GREMLIN Database
RNH - Ribonuclease HI
UniProt: Q9HSF6 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 199 (176)
Sequences: 1131 (766)
Seq/√Len: 57.7

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
74_F138_G5.2071.00
25_G31_L3.2211.00
141_Q145_K3.0101.00
79_R193_N2.7981.00
72_A122_A2.6591.00
152_D166_R2.6511.00
124_E164_R2.5431.00
119_L136_L2.4841.00
137_R178_T2.3441.00
120_I168_L2.2831.00
115_E139_D2.1341.00
121_A124_E2.1041.00
22_F25_G2.0391.00
23_S31_L2.0241.00
138_G144_E1.9851.00
22_F31_L1.9791.00
27_S30_E1.9621.00
120_I165_A1.9491.00
21_S32_W1.9301.00
117_D161_K1.9291.00
31_L34_A1.9161.00
135_E178_T1.9161.00
23_S27_S1.9031.00
116_Y146_Q1.8921.00
27_S31_L1.8651.00
144_E177_I1.8451.00
147_L165_A1.8370.99
116_Y142_L1.8100.99
119_L143_V1.8050.99
114_A188_A1.8020.99
28_E32_W1.7750.99
165_A177_I1.7450.99
158_L162_R1.7050.99
24_D34_A1.6960.99
192_A196_L1.6680.99
144_E175_W1.6000.99
75_D139_D1.6000.99
22_F27_S1.5990.99
145_K149_G1.5970.99
123_L172_F1.5430.98
127_A171_G1.4780.98
169_L175_W1.4550.97
77_A193_N1.4390.97
38_D41_A1.4290.97
132_D173_D1.4280.97
38_D43_A1.4050.97
24_D27_S1.3920.97
21_S30_E1.3850.96
24_D31_L1.3770.96
131_F134_I1.3680.96
88_G188_A1.3600.96
102_G105_T1.3060.95
126_A134_I1.2970.95
79_R196_L1.2910.95
25_G28_E1.2200.93
150_A154_N1.2180.93
22_F26_N1.2170.93
135_E176_S1.2080.93
71_H137_R1.1960.92
112_N143_V1.1900.92
181_P184_T1.1810.92
88_G195_A1.1630.91
142_L146_Q1.1530.91
21_S24_D1.1420.90
71_H135_E1.1310.90
23_S26_N1.1280.90
30_E33_H1.1220.89
85_A89_W1.1120.89
130_G168_L1.1110.89
68_G132_D1.1020.89
25_G30_E1.1010.89
40_H43_A1.0960.88
136_L175_W1.0930.88
49_V55_P1.0710.87
54_S57_D1.0680.87
116_Y143_V1.0660.87
103_G121_A1.0650.87
188_A192_A1.0600.87
44_Y48_L1.0540.86
60_A63_Q1.0400.86
141_Q151_W1.0380.85
87_V114_A1.0310.85
73_Y111_N1.0210.84
98_I102_G1.0190.84
185_N189_D1.0020.83
146_Q149_G0.9890.83
88_G126_A0.9550.80
36_L42_V0.9500.80
144_E147_L0.9490.80
166_R170_T0.9480.80
25_G35_D0.9480.80
142_L179_H0.9470.80
22_F29_H0.9460.80
150_A155_D0.9400.79
70_V134_I0.9350.79
143_V146_Q0.9310.79
22_F34_A0.9300.78
190_A194_E0.9250.78
47_K50_V0.9230.78
21_S28_E0.9210.78
62_V65_D0.9160.77
72_A136_L0.9140.77
74_F153_T0.9120.77
193_N196_L0.9100.77
21_S27_S0.9050.77
109_A113_Q0.9010.76
87_V109_A0.8950.76
89_W103_G0.8890.75
126_A142_L0.8790.74
80_G192_A0.8790.74
58_I61_V0.8790.74
23_S30_E0.8760.74
123_L168_L0.8750.74
120_I124_E0.8740.74
23_S29_H0.8650.73
188_A195_A0.8640.73
116_Y158_L0.8490.72
146_Q162_R0.8460.72
75_D115_E0.8450.71
21_S26_N0.8390.71
25_G33_H0.8390.71
87_V103_G0.8380.71
40_H44_Y0.8380.71
89_W125_A0.8360.71
21_S33_H0.8360.71
25_G34_A0.8330.70
142_L162_R0.8330.70
77_A196_L0.8210.69
44_Y47_K0.8160.69
133_D167_E0.8110.68
119_L138_G0.8100.68
116_Y182_R0.8070.68
182_R188_A0.8010.67
50_V54_S0.8010.67
141_Q179_H0.7980.67
151_W156_P0.7980.67
109_A136_L0.7930.67
43_A47_K0.7930.67
28_E31_L0.7930.67
