GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcE in Cupriavidus basilensis 4G11

Align D-lactate oxidase, FAD binding subunit (EC 1.1.3.15) (characterized)
to candidate RR42_RS17310 RR42_RS17310 glycolate oxidase

Query= reanno::Cup4G11:RR42_RS17310
         (374 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS17310 RR42_RS17310 glycolate
           oxidase
          Length = 374

 Score =  746 bits (1925), Expect = 0.0
 Identities = 374/374 (100%), Positives = 374/374 (100%)

Query: 1   MPATPADQQATLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDY 60
           MPATPADQQATLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDY
Sbjct: 1   MPATPADQQATLTAFRDAIRHATGTRTPLRLRGGGSKDFYGQHPQGTLLDTRAYSGIVDY 60

Query: 61  DPPELVITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPR 120
           DPPELVITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPR
Sbjct: 61  DPPELVITARCGTPLAQIEAALAERRQMLAFEPPHFSTGADGSDVATIGGAVAAGLSGPR 120

Query: 121 RQAVGALRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKV 180
           RQAVGALRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKV
Sbjct: 121 RQAVGALRDFVLGTRVMDGRGDVLSFGGQVMKNVAGYDVSRLMSGSLGTLGLILEVSLKV 180

Query: 181 LPVPFDDATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARAR 240
           LPVPFDDATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARAR
Sbjct: 181 LPVPFDDATLRFALDEAAALDRLNDWGGQPLPIAASAWHDGVLHLRLSGAAAALRAARAR 240

Query: 241 LGGEAVDAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGG 300
           LGGEAVDAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGG
Sbjct: 241 LGGEAVDAAQADALWRALREHSHAFFAPVQAGRALWRIAVPTTAAPLALPGGQLIEWGGG 300

Query: 301 QRWWLGGSDSAADSAIVRAAAKAAGGHATLFRNGDKAVGVFTPLSAPVAAIHQRLKATFD 360
           QRWWLGGSDSAADSAIVRAAAKAAGGHATLFRNGDKAVGVFTPLSAPVAAIHQRLKATFD
Sbjct: 301 QRWWLGGSDSAADSAIVRAAAKAAGGHATLFRNGDKAVGVFTPLSAPVAAIHQRLKATFD 360

Query: 361 PAGIFNPQRMYAGL 374
           PAGIFNPQRMYAGL
Sbjct: 361 PAGIFNPQRMYAGL 374


Lambda     K      H
   0.321    0.136    0.414 

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: 616
Number of extensions: 10
Number of successful extensions: 1
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: 374
Length of database: 374
Length adjustment: 30
Effective length of query: 344
Effective length of database: 344
Effective search space:   118336
Effective search space used:   118336
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 (21.8 bits)
S2: 50 (23.9 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