GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Cronobacter condimenti 1330

Align ADP-specific glucokinase (EC 2.7.1.147) (characterized)
to candidate WP_007679976.1 BN137_RS02630 fructokinase

Query= BRENDA::Q8R8N4
         (312 letters)



>NCBI__GCF_000319285.1:WP_007679976.1
          Length = 303

 Score =  127 bits (318), Expect = 4e-34
 Identities = 98/320 (30%), Positives = 153/320 (47%), Gaps = 31/320 (9%)

Query: 1   MRIGVDLGGTNIAVGLVEEDGKIIATGSRPTKPERGYEAIARDIAELSFELLQRMGISVK 60
           MRIG+DLGGT   V  + +DG+       PT P   Y      IA L  EL +R      
Sbjct: 1   MRIGIDLGGTKTEVIALSDDGEQRFRHRVPT-PRNDYPQTVETIAGL-VELAER---ETG 55

Query: 61  DVKSMGIGVPGVADNEKGIVIRAVNLFWTKVPLAKEIRKYIDLPIYMENDANVAALAEAT 120
           +  ++G+G+PG      G+V  A + +     L K++   +   + + NDAN  A++EA 
Sbjct: 56  ERGTVGVGIPGTLSPYTGVVKNANSTWLNGQALDKDLSARLAREVRLANDANCFAVSEAV 115

Query: 121 FGAGRGSKSSVTITLGTGVGSGFILDGKIYSGAHHFAPEIGHMVI---GDNGIR------ 171
            GA  G+++   + +GTG GSG  L G+ + GA+  A E GH  +    D+ +R      
Sbjct: 116 DGAAAGAQTVFAVIIGTGCGSGIALGGRSHIGANGNAGEWGHNPLPWMDDDELRYREEVP 175

Query: 172 CNCGKIGCFETYASATALIREGKKAAKRNPNTLILKFANGDIEGITAKNVIDAAKQYDEE 231
           C CGK GC ETY S T    +  + +                + +    +I    + D  
Sbjct: 176 CYCGKQGCIETYISGTGFATDYHRLSG---------------QPLKGSEIIRLVDEQDAL 220

Query: 232 ALKIFEEYVKYLAVGIVNIINLFDPEVIILGGGVANAGDFLLKPLKKEVAENILFKELPY 291
           A      Y   LA  + +I+N+ DP+VI+LGGG++N  D L K +   + ++ +F     
Sbjct: 221 AELALSRYELRLAKSLAHIVNVLDPDVIVLGGGMSNV-DRLYKTV-PPLMKHWVFGGECE 278

Query: 292 ADIRKAELGNDAGIIGAAIL 311
             +RKA  G+ +G+ GAA L
Sbjct: 279 TPVRKAVHGDSSGVRGAAWL 298


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: 268
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: 312
Length of database: 303
Length adjustment: 27
Effective length of query: 285
Effective length of database: 276
Effective search space:    78660
Effective search space used:    78660
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 24 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