GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Sphingomonas koreensis DSMZ 15582

Align glucokinase (EC 2.7.1.1; EC 2.7.1.2; EC 2.7.1.8) (characterized)
to candidate Ga0059261_0355 Ga0059261_0355 glucokinase, proteobacterial type

Query= ecocyc::GLUCOKIN-MONOMER
         (321 letters)



>FitnessBrowser__Korea:Ga0059261_0355
          Length = 323

 Score =  160 bits (405), Expect = 4e-44
 Identities = 107/314 (34%), Positives = 156/314 (49%), Gaps = 8/314 (2%)

Query: 9   DVGGTNARLALCDIASGE---ISQAKTYSGLDYPSLEAVIRVYLEEHKVEV-KDGCIAIA 64
           D+GGT+AR A+ ++  G    I +  T    ++ S +   +        E+ +   IAIA
Sbjct: 7   DIGGTHARFAIAEVEGGRVVSIGEPVTQKTAEHGSFQLAWQASARALGREMPRAAAIAIA 66

Query: 65  CPITGDWVAMTNHTWAFSIAEMKKNLGFSHLEIINDFTAVSMAIPMLKKEHLIQFGGAEP 124
            PI  + + +TN+ W      +K+ L      +INDF AV  A+  L  EH +   G + 
Sbjct: 67  SPINDELIKLTNNPWIIRPPLIKERLEVDSYSLINDFGAVGHAVAQLPSEHFLHICGPDA 126

Query: 125 --VEGKPIAVYGAGTGLGVAHLVHVDK-RWVSLPGEGGHVDFAPNSEEEAIILEILRAEI 181
              E   I V G GTGLGVA +       +  +  EGGH+DFAP    E  I++ LR+  
Sbjct: 127 PFAEKGAITVCGPGTGLGVAQVFRTGPLSYHVISTEGGHMDFAPLDGIEDSIVKRLRSTY 186

Query: 182 GHVSAERVLSGPGLVNLYRAIVKADNRLPENLKPKDITERALADSCTDCRRALSLFCVIM 241
             VSAER+++GPG+V +Y  + + + +    L  K+I   A     +    AL  FC+ +
Sbjct: 187 TRVSAERIVAGPGIVPIYETLAEIEGKRTHRLNDKEIWTLAFEGKDSLAMAALDRFCLSL 246

Query: 242 GRFGGNLALNLGTFGGVFIAGGIVPRFLEFFKASGFRAAFEDKGRFKEYVHDIPVYLIVH 301
           G   G+LAL  G   GV IAGG+  +  +    SGF   F  KGRF+  +  IPV LI H
Sbjct: 247 GAVAGDLALAHGP-TGVVIAGGLGLKLKDHLVNSGFGQRFIAKGRFQALMSSIPVKLITH 305

Query: 302 DNPGLLGSGAHLRQ 315
             PGL G+ A   Q
Sbjct: 306 PQPGLYGAAAAYAQ 319


Lambda     K      H
   0.322    0.141    0.426 

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: 294
Number of extensions: 16
Number of successful extensions: 5
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: 321
Length of database: 323
Length adjustment: 28
Effective length of query: 293
Effective length of database: 295
Effective search space:    86435
Effective search space used:    86435
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 (21.9 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