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Table 1 Representative search hits supporting the SUMO relationship of globular segments in RENi family members. RENi family members (column 1) have been initially split into likely globular segments (column 2). These sequences have been submitted to sequence-based domain and fold-recognition methods (RPS-BLAST [8], FFAS03 [37], column 3) as well as a structure-based similarity method (INBGU [41]) (column 4). For FFAS03 scores below -9.5 are considered significant, for the Fischer fold prediction method (INBGU) it is a score of 12 and above. The following database identifiers correspond to the tabulated domains: COG5227 for the SMT3 domain in COG, smart00213 for UBQ (ubiquitin and ubiquitin-like) in SMART. The mentioned PDB identifiers represent structures of the following molecules: 1A5R Sumo-1 in human, 1L2NA Smt3, the SUMO homolog in budding yeast, 1EUVB Smt3 in budding yeast. The sequence-only similarity methods can be ordered with increasing sensitivity as: (i) RPS-BLAST, (ii) FFAS03 against a sequence database (COG), and (iii) FFAS03 against a structure database (SCOP). Only the significant hit with the lowest sensitivity method is reported for each sequence.

From: Proteins with two SUMO-like domains in chromatin-associated complexes: The RENi (Rad60-Esc2-NIP45) family

Species/Accession

Segment

Method/DB/Hit/E-value

Hit/Score

D. melanogaster/ NP_651134

220–325

FFAS03/COG/SMT3/-10.400

1A5R/27.1

1L2NA/13.6

 

325–424

RPS-BLAST/COG/SMT3/9e-04

1L2NA/42.4

1A5R/24.4

S. pombe/ NP_595995

200–315

FFAS03/scop165/1euvb/-11.4

1L2NA/26.4

1A5R/19.7

 

315–406

FFAS03/COG/SMT3/-16.3

1A5R/16.1

1L2NA/15.2

S. cerevisiae/ NP_010650

330–456

FFAS03/COG/SMT3/-36.6

1A5R/89.7

1L2NA/35.0

C. elegans/ NP_497960

115–225

FFAS03/COG/SMT3/-11.8

1A5R/27.2

 

225–328

FFAS03/COG/SMT3/-15.3

1A5R/38.5

1L2NA/17.6

M. musculus/ NP_035030

220–320

RPS-BLAST/SMART/UBQ/3e-05

FFAS03/COG/SMT3/-11

1L2NA/24.3

1A5R/19.9

 

320–412

RPS-BLAST/COG/SMT3/1e-04

1L2NA/89.4

1A5R/71.6

A. nidulans/ EAA62889

160–300

FFAS03/COG/SMT3/-8.3

1A5R/22.5

 

300–404

RPS-BLAST/SMART/UBQ/3e-04

FFAS03/COG/SMT3/-39.100

1A5R/87.4

1L2NA/30.6

A thaliana/ NP_564924

130–213

RPS-BLAST/COG/SMT3/4e-06

1L2NA/119.1

1A5R/51.4

D discoideus/ JC3V1_0C0008_11033

230–340

RPS-BLAST/COG/SMT3/0.001

1A5R/141.9

1L2NA/57.0

 

340–449

FFAS03/COG/SMT3/-33.600

1A5R/51.3

1L2NA/39.4