GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ligI in Cupriavidus basilensis 4G11

Align 2-pyrone-4,6-dicarboxylate hydrolase; PDC hydrolase; 2-pyrone-4,6-dicarboxylate lactonase; EC 3.1.1.57 (characterized)
to candidate RR42_RS15075 RR42_RS15075 hypothetical protein

Query= SwissProt::O87170
         (293 letters)



>FitnessBrowser__Cup4G11:RR42_RS15075
          Length = 240

 Score = 90.5 bits (223), Expect = 3e-23
 Identities = 65/196 (33%), Positives = 96/196 (48%), Gaps = 23/196 (11%)

Query: 65  GFARNVIVQASCHGTDNAATLDAIARAQGKARGIAVVDPAIDEAELAALHEGGMRGIRFN 124
           G    V+VQ S  G DN+  L+A   A    RG+ VV P     ELA LH  G+RG+R+N
Sbjct: 21  GVRAGVVVQPSFFGCDNSE-LEAALAASPALRGVCVVGPEASAGELARLHGLGVRGLRWN 79

Query: 125 FLKRLVD----DAPKDKFLEVAGRLPAGWHVVIYFEADILEELRPFMDAIPVPIVIDHMG 180
            + R  D    DA     LE A  L  GWH+ ++ +   L ELR ++ A+P+ +V+DH G
Sbjct: 80  MVGRHDDASWRDARWPALLEAAHAL--GWHLELHTDPGRLNELRAWLPAVPIALVLDHFG 137

Query: 181 RPDVRQGPDGADMKAFRRLLDSREDIWFKATCPDRLDPAGPPWDDFARSVAPLVADY--- 237
           +P      D A M A       + +++ K + P R+          A  +A +VA +   
Sbjct: 138 KPAPGAQAD-APMLACAAHWRGQREVYVKLSAPYRV----------AADLAGVVAGWHHC 186

Query: 238 --ADRVIWGTDWPHPN 251
                ++WG+DWP  N
Sbjct: 187 LGEQGLLWGSDWPWTN 202


Lambda     K      H
   0.323    0.140    0.455 

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: 242
Number of extensions: 15
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: 293
Length of database: 240
Length adjustment: 25
Effective length of query: 268
Effective length of database: 215
Effective search space:    57620
Effective search space used:    57620
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: 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