142_L158_L0.7810.65
32_W36_L0.7780.65
23_S33_H0.7760.65
74_F118_A0.7720.65
100_A104_D0.7720.65
146_Q153_T0.7710.64
73_Y106_I0.7670.64
184_T190_A0.7660.64
86_A89_W0.7650.64
119_L177_I0.7650.64
116_Y162_R0.7610.63
24_D29_H0.7570.63
119_L165_A0.7550.63
21_S25_G0.7540.63
42_V47_K0.7500.62
147_L169_L0.7480.62
83_G102_G0.7460.62
72_A91_L0.7420.61
82_P86_A0.7390.61
36_L39_A0.7360.61
187_R190_A0.7340.61
87_V105_T0.7310.60
171_G176_S0.7290.60
38_D47_K0.7190.59
101_E187_R0.7190.59
43_A46_D0.7180.59
29_H32_W0.7160.59
151_W155_D0.7130.58
24_D28_E0.7110.58
22_F35_D0.7080.58
42_V52_G0.7060.58
29_H33_H0.7050.57
49_V52_G0.7040.57
142_L182_R0.7040.57
26_N31_L0.7020.57
40_H45_A0.7000.57
46_D53_G0.6970.57
50_V62_V0.6950.56
167_E178_T0.6910.56
90_V93_S0.6910.56
148_T177_I0.6890.56
119_L148_T0.6880.56
23_S34_A0.6820.55
127_A172_F0.6760.54
75_D111_N0.6750.54
142_L161_K0.6740.54
74_F182_R0.6670.53
23_S28_E0.6670.53
76_G81_N0.6630.53
104_D107_G0.6520.52
26_N35_D0.6510.52
35_D44_Y0.6500.51
116_Y153_T0.6450.51
100_A105_T0.6380.50
87_V93_S0.6370.50
191_L195_A0.6340.50
77_A192_A0.6330.50
101_E125_A0.6280.49
42_V45_A0.6200.48
27_S32_W0.6130.47
143_V162_R0.6100.47
26_N32_W0.6070.47
133_D174_D0.6070.47
53_G57_D0.6060.47
128_D135_E0.6060.47
37_G44_Y0.6060.47
151_W180_V0.6030.46
39_A47_K0.6020.46
32_W37_G0.6020.46
44_Y50_V0.5980.46
112_N140_S0.5980.46
58_I62_V0.5950.45
163_V171_G0.5920.45
56_T64_P0.5890.45
50_V53_G0.5870.45
26_N30_E0.5870.45
32_W35_D0.5860.44
103_G106_I0.5790.44
92_V135_E0.5780.44
22_F33_H0.5760.43
126_A189_D0.5740.43
34_A39_A0.5740.43
99_V104_D0.5710.43
87_V96_G0.5710.43
31_L35_D0.5700.43
154_N194_E0.5690.43
69_R134_I0.5690.43
35_D40_H0.5670.42
39_A43_A0.5650.42
42_V54_S0.5640.42
42_V46_D0.5580.41
54_S167_E0.5550.41
138_G153_T0.5550.41
25_G29_H0.5470.40
36_L40_H0.5460.40
144_E179_H0.5440.40
92_V134_I0.5440.40
25_G111_N0.5420.40
26_N33_H0.5410.40
37_G41_A0.5390.39
37_G47_K0.5390.39
46_D56_T0.5390.39
192_A195_A0.5370.39
27_S34_A0.5350.39
36_L44_Y0.5340.39
100_A107_G0.5330.39
21_S29_H0.5330.39
127_A168_L0.5330.39
148_T171_G0.5300.38
146_Q182_R0.5300.38
85_A91_L0.5290.38
90_V192_A0.5240.38
75_D112_N0.5210.38
118_A149_G0.5180.37
58_I64_P0.5170.37
66_R69_R0.5140.37
56_T59_T0.5130.37
191_L194_E0.5100.36
156_P159_R0.5100.36
167_E170_T0.5090.36
89_W102_G0.5090.36
127_A165_A0.5030.36
99_V177_I0.5000.35
68_G119_L0.5000.35
139_D143_V0.5000.35
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
4mh8A 1 0.191 100 0.4 Contact Map
4e19A 1 0.6683 100 0.407 Contact Map
2qkbA 1 0.6834 100 0.483 Contact Map
3u3gD 1 0.6683 100 0.495 Contact Map
3hstB 1 0.6683 100 0.499 Contact Map
2ehgA 1 0.6482 100 0.5 Contact Map
3qioA 1 0.6432 100 0.502 Contact Map
1mu2A 2 0.8342 100 0.502 Contact Map
3p1gA 1 0.7236 100 0.503 Contact Map
2lsnA 1 0.6834 100 0.506 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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