GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ivdG in Dyella japonica UNC79MFTsu3.2

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate N515DRAFT_0944 N515DRAFT_0944 3-oxoacyl-[acyl-carrier protein] reductase

Query= metacyc::MONOMER-11802
         (255 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_0944 N515DRAFT_0944
           3-oxoacyl-[acyl-carrier protein] reductase
          Length = 242

 Score = 92.0 bits (227), Expect = 1e-23
 Identities = 77/252 (30%), Positives = 128/252 (50%), Gaps = 26/252 (10%)

Query: 9   IVSGAASGLGAATAQMLVEAGAKVMLVDLN----AQAVEAKARELGDNARFAVADISDEQ 64
           +V+G++ G+G A A  L +AG  ++L   +    A+AV+A  + LG  AR    DI+D  
Sbjct: 6   LVTGSSRGIGRAIALRLAQAGYDLVLHCRSRRDEAEAVQAAIQALGRQARVLQFDIADRA 65

Query: 65  AAQSAVDAAVSAFGSLHGLVNCAGIV--GAEKVLGKQGPHGLASFAKVINVNLIGSFNLL 122
           A  +A++A ++A G+ +G+V  AG+   GA   L  +       + +V+  NL G +N+L
Sbjct: 66  ACAAALEADLAAHGAYYGVVCNAGLTRDGAFPALTDE------DWDQVLRTNLDGFYNVL 119

Query: 123 RLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAARELARF 182
                 M    A      G I+   S++   G  GQ  Y+ASK  +       A ELA+ 
Sbjct: 120 HPLVMPMIRRRAP-----GRIVCITSVSGLIGNRGQVNYSASKAGVIGAAKALALELAKR 174

Query: 183 GIRVMTIAPGIFETPMM-AGMS-DEVRASLAAGVPFPPRLGRPQEYAALARHII--ENSM 238
            I V  +APG+ +T M+ AG+  DE+ A++        R+G P E AA  + ++  E   
Sbjct: 175 RITVNCVAPGLIDTDMVDAGLPLDEILAAIPM-----QRMGTPDEVAAAVQFLLSPEAGY 229

Query: 239 LNGEVIRLDGAL 250
           +  +V+ ++G L
Sbjct: 230 ITRQVLAVNGGL 241


Lambda     K      H
   0.318    0.131    0.358 

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: 118
Number of extensions: 5
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: 255
Length of database: 242
Length adjustment: 24
Effective length of query: 231
Effective length of database: 218
Effective search space:    50358
Effective search space used:    50358
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: 46 (22.3 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, the preprint on GapMind for carbon sources, 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