GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Korea:Ga0059261_0355 Ga0059261_0355
           glucokinase, proteobacterial type
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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