Table 1 |
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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. |
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Species/Accession |
Segment |
Method/DB/Hit/E-value |
Hit/Score |
|
|
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|
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 |
|
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Novatchkova et al. BMC Bioinformatics 2005 6:22 doi:10.1186/1471-2105-6-22 |
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