GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_1164 N515DRAFT_1164
           enoyl-CoA hydratase
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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