GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badK in Dyella japonica UNC79MFTsu3.2

Align BadK (characterized)
to candidate N515DRAFT_1164 N515DRAFT_1164 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1164
          Length = 260

 Score =  171 bits (434), Expect = 1e-47
 Identities = 102/250 (40%), Positives = 145/250 (58%), Gaps = 2/250 (0%)

Query: 11  QGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAG-NTRAFAAGADIAS 69
           +G V IIT+NRPD LNALN   ++ L  A      DD +  +V+AG   +AF AGADIA 
Sbjct: 11  RGAVRIITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDKAFVAGADIAE 70

Query: 70  MAAWSYSDVYG-SNFITRNWETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKF 128
           M  ++     G S    R   +I ++ KPV+A + G A GGG ELA+AC + +A   A+F
Sbjct: 71  MNGYTPVQAQGFSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACHLRVASEKARF 130

Query: 129 ALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRD 188
             PEI LGL+PG GGTQRL R  G+  A+++CL+   + A+ A   G+V+RVV  + L +
Sbjct: 131 GQPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVNRVVAPEALDE 190

Query: 189 ETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFL 248
              ALA  +AA +  A   + +++ +  E  L +G+ FE +     F++ D REG  AFL
Sbjct: 191 TVDALADQLAASAPLAAAGILDAILQGGEMALDQGLEFETQAFALAFSTEDMREGTTAFL 250

Query: 249 EKRAPCFSHR 258
           EKR   F  R
Sbjct: 251 EKRKAEFKGR 260


Lambda     K      H
   0.321    0.135    0.389 

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: 134
Number of extensions: 7
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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