GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucD in Desulfitobacterium hafniense DCB-2

Align L-fuconate dehydratase; L-rhamnonate dehydratase (EC 4.2.1.68; EC 4.2.1.90) (characterized)
to candidate WP_011460067.1 DHAF_RS16340 UxaA family hydrolase

Query= reanno::BFirm:BPHYT_RS34230
         (431 letters)



>NCBI__GCF_000021925.1:WP_011460067.1
          Length = 385

 Score =  229 bits (584), Expect = 1e-64
 Identities = 151/399 (37%), Positives = 212/399 (53%), Gaps = 33/399 (8%)

Query: 10  LEGYLRGDGRKGIRNVVAVAYLVECAHHVAREIVTQFREPLDAFDDPSAEREPPVHLIGF 69
           L G+ R DG  GIRN + +     CA  VA  I  Q          P A     V +   
Sbjct: 3   LWGFRRPDGLFGIRNHLLILPTSVCATTVAANIAAQV---------PGA-----VAIANQ 48

Query: 70  PGCYPNG--YAEKM--LERLTTHPNVGAVLFVSLGCESMNKHYLVDVVRASGRPVEVLTI 125
            GC   G  Y + +  L  +  +PNVGAVL V LGCE +   +  + +  SG+PV+ L I
Sbjct: 49  HGCCQLGADYEQTLRTLIGIGRNPNVGAVLVVGLGCEGIPILHTAEEIAKSGKPVQSLII 108

Query: 126 QEKGGTRSTIQYGVDWIRGAREQLAAQQKVPMALSELVIGTICGGSDGTSGITANPAVGR 185
           QE GGT  T   GV         L+  ++    LSEL +G  CGGSD TSG+ ANPA G 
Sbjct: 109 QEHGGTLKTTALGVQVAAQMARTLSMLKREEAPLSELSLGVECGGSDFTSGLAANPAAGT 168

Query: 186 AFDHLIDAGATCIFEETGELVGCEFHMKTRAARPALGDEIVACV----AKAARYYSILGH 241
           A D ++ AG T +  ET E +G E  +  RA  P +  +++  V     +A + +  L  
Sbjct: 169 ASDLVVKAGGTAMLSETTEFIGAEHVLAKRAKSPEVAAKLLGIVKETELRARQLHVDLRD 228

Query: 242 GSFAVGNADGGLTTQEEKSLGAYAKSGASPIVGIIKPGDIPPTGGLYLLDVVPDGEPRFG 301
           G    GN  GG+++ EEKSLG   K+G S I  I+  G+ P   GLY++D          
Sbjct: 229 GQPTPGNIAGGISSIEEKSLGCIYKAGHSTIQDILAYGEAPQGKGLYVMDT--------- 279

Query: 302 FPNISDNAEIGELIACGAHVILFTTGRGSVVGSAISPVIKVCANPATYRNLSGDMDVDAG 361
            P     + IG ++A G  +I+FTTGRG+  GS I+PVIKV AN  TY N++ ++D+D  
Sbjct: 280 -PGQDVESMIG-MLAGGIQIIVFTTGRGTPTGSPIAPVIKVTANADTYLNMADNIDLDLS 337

Query: 362 RILEGRGTLDEVGREVFEQTVAVSRGAASKSETLGHQEF 400
            IL G  T+++ GR +F++ + V+ G  +KSE+LGHQEF
Sbjct: 338 PILSGAETIEDSGRRIFKEIIEVANGKLTKSESLGHQEF 376


Lambda     K      H
   0.318    0.137    0.408 

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: 487
Number of extensions: 27
Number of successful extensions: 4
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: 431
Length of database: 385
Length adjustment: 31
Effective length of query: 400
Effective length of database: 354
Effective search space:   141600
Effective search space used:   141600
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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