GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dhaD in Cronobacter universalis NCTC 9529

Align NAD-dependent glycerol dehydrogenase; Dha-forming NAD-dependent glycerol dehydrogenase; EC 1.1.1.6 (characterized)
to candidate WP_007700802.1 AFK65_RS15785 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= SwissProt::Q92EU6
         (254 letters)



>NCBI__GCF_001277175.1:WP_007700802.1
          Length = 253

 Score =  149 bits (376), Expect = 5e-41
 Identities = 86/245 (35%), Positives = 142/245 (57%), Gaps = 3/245 (1%)

Query: 10  FNITDKVAVVTGAASGIGKAMAELFSEKGAYVVLLDIKEDVKDVAAQINPSRT-LALQVD 68
           F++  KVA+VTG  +G+G+ MA   +E G  +V ++I E  + +       R  L+L  D
Sbjct: 6   FSLQGKVAIVTGCDTGLGQGMALGLAEAGCDIVGINIVEPTETIERVTALGRRFLSLTAD 65

Query: 69  ITKKENIEKVVAEIKKVYPKIDILANSAGVALLEKAEDLPEEYWDKTMELNLKGSFLMAQ 128
           + K + I +++      +  +D+L N+AG+   E A +  E+ WD  M LN+K  F M+Q
Sbjct: 66  LRKIDAIPELIERAVAEFGHVDVLVNNAGLIRREDAINFSEQDWDDVMNLNIKSVFFMSQ 125

Query: 129 IIGREMIATG-GGKIVNMASQASVIALDKHVAYCASKAAIVSMTQVLAMEWAPYNINVNA 187
            + ++ IA G GGKI+N+AS  S     +  +Y ASK+ ++ +T+++A EWA +NINVNA
Sbjct: 126 TVAKQFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGITRLMANEWAKHNINVNA 185

Query: 188 ISPTVILTELGKKAWAG-QVGEDMKKLIPAGRFGYPEEVAACALFLVSDAASLITGENLI 246
           I+P  + T   ++  A  Q   ++   IPAGR+G P ++    +FL S A+  I G  + 
Sbjct: 186 IAPGYMATNNTQQLRADEQRSAEILDRIPAGRWGLPSDLMGPVVFLASSASDYINGYTVA 245

Query: 247 IDGGY 251
           +DGG+
Sbjct: 246 VDGGW 250


Lambda     K      H
   0.316    0.133    0.369 

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: 148
Number of extensions: 6
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: 254
Length of database: 253
Length adjustment: 24
Effective length of query: 230
Effective length of database: 229
Effective search space:    52670
Effective search space used:    52670
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 (21.6 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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 (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