GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Cronobacter universalis NCTC 9529

Align 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale)
to candidate WP_007700802.1 AFK65_RS15785 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD

Query= uniprot:Q8EGC1
         (252 letters)



>NCBI__GCF_001277175.1:WP_007700802.1
          Length = 253

 Score =  108 bits (270), Expect = 1e-28
 Identities = 80/256 (31%), Positives = 128/256 (50%), Gaps = 23/256 (8%)

Query: 3   LKDKVVVITGGAGGLGLAMAHNFAQAGAKLALIDVDQ--DKLERACADLGSSTEVQGYAL 60
           L+ KV ++TG   GLG  MA   A+AG  +  I++ +  + +ER  A LG          
Sbjct: 8   LQGKVAIVTGCDTGLGQGMALGLAEAGCDIVGINIVEPTETIERVTA-LGR--RFLSLTA 64

Query: 61  DITDEEDVVAGFAYILEDFGKINVLVNNAGILRDGMLVKAKDGKVTDRMSFDQ--FQSVI 118
           D+   + +       + +FG ++VLVNNAG++R             D ++F +  +  V+
Sbjct: 65  DLRKIDAIPELIERAVAEFGHVDVLVNNAGLIRR-----------EDAINFSEQDWDDVM 113

Query: 119 NVNLTGTFLCGREAAAAMIESGQAGVIVNISS-LAKAGNVGQSNYAASKAGVAAMSVGWA 177
           N+N+   F   +  A   I  G  G I+NI+S L+  G +   +Y ASK+GV  ++   A
Sbjct: 114 NLNIKSVFFMSQTVAKQFIAQGNGGKIINIASMLSFQGGIRVPSYTASKSGVMGITRLMA 173

Query: 178 KELARYNIRSAAVAPGVIATEMTAAMKPEALERLEKL--VPVGRLGHAEEIASTVRFIIE 235
            E A++NI   A+APG +AT  T  ++ +     E L  +P GR G   ++   V F+  
Sbjct: 174 NEWAKHNINVNAIAPGYMATNNTQQLRADEQRSAEILDRIPAGRWGLPSDLMGPVVFLAS 233

Query: 236 --NDYVNGRVFEVDGG 249
             +DY+NG    VDGG
Sbjct: 234 SASDYINGYTVAVDGG 249


Lambda     K      H
   0.317    0.134    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: 163
Number of extensions: 15
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: 252
Length of database: 253
Length adjustment: 24
Effective length of query: 228
Effective length of database: 229
Effective search space:    52212
Effective search space used:    52212
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: 46 (22.3 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