GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Shewanella sp. ANA-3

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate 7025639 Shewana3_2790 fructokinase (RefSeq)

Query= BRENDA::Q8R8N4
         (312 letters)



>FitnessBrowser__ANA3:7025639
          Length = 306

 Score =  127 bits (319), Expect = 3e-34
 Identities = 82/273 (30%), Positives = 135/273 (49%), Gaps = 19/273 (6%)

Query: 1   MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60
           +R+G+DLGGT I +  + E+G  +    +     R Y+     I +L  E    +G    
Sbjct: 2   IRMGIDLGGTKIELVALSEEGNELFR--KRINTPRDYQGTLNAIVDLVNEAEATLG---- 55

Query: 61  DVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEAT 120
           +  ++G+G+PGV     G+V  A + +    PL   + + +   + + NDAN  A++EA 
Sbjct: 56  EKGTVGVGIPGVISPYSGLVKNANSTWINGHPLDVNLGELLGREVRVANDANCFAVSEAV 115

Query: 121 FGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVI------GDNGIRCNC 174
            GA  G      + +GTG G+G  ++GK+++G +    E GH  +        N  RC C
Sbjct: 116 DGAAAGKSVVFGVIIGTGCGAGVAINGKVHAGGNGIGGEWGHNPLPWMTKEEFNTTRCFC 175

Query: 175 GKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEEALK 234
           G   C ET+ S T  +R+  +A  R  N      A     G     ++DA    DE A+ 
Sbjct: 176 GNPDCIETFISGTGFVRDYNEALSRAVNVQ----AAPAKSGTEIMALVDAG---DEMAIA 228

Query: 235 IFEEYVKYLAVGIVNIINLFDPEVIILGGGVAN 267
            F+ Y+  LA  + ++IN+ DP+ I+LGGG++N
Sbjct: 229 AFDRYMDRLARSLAHVINMLDPDAIVLGGGMSN 261


Lambda     K      H
   0.318    0.140    0.397 

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: 292
Number of extensions: 13
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: 312
Length of database: 306
Length adjustment: 27
Effective length of query: 285
Effective length of database: 279
Effective search space:    79515
Effective search space used:    79515
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 (21.7 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