GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Rhodobacter viridis JA737

Align Methylglutaconyl-CoA hydratase, mitochondrial; AU-specific RNA-binding enoyl-CoA hydratase; AU-binding enoyl-CoA hydratase; muAUH; Itaconyl-CoA hydratase; EC 4.2.1.18; EC 4.2.1.56 (characterized)
to candidate WP_110804971.1 C8J30_RS06890 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q9JLZ3
         (314 letters)



>NCBI__GCF_003217355.1:WP_110804971.1
          Length = 728

 Score = 70.9 bits (172), Expect = 9e-17
 Identities = 55/171 (32%), Positives = 78/171 (45%), Gaps = 15/171 (8%)

Query: 76  NALSKNLLKMLSKAVDALKSDKKVRTIIIRSEVPGIFCAGADLKERAKMHSSEVGPF--- 132
           N +S      LS  VD   +D   + I++ S     F  G DL   AKM +         
Sbjct: 26  NVMSLEGFAQLSALVDGCLADPACKGIVLTSGKKD-FAGGMDLNVIAKMRAGGAEAIFAG 84

Query: 133 VSKIRSVINDIANLPV---------PTIAAIDGLALGGGLELALACDIRVAASS--AKMG 181
           V ++ +V+  I    +         P    + G ALG GLEL L+C    AA +  AK+G
Sbjct: 85  VMQMHAVLRKIERAGMDPKTLKGAKPIACVLPGTALGIGLELPLSCHRIFAAENPKAKIG 144

Query: 182 LVETKLAIIPGGGGTQRLPRAIGMSLAKELIFSARVLDGQEAKAVGLISHV 232
           L E  + I PG GGT RL R +G  +A   +   ++ D + AKA G+I  V
Sbjct: 145 LPEIMVGIFPGAGGTTRLVRKMGAMMAAPFLLEGKLSDPKAAKAAGIIDEV 195


Lambda     K      H
   0.318    0.135    0.377 

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: 400
Number of extensions: 25
Number of successful extensions: 1
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: 314
Length of database: 728
Length adjustment: 33
Effective length of query: 281
Effective length of database: 695
Effective search space:   195295
Effective search space used:   195295
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: 51 (24.3 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