GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glk in Escherichia coli BW25113

Align glucokinase (EC 2.7.1.2) (characterized)
to candidate 15241 b1119 N-acetyl-D-glucosamine kinase (NCBI)

Query= reanno::SB2B:6938110
         (299 letters)



>FitnessBrowser__Keio:15241
          Length = 303

 Score =  206 bits (524), Expect = 5e-58
 Identities = 125/300 (41%), Positives = 173/300 (57%), Gaps = 7/300 (2%)

Query: 2   MRMGVDLGGTKIELVALGEDGSELFRKRIATPRE-YQGTLNAVVTLVNEAEATLGTQGSL 60
           M  G D+GGTKI L          + KR+ TPR+ Y   L+AV  LV EA+   G +GS+
Sbjct: 1   MYYGFDIGGTKIALGVFDSGRQLQWEKRVPTPRDSYDAFLDAVCELVAEADQRFGCKGSV 60

Query: 61  GIGIPGVISPYTGLVKNANSTWINGHPLDRDLGALLNREVRVANDANCFAVSEAVDGAAA 120
           GIGIPG+     G +  AN    +G PL  DL A L+R+VR+ NDANCFA+SEA D    
Sbjct: 61  GIGIPGMPETEDGTLYAANVPAASGKPLRADLSARLDRDVRLDNDANCFALSEAWDDEFT 120

Query: 121 GKRVVFGAILGTGCGAGLAFDGRVHEGGNGIGGEWGHNPLP----WMRPDEFNTTECFCG 176
              +V G ILGTG G GL F+G+   G + I GE+GH  LP     M   +F    C CG
Sbjct: 121 QYPLVMGLILGTGVGGGLIFNGKPITGKSYITGEFGHMRLPVDALTMMGLDFPLRRCGCG 180

Query: 177 NKDCIETFVSGTGFVRDFRNSGGTAQNGAEIMSLVDAGDELANLVFDRYLDRLARSLAHV 236
              CIE ++SG GF   +++         EI++L D GDE A    +RYLD LA  L ++
Sbjct: 181 QHGCIENYLSGRGFAWLYQHYYHQPLQAPEIIALYDQGDEQARAHVERYLDLLAVCLGNI 240

Query: 237 INMLDPDAIVLGGGMSNVQAIYARLPAILPKYVVGRECRTPVVQNL-YGCSSGVRGAAWL 295
           + ++DPD +V+GGG+SN  AI  +L   LP++++    R P ++   +G + G+RGAA+L
Sbjct: 241 LTIVDPDLVVIGGGLSNFPAITTQLADRLPRHLL-PVARVPRIERARHGDAGGMRGAAFL 299


Lambda     K      H
   0.320    0.139    0.429 

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: 295
Number of extensions: 17
Number of successful extensions: 3
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: 299
Length of database: 303
Length adjustment: 27
Effective length of query: 272
Effective length of database: 276
Effective search space:    75072
Effective search space used:    75072
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 (21.8 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