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_1776 Ga0059261_1776 Transcriptional regulator/sugar kinase

Query= BRENDA::Q8RDE9
         (315 letters)



>FitnessBrowser__Korea:Ga0059261_1776
          Length = 335

 Score = 96.3 bits (238), Expect = 9e-25
 Identities = 95/329 (28%), Positives = 142/329 (43%), Gaps = 62/329 (18%)

Query: 5   LCGVDLGGTKISTGIVDENGNIIKSIKIPTMAEKGPDVVIERIEESIYQVLKDTGLEMSN 64
           L  V+ GGTK   GI D  G+++   +IPT     P   ++       + +   G     
Sbjct: 19  LGAVEAGGTKFLCGIADRTGSVLAQTRIPTTT---PAETLDAATAFFAEHVARHG----P 71

Query: 65  LKGIGIGSPGPLNAKK-----GIVISPPNLPHWSNVPIVEILSKRLGIEVRLENDANAAA 119
           L    +GS GPL+        G + S P  P W +V ++    + +   + L+ D N AA
Sbjct: 72  LSAFSVGSFGPLSLDPIAPDYGSITSTPK-PGWQDVDLLGYFRQMIDAPMALDTDVNCAA 130

Query: 120 IGEHLFGSGRGVDNFVYITVSTGIGGGVIIEGKLYSGENSNAAEIGHHTI-------NFD 172
           +GE LFGSGRG+D F Y+TV TGIG G+++ G  + G  +N  E GH  +       +F 
Sbjct: 131 VGERLFGSGRGLDTFCYVTVGTGIGVGLLVGGAPHGG--ANHPEAGHIRLPRAPGDHDFA 188

Query: 173 GPRCNCGNYG-CFEAYASGTAIARFAREGIEKGIKTKIKELAGEGEVKAEHVFEAAKL-G 230
           G    C  +G C E  A G A                         +KA     A  L G
Sbjct: 189 G---ICPFHGDCLEGLACGPA-------------------------MKARWGAAAETLPG 220

Query: 231 DEFAKELVEKEAFYLGVGIANIMAFYNPRKIAIGGGVSAQWDMLYEKMMETVRKKALKPN 290
           D  A ++   EA YL    A +     P +I +GGGV  +  +++ ++  T+  K    +
Sbjct: 221 DHPAWDI---EADYLAGLCATLTYIVRPDRIILGGGV-MESHLMHARVRRTLVAKLAGYD 276

Query: 291 AEVCE------VVKAQLGENIGVLGAAAL 313
           A +        VV    G + G+ GA AL
Sbjct: 277 ASMRSLDMDEYVVPPTAGPSAGLTGAFAL 305


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: 242
Number of extensions: 14
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: 315
Length of database: 335
Length adjustment: 28
Effective length of query: 287
Effective length of database: 307
Effective search space:    88109
Effective search space used:    88109
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: 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