAGAG 121

Query: 120 QGHDDVICITLGTGLGGGIIIGNKLRRGRFGVAAEFGHIRVV-----PDGLLCGCGSQGC 174
           QG   +  +T+GTG+G G+    +   G   +  E GH+ V+     P    C   S GC
Sbjct: 122 QGCSSLAYVTVGTGIGAGLARDGRTLTG--ALHPEMGHVPVLRFEGDPTPSACPFHS-GC 178

Query: 175 WEQYASGRALVRYAKQRANATPENAAVLLGLGDGSVDGIEGKHISEAARQGDPVAVDSFR 234
            E  A+G A+ R                          + GK + ++           F 
Sbjct: 179 AEGMAAGPAVQR-------------------------RLGGKLLEDSPA--------DFA 205

Query: 235 ELARWAGAGLADLASLFDPSAFIVGGGVSDE---GELVLDPIRKSFRRWLIGGEWRPHAQ 291
            +A + G   A +   + P   +VGGGV D    G+     +R +   + +G        
Sbjct: 206 AVADYLGQLFATIVLAWSPHRIVVGGGVMDVPGLGKAATVRMRVALGGYGVGSAVGEADF 265

Query: 292 VLAAQLGGKAGLVGAADLARQ 312
           + +A L   AGL GA  LARQ
Sbjct: 266 IRSAAL-EHAGLEGALILARQ 285


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: 296
Number of extensions: 17
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 313
Length of database: 291
Length adjustment: 27
Effective length of query: 286
Effective length of database: 264
Effective search space:    75504
Effective search space used:    75504
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 17 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