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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.