Hit# SCOP Id Protein Name SCOP Superfamily SCOP Fold SCOP Class Comb score SVM score HH prob DALI Z FAST SN TM score SCOP domains with score better than threshold (Comb score > 2.0 OR SVM score > 0.6 OR HH prob > 0.9) 1 d1ri7a1 Putative transcriptional regulator PH1519 "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 2.97 1.406 3.0 4.5 0.42 0.05 2 d1je8a_ Nitrate/nitrite response regulator (NarL) C-terminal effector domain of the bipartite response regulators DNA/RNA-binding 3-helical bundle All a 2.57 0.907 3.2 5.0 0.44 0.04 3 d1uhsa_ Homeodomain-only protein, Hop Homeodomain-like DNA/RNA-binding 3-helical bundle All a 2.49 0.632 3.5 4.2 0.49 0.03 4 d1a9xa1 Carbamoyl phosphate synthetase, large subunit connection domain Carbamoyl phosphate synthetase, large subunit connection domain Carbamoyl phosphate synthetase, large subunit connection domain All a 2.37 0.994 2.9 3.7 0.51 0.03 5 d1hcra_ HIN recombinase (DNA-binding domain) Homeodomain-like DNA/RNA-binding 3-helical bundle All a 2.34 1.399 2.4 3.8 0.42 0.02 6 d1sfua_ 34L "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 2.18 0.905 3.3 4.8 0.46 0.02 7 d1u5ta2 Vacuolar sorting protein SNF8 (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 2.05 0.901 2.7 3.9 0.43 0.01 8 d1mkma1 Transcriptional regulator IclR, N-terminal domain "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 2.04 0.908 2.3 4.9 0.46 0.11 9 d1fsea_ Germination protein GerE C-terminal effector domain of the bipartite response regulators DNA/RNA-binding 3-helical bundle All a 2.02 0.906 1.8 4.9 0.44 0.04 10 d1l3la1 Quorum-sensing transcription factor TraR, C-terminal domain C-terminal effector domain of the bipartite response regulators DNA/RNA-binding 3-helical bundle All a 1.94 0.899 1.9 5.0 0.43 0.04 11 d1sfxa_ Hypothetical protein AF2008 "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.92 0.901 3.0 4.1 0.45 0.03 12 d1igna1 DNA-binding domain of rap1 Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.86 0.729 2.0 3.2 0.46 0.01 13 d1fjla_ Paired protein Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.85 0.728 2.8 4.5 0.48 0.01 14 d1on2a1 Manganese transport regulator MntR "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.80 1.311 1.6 4.6 0.41 0.04 15 d1lvaa3 C-terminal fragment of elongation factor SelB "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.77 0.723 2.6 4.8 0.44 0.03 16 d1sfea1 Ada DNA repair protein Methylated DNA-protein cysteine methyltransferase, C-terminal domain DNA/RNA-binding 3-helical bundle All a 1.59 0.724 1.9 3.1 0.44 0.01 17 d1qbja_ Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.52 1.021 2.0 4.9 0.46 0.02 18 d1ldda_ Anaphase promoting complex (APC) (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.48 0.897 1.8 3.8 0.44 0.03 19 d1t56a1 Ethr repressor Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.45 0.902 2.3 2.8 0.40 0.03 20 d1in4a1 Holliday junction helicase RuvB "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.42 0.906 0.9 3.8 0.41 0.02 21 d1bl0a2 MarA Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.40 0.641 1.3 2.9 0.38 0.05 22 d1r71a_ Transcriptional repressor protein KorB DNA-binding domain KorB DNA-binding domain-like DNA/RNA-binding 3-helical bundle All a 1.34 0.898 0.2 3.2 0.38 0.17 23 d1o57a1 N-terminal domain of Bacillus PurR "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.29 0.895 0.8 4.6 0.46 0.01 24 d1biaa1 Biotin repressor, N-terminal domain "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.29 1.297 1.5 4.2 0.40 0.02 25 d1qdma1 (Pro)phytepsin Saposin Saposin-like All a 1.25 0.726 1.8 3.2 0.43 0.02 26 d1j75a_ Dlm-1 (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.23 0.900 1.1 4.4 0.43 0.08 27 d1hlva1 DNA-binding domain of centromere binding protein B (CENP-B) Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.22 1.591 1.1 3.8 0.39 0.04 28 d1mgta1 O6-alkylguanine-DNA