GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davA in Acidovorax caeni R-24608

Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_054254879.1 BN2503_RS01565 aliphatic amidase

Query= BRENDA::B3IVI7
         (264 letters)



>NCBI__GCF_001298675.1:WP_054254879.1
          Length = 348

 Score = 67.8 bits (164), Expect = 3e-16
 Identities = 56/202 (27%), Positives = 87/202 (43%), Gaps = 6/202 (2%)

Query: 33  GAQLLVCPEMFLTGYNIGLAQVERLAEAADGPAAMTVVEIAQAHRIAIVYGYP----ERG 88
           G  L++ PE    G      ++   A A  G       E  +  ++  V+       E  
Sbjct: 51  GMDLVIFPEYSTHGIMYDAKEMYDTAAAVPGEETAIFAEACRKAKVWGVFSLTGERHEEH 110

Query: 89  DDGAIYNSVQLIDAHGRSLSNYRKTHLFGELDRSMFSPGADHFPVVELEGWKVGLLICYD 148
            + A YN++ L++  G  +  YRK   +  ++   + PG   +     +G KV L+IC D
Sbjct: 111 PNKAPYNTLILMNDQGEIVQKYRKIMPWVPIEG--WYPGNCTYVSEGPKGLKVSLIICDD 168

Query: 149 IEFPENARRLALDGAELILVPTANMTPYDFTCQVTVRARAQENQCYLVYANYCGAEDEIE 208
             +PE  R  A+ GAELI+     M P      +  +A A  N  Y+  AN  G +    
Sbjct: 169 GNYPEIWRDCAMKGAELIVRCQGYMYPAKDQQVLMAKAMAWANNSYVAVANATGWDGVYS 228

Query: 209 YCGQSSIIGPDGSLLAMAGRDE 230
           Y G S++IG DG  L   G +E
Sbjct: 229 YFGHSALIGFDGRTLGECGEEE 250


Lambda     K      H
   0.322    0.139    0.416 

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: 226
Number of extensions: 8
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: 264
Length of database: 348
Length adjustment: 27
Effective length of query: 237
Effective length of database: 321
Effective search space:    76077
Effective search space used:    76077
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: 48 (23.1 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