GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_4061 Ga0059261_4061
           Transcriptional regulator/sugar kinase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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