alkyltransferase Methylated DNA-protein cysteine methyltransferase, C-terminal domain DNA/RNA-binding 3-helical bundle All a 1.22 0.903 1.6 3.7 0.42 0.00 29 d2bbya_ DNA-binding domain from rap30 (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.21 0.897 1.1 4.3 0.44 0.01 30 d1pb6a1 Hypothetical transcriptional regulator YcdC Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.18 0.904 1.9 3.0 0.26 0.02 31 d1j5ya1 Putative transcriptional regulator TM1602, N-terminal domain "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.18 1.541 1.2 4.7 0.44 0.10 32 d1rp3a1 Sigma factor sigma-28 (FliA) Sigma3 and sigma4 domains of RNA polymerase sigma factors DNA/RNA-binding 3-helical bundle All a 1.18 0.895 1.6 3.9 0.36 0.03 33 d1or7a1 SigmaE factor (RpoE) Sigma3 and sigma4 domains of RNA polymerase sigma factors DNA/RNA-binding 3-helical bundle All a 1.17 1.037 5.4 0.42 0.05 34 d1dpua_ C-terminal domain of RPA32 (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.15 0.994 0.5 4.7 0.45 0.04 35 d1d5ya2 Rob transcription factor, N-terminal domain Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.14 0.901 1.3 2.8 0.37 0.03 36 d1hsta_ Histone H5, globular domain (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.12 0.907 1.3 2.8 0.38 0.01 37 d1ufma_ COP9 signalosome complex subunit 4, GSN4 (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.11 0.729 0.4 3.6 0.41 0.01 38 d1p6ra_ Penicillinase repressor BlaI "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.09 0.910 0.8 3.8 0.42 0.01 39 d1ucra_ Dissimilatory sulfite reductase DsvD "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.04 0.906 1.5 3.7 0.39 0.01 40 d1sd4a_ Penicillinase repressor BlaI "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 1.02 0.911 1.1 3.2 0.44 0.03 41 d1gdta1 gamma,delta resolvase (C-terminal domain) Homeodomain-like DNA/RNA-binding 3-helical bundle All a 0.95 1.647 4.6 0.39 0.15 42 d1bjaa_ Transcription factor MotA, activation domain "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.93 0.905 1.3 4.0 0.45 0.01 43 d1lvaa1 C-terminal fragment of elongation factor SelB "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.91 0.723 0.1 4.5 0.44 0.01 44 d2foka2 Restriction endonuclease FokI, N-terminal (recognition) domain (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.88 0.712 0.9 2.7 0.33 0.01 45 d1pdnc_ Paired protein (prd) Homeodomain-like DNA/RNA-binding 3-helical bundle All a 0.88 0.843 0.0 3.9 0.47 0.04 46 d1u78a2 Transposase tc3a1-65 Homeodomain-like DNA/RNA-binding 3-helical bundle All a 0.88 1.664 4.9 0.40 0.02 47 d1u5tb2 Vacuolar protein sorting-associated protein VPS36 (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.78 0.899 0.7 4.4 0.44 0.01 48 d2foka3 Restriction endonuclease FokI, N-terminal (recognition) domain (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.76 0.896 0.8 3.9 0.39 0.01 49 d1tqia1 Rio2 serine protein kinase N-terminal domain "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.75 0.906 0.5 3.7 0.42 0.05 50 d1rp3a2 Sigma factor sigma-28 (FliA) Sigma3 and sigma4 domains of RNA polymerase sigma factors DNA/RNA-binding 3-helical bundle All a 0.73 1.099 0.0 5.4 0.41 0.07 51 d1hw1a1 Fatty acid responsive transcription factor FadR, N-terminal domain "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.70 0.896 3.6 0.42 0.05 52 d1ft9a1 CO-sensing protein CooA, C-terminal domain "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.69 0.910 0.5 3.5 0.42 0.02 53 d1tc3c_ Transposase tc3a1-65 Homeodomain-like DNA/RNA-binding 3-helical bundle All a 0.68 1.664 4.9 0.42 0.01 54 d1hkqa_ Replication protein A, repA "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.58 0.728 1.0 1.9 0.44 0.01 55 d1smyf1 Sigma70 Sigma3 and sigma4 domains of RNA polymerase sigma factors DNA/RNA-binding 3-helical bundle All a 0.54 0.906 3.7 0.37 0.03 56 d1lnwa_ MexR repressor "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.39 0.901 1.1 2.1 0.43 0.05 57 d1hq1a_ Signal sequence binding protein Ffh Signal peptide-binding domain Signal peptide-binding domain All a 0.37 0.866 0.0 4.0 0.44 0.01 58 d1gvda_ c-Myb, DNA-binding domain Homeodomain-like DNA/RNA-binding 3-helical bundle All a 0.33 0.896 0.0 3.6 0.41 0.01 59 d1fnna1 CDC6, C-terminal domain "Winged helix" DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.26 0.905 0.5 2.4 0.42 0.01 60 d1kqpa_ NH3-dependent NAD+-synthetase Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b 0.17 -0.531 -0.531 0.0 1.5 0.35 61 d1mswd_ T7 RNA polymerase DNA/RNA polymerases DNA/RNA polymerases multi 0.12 0.897 0.9 1.0 0.33 0.01 62 d1u5ta1 Vacuolar sorting protein SNF8 (Winged helix( DNA-binding domain DNA/RNA-binding 3-helical bundle All a 0.09 0.703 0.4 1.2 0.36 0.00 63 d6paxa2 Pax-6 Homeodomain-like DNA/RNA-binding 3-helical bundle All a 0.03 1.285 0.0 5.0 0.45 0.02 64 d1e3oc1 Oct-1 POU Homeodomain Homeodomain-like DNA/RNA-binding 3-helical bundle All a -0.03 0.763 0.0 4.1 0.46 0.01 65 d1ru8a_ Putative N-type ATP pyrophosphatase PF0828 Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.08 -0.488 -0.488 0.0 0.9 0.35 66 d1jgta1 beta-Lactam synthetase Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.15 -0.566 -0.566 0.0 1.1 0.38 67 d1q15a1 beta-Lactam synthetase Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.19 -0.600 -0.600 0.0 1.7 0.39 68 d1ni5a1 Putative cell cycle protein MesJ, N-terminal domain Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.28 -0.485 -0.485 0.0 0.9 0.35 69 d1ct9a1 Asparagine synthetase B, C-terminal domain Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.30 -0.676 -0.676 0.0 1.0 0.37 70 d1k92a1 Argininosuccinate synthetase, N-terminal domain Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.43 -0.257 -0.257 0.0 1.1 0.37 71 d1vl2a1 Argininosuccinate synthetase, N-terminal domain Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.44 -0.289 -0.289 0.0 1.3 0.38 72 d1sura_ Phosphoadenylyl sulphate (PAPS) reductase Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.56 -0.424 -0.424 0.0 1.0 0.28 73 d1gpma1 GMP synthetase, central domain Adenine nucleotide alpha hydrolases-like Adenine nucleotide alpha hydrolase-like a/b -0.70 -0.281 -0.281 0.0 1.0 0.29 SCOP domains with score worse than threshold 74 d1mija_ Homeo-prospero domain of Prospero protein Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.47 0.558 0.01 3.0 2.9 0.55 75 d2ezha_ Transposase Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.35 -0.699 0.01 1.7 3.2 0.43 76 d1wdka1 Fatty oxidation complex alpha subunit, C-terminal domain 6-phosphogluconate dehydrogenase C-terminal domain-like 6-phosphogluconate dehydrogenase C-terminal domain-like All a 1.32 -1.348 0.03 1.2 1.4 0.47 77 d1t4ga1 DNA repair protein Rad51, N-terminal domain Rad51 N-terminal domain-like SAM domain-like All a 1.29 -1.092 0.05 0.0 3.5 0.43 78 d1c20a_ DNA-binding domain from the dead ringer protein ARID-like DNA/RNA-binding 3-helical bundle All a 1.23 -1.201 0.02 0.9 2.1 0.44 79 d2ezla_ Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase Homeodomain-like DNA/RNA-binding 3-helical bundle All a 1.13 -0.841 0.01 1.8 2.5 0.37 80 d1ikpa3 Exotoxin A, middle domain Exotoxin A, middle domain Toxins' membrane translocation domains mem 1.12 -0.854 0.02 1.1 2.8 0.49 81 d1kb4b_ Vitamin D3 receptor, VDR, DNA-binding domain Glucocorticoid receptor-like (DNA-binding domain) Glucocorticoid receptor-like (DNA-binding domain) small 1.09 -1.282 0.01 1.0 1.9 0.38 82 d1f14a1 Short chain L-3-hydroxyacyl CoA dehydrogenase 6-phosphogluconate dehydrogenase C-terminal domain-like 6-phosphogluconate dehydrogenase C-terminal domain-like All a 1.04 -0.973 0.02 1.3 1.7 0.46 83 d1u9la_ Transcription elongation protein NusA Rad51 N-terminal domain-like SAM domain-like All a 1.03 -1.425 0.10 0.8 3.5 0.42