GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Dinoroseobacter shibae DFL-12

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate 3610445 Dshi_3826 3-hydroxyacyl-CoA dehydrogenase NAD-binding (RefSeq)

Query= BRENDA::O87873
         (258 letters)



>FitnessBrowser__Dino:3610445
          Length = 673

 Score = 70.9 bits (172), Expect = 7e-17
 Identities = 50/178 (28%), Positives = 78/178 (43%), Gaps = 7/178 (3%)

Query: 12  LERDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVD 71
           ++ D  L  + +  P  N    A+   +  A+    +    R  +L   G  F  G  + 
Sbjct: 9   VDTDTGLAWVTVDNPPVNATSTAVRQGLLDAV---TRVQGARLAILRCAGRTFIAGGDMR 65

Query: 72  EHMPDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAKFGQ 131
           E            L  +V  +  S  P +  ++G  LGGGLE+A       AAP  +FG 
Sbjct: 66  EF---DAPPQPPDLPDVVDAIEASATPFVAVMQGTVLGGGLEIAMGCAYRIAAPGTRFGL 122

Query: 132 PEIRLGVFAPAASCLLPPRV-GQACAEDLLWSGRSIDGAEGHRIGLIDVLAEDPEAAA 188
           PE+ +G+   A      PR+ G   A D+  +G+ +   E H  G +D +A+DPEAAA
Sbjct: 123 PEVTVGLIPGAGGTQRAPRLFGWDAAIDMACAGKLLSAQEAHARGALDAIADDPEAAA 180


Lambda     K      H
   0.321    0.135    0.402 

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: 478
Number of extensions: 27
Number of successful extensions: 2
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: 258
Length of database: 673
Length adjustment: 31
Effective length of query: 227
Effective length of database: 642
Effective search space:   145734
Effective search space used:   145734
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 (21.9 bits)
S2: 50 (23.9 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