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Table 4 Homology detection results of OB-fold structures using reconstructed ancestral sequences

From: Reconstruction of ancestral protein sequences and its applications

SCOP Superfamily/family

PDB structure

New homologs

NCBI annotation

Nucleic acid-binding proteins/ Anticodon-binding domain

1b7yB, 39–151

N/A

-

 

1b8aA, 1–102

N/A

-

 

1bbuA, 64–151

13431467

DNA polymerase II small subunit

  

15598836

DNA polymerase III, alpha chain

 

1c0aA, 1–106

11261591

DNA polymerase III, alpha chain

  

11499379

conserved hypothetical protein

  

1169392

DNA polymerase III alpha subunit

  

118794

DNA polymerase III alpha subunit

  

13620707

putative DNA polymerase III, alpha chain

  

14194684

DNA polymerase III alpha subunit

  

14194702

DNA polymerase III alpha subunit

  

14195653

DNA polymerase III alpha subunit

  

14195659

DNA polymerase III alpha subunit

  

15594924

DNA polymerase III, subunit alpha

  

15598836

DNA polymerase III, alpha chain

  

15601899

DnaE

  

15642243

DNA polymerase III, alpha subunit

  

15669005

M. jannaschii predicted coding region MJ0818

  

15679404

DNA polymerase delta small subunit

  

3914611

ATP-dependent DNA helicase recG

 

1cuk, 1–64

N/A

-

 

1e1oA, 64–148

11261591

DNA polymerase III, alpha chain XF0204

  

14194684

DNA polymerase III alpha subunit

 

1fguA, 181–298

15219507

hypothetical protein

  

15230563

putative protein

  

15790309

Vng1255c from Halobacterium sp.

  

6166145

DNA polymerase III alpha subunit

  

8778702

T1N15.20

 

1fl0A

10957481

hypothetical protein

 

1g51A, 1–104

14520587

hypothetical protein

  

14591565

hypothetical protein

  

15595886

hypothetical protein

  

3914638

ATP-dependent DNA helicase recG

 

1otcB, 36–126

N/A

-

 

1quqA, 62–152

15387767

probable replication protein a 28 Kd subunit

 

1qvcA, 1–114

N/A

-

Nucleic acid-binding proteins/Cold shock DNA-binding domain like

1a62, 48–125

N/A

-

 

1ah9

N/A

-

 

1bkb, 75–139

15790688

translation initiation factor eIF-5A; Eif5a

 

1c9oA

6014735

Cold shock protein CspSt

 

1csp

N/A

-

 

1d7qA

N/A

-

 

1mjc

N/A

-

 

1rl2

N/A

-

 

1sro

15671445

N utilization substance protein A

  

15794781

N utilisation substance protein A

  

15803711

transcription pausing; L factor

 

2eifA, 73–132

N/A

-

Nucleic acid-binding proteins/DNA ligase, mRNA capping enzyme, domain2

1a0i, 241–349

N/A

-

 

1dgsA, 315–400

N/A

-

 

1ckmA, 238–302

N/A

-

 

1fviA, 190–293

N/A

-

Nucleic acid-binding proteins/Phage ssDNA-binding proteins

1gpc

N/A

-

 

1gvp

N/A

-

 

1pfs

N/A

-

Nucleic acid-binding proteins/RNA polymerase subunit RBP8

1a1d

N/A

-

Staphylococcal nuclease/Staphylococcal nuclease

1eyd

13422779

aldose 1-epimerase *

Bacterial enterotoxins/Bacterial AB5 toxins, B units

1c4qA

N/A

-

 

1prtF

N/A

-

Bacterial enterotoxins/Superantigen toxins

1an8, 19–94

N/A

-

TIMP-like/Tissue inhibitor of metalloproteases

1ueaB, 14–106

N/A

-

Inorganic pyrophosphatase/ Inorganic pyrophosphatase

2prd

N/A

-

MOP-like/BiMOP, duplicated molybdate-binding domain

1b9mA, 127–262

10639288

probable ATP-binding protein

  

10955070

AgtA

  

1175513

Putative ferric transport ATP-binding protein afuC

  

15598450

probable ATP-binding component of ABC transporter

  

3978166

ATPase FbpC

  

4895001

glucose ABC transporter ATPase *

Histidine kinase CheA, C-terminal domain/ Histidine kinase CheA, C-terminal domain

1b3qA, 540–671

N/A

-

  1. * Putative false positives as assessed by manual inspection.
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BMC Ecology and Evolution

ISSN: 2730-7182

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