GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praD in Ruegeria conchae TW15

Align 4-oxalocrotonate decarboxylase; EC 4.1.1.77 (characterized)
to candidate WP_010443489.1 G7G_RS0121215 hydratase/decarboxylase

Query= SwissProt::Q9KWS3
         (256 letters)



>NCBI__GCF_000192475.1:WP_010443489.1
          Length = 258

 Score = 96.7 bits (239), Expect = 4e-25
 Identities = 69/218 (31%), Positives = 104/218 (47%), Gaps = 14/218 (6%)

Query: 22  QLTGDDAVTVREAAEIQRLLIAHRIERGARQVGLKMGFTSRAKMAQMGVSDLIWGRLTSD 81
           QLT D+A ++  A+ ++ L       +G ++VG K+GFT+R      GV   IWG++ +D
Sbjct: 31  QLTLDEAYSI--ASRVREL-------QGKKRVGRKVGFTNRTIWPVYGVDQPIWGQVYAD 81

Query: 82  MWVEEGGEIDLAHYVHPRVEPEICYLLGKRLEGNVTPLEALAAVEAVAPAMEIIDSRYRD 141
                   ++LA Y  PR+EPEI   L       +   +    VE VAP  EI+ S Y D
Sbjct: 82  GLFSTDQPVNLARYSEPRIEPEIVVGLKHAPTAEMNNEQLAGCVEWVAPGFEIVQSIYPD 141

Query: 142 FKFSLPDVIADNASSSGFVVG----AWHKPETDVSNLGMVMSFDGRAVELGTSAAILGSP 197
           +KFS+ D IA        V+G    A     T ++ + + +   G A+E G     LG P
Sbjct: 142 WKFSVEDSIAAQGLHGCLVLGDKIAATQDVLTGLAEVPIALFKGGEAIESGKGENALGGP 201

Query: 198 IRALVAAARLAAQQGEALEAGSLILAGAATAAVALRPG 235
           I  L     L + + + L+ G L+  G  T A  + PG
Sbjct: 202 IEVLAHLVSLLS-EADQLQGGELVTTGTLTDAWPVSPG 238


Lambda     K      H
   0.318    0.132    0.372 

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: 122
Number of extensions: 6
Number of successful extensions: 2
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: 256
Length of database: 258
Length adjustment: 24
Effective length of query: 232
Effective length of database: 234
Effective search space:    54288
Effective search space used:    54288
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: 47 (22.7 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