GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS15640
          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:

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