GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Rhodobacter viridis JA737

Align Enoyl-CoA hydratase (characterized, see rationale)
to candidate WP_110804971.1 C8J30_RS06890 3-hydroxyacyl-CoA dehydrogenase

Query= uniprot:A0A2Z5MEB0
         (258 letters)



>NCBI__GCF_003217355.1:WP_110804971.1
          Length = 728

 Score = 79.0 bits (193), Expect = 3e-19
 Identities = 57/173 (32%), Positives = 84/173 (48%), Gaps = 15/173 (8%)

Query: 23  KALNALNDALMDELGVALREFDADDAIGAIVLTGSEKAFAAGADIGMMSTYS-------Y 75
           K++N ++     +L   +    AD A   IVLT  +K FA G D+ +++          +
Sbjct: 23  KSMNVMSLEGFAQLSALVDGCLADPACKGIVLTSGKKDFAGGMDLNVIAKMRAGGAEAIF 82

Query: 76  MDVYKGDYITRNWETV----RSIR--KPIIAAVAGFALGGGCELAMMCDMIFAADT--AK 127
             V +   + R  E      ++++  KPI   + G ALG G EL + C  IFAA+   AK
Sbjct: 83  AGVMQMHAVLRKIERAGMDPKTLKGAKPIACVLPGTALGIGLELPLSCHRIFAAENPKAK 142

Query: 128 FGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAGLVSRV 180
            G PEI +GI PGAGGT RL R +    A    L  +  D   A+ AG++  V
Sbjct: 143 IGLPEIMVGIFPGAGGTTRLVRKMGAMMAAPFLLEGKLSDPKAAKAAGIIDEV 195


Lambda     K      H
   0.322    0.135    0.383 

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: 442
Number of extensions: 32
Number of successful extensions: 3
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: 728
Length adjustment: 32
Effective length of query: 226
Effective length of database: 696
Effective search space:   157296
Effective search space used:   157296
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: 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