GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glk in Pedobacter sp. GW460-11-11-14-LB5

Align glucokinase; EC 2.7.1.2 (characterized)
to candidate CA265_RS15640 CA265_RS15640 sugar kinase

Query= CharProtDB::CH_014478
         (324 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS15640 CA265_RS15640 sugar
           kinase
          Length = 395

 Score =  148 bits (374), Expect = 2e-40
 Identities = 88/262 (33%), Positives = 142/262 (54%), Gaps = 5/262 (1%)

Query: 65  KSRLVGIGIGAPGPVNFANGSIEVAVNLGWEKFPIKDILEVETSLPVVVDNDANIAAIGE 124
           K  L+GIGIG PG VN   G     + +      ++D L  +  LPV +DND+++ A+ E
Sbjct: 137 KENLLGIGIGMPGFVNAEKGMNYSFMQVE-NDISLQDYLAKKLRLPVYIDNDSSLIALAE 195

Query: 125 MWKGAGDGAKDLLCVTLGTGVGGGVIANGEIVQGVNGAAGEIGHITSIPEGGAPCNCGKT 184
           +  G     KD+L V +G G G G+I NG++ +G +G AGE  HI  +      C+CGK 
Sbjct: 196 LNFGEARNLKDVLVVNIGWGTGLGMIINGKLYRGSSGYAGEFSHIP-LSNSNTLCSCGKR 254

Query: 185 GCLETIASATGIVRLTMEELTETDKPSELRTVLEQNGQVTSKDVFDAARSKDGLAMHVVD 244
           GCLE   S   +V+   EE  +  + + L+T+     +       +A   +D +A+ ++ 
Sbjct: 255 GCLEVETSLLVMVQKA-EEAVKNGEETSLKTLFNDKSKSHVDHFLNAVVKQDPVAISILA 313

Query: 245 KVAFHLGLALANSANALNPEKIVLGGGVSRAGEVLLAPVRDYFKRFAFPRVAQGAELAIA 304
             AF +G  LA   + +NPE+IVL G  ++AG++LL P++     F  PRVA+  E+  +
Sbjct: 314 DAAFQIGKGLATLIHIMNPERIVLSGRGAKAGKMLLPPIQQAINEFCIPRVAEQTEIKCS 373

Query: 305 TLGNDAGIIGGAWLV--KSYFE 324
           +L ++A ++  A L+   S FE
Sbjct: 374 SLSDEAELLAAASLMVENSLFE 395


Lambda     K      H
   0.316    0.137    0.404 

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: 255
Number of extensions: 14
Number of successful extensions: 4
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: 324
Length of database: 395
Length adjustment: 29
Effective length of query: 295
Effective length of database: 366
Effective search space:   107970
Effective search space used:   107970
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: 49 (23.5 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