GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Dechlorosoma suillum PS

Align BadI (characterized)
to candidate Dsui_2807 Dsui_2807 enoyl-CoA hydratase/carnithine racemase

Query= metacyc::MONOMER-892
         (260 letters)



>FitnessBrowser__PS:Dsui_2807
          Length = 262

 Score =  103 bits (256), Expect = 5e-27
 Identities = 77/249 (30%), Positives = 118/249 (47%), Gaps = 13/249 (5%)

Query: 12  NGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDRAFCTGGDQSTH 71
           +G   +++NRP + N+      + L+  L     DK V  +VL GAG +AFC G D    
Sbjct: 15  DGRTTLVLNRPAQFNSLSNAMLETLLAELQSIAADKTVRVVVLQGAG-KAFCAGHDLKEM 73

Query: 72  DGNYDGRGTVGL--PMEELHTAIRDVPKPVIARVQGYAIGGGNVLATICDLTICSEKAIF 129
             N+D      L     ++   I+++P+PVIAR+ G A   G  L ++CDL + ++ A F
Sbjct: 74  RSNHDKAFMQALFKLCAKVMLTIQEMPQPVIARIHGIATAAGCQLVSMCDLAVAADVAKF 133

Query: 130 GQVGPKMG--SVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAEAMGLANLCVPHDEL 187
              G  +G     P  G   LAR +G K+A E+    +     EA+  GL N  V   +L
Sbjct: 134 AVSGINVGLFCSTPAVG---LARNMGRKEALEMLLTGEFIDAGEAQRRGLVNRVVALGDL 190

Query: 188 DAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYA---LKLYYDTDESREGV 244
           D  V+   + +  +SP A+A  K+ F      + GI     YA   +       ++ EG+
Sbjct: 191 DEAVEHLVQSILAKSPVAVATGKQMFYKQL--EMGIEAAYQYAGEVMACNMMAGDAAEGI 248

Query: 245 KALQEKRKP 253
            A  EKRKP
Sbjct: 249 DAFIEKRKP 257


Lambda     K      H
   0.319    0.138    0.418 

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: 171
Number of extensions: 8
Number of successful extensions: 5
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: 260
Length of database: 262
Length adjustment: 25
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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 (21.7 bits)
S2: 47 (22.7 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