GREMLIN Database
RND - Ribonuclease D
UniProt: P09155 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10858
Length: 375 (355)
Sequences: 2053 (1398)
Seq/√Len: 74.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
123_E129_T4.4931.00
219_L281_K4.4221.00
18_A51_H3.8341.00
216_C279_V3.7791.00
8_T11_A3.6261.00
20_R72_D3.4591.00
212_R290_L3.0311.00
7_T11_A2.9741.00
15_L53_A2.8641.00
247_V279_V2.7581.00
184_R187_Q2.7181.00
220_L244_L2.7081.00
107_A121_M2.6741.00
254_S257_E2.5521.00
216_C251_M2.5481.00
128_V158_Y2.5231.00
285_L290_L2.3881.00
175_W178_A2.3201.00
286_P289_A2.2851.00
285_L289_A2.2771.00
317_V365_A2.1691.00
318_S328_L2.1641.00
46_L55_I2.1551.00
220_L275_L2.1541.00
78_F160_L2.1301.00
73_P98_Q2.0991.00
77_K99_P2.0881.00
176_L180_L2.0861.00
9_D13_A2.0711.00
124_E169_E2.0651.00
255_L273_K2.0581.00
47_F52_L2.0511.00
15_L19_V2.0401.00
203_I217_L2.0201.00
125_Y169_E2.0121.00
146_E150_E1.9961.00
16_C65_P1.9911.00
27_L79_L1.9801.00
80_H103_T1.9641.00
317_V320_T1.9611.00
56_D142_R1.9581.00
184_R188_M1.9341.00
282_A285_L1.9121.00
25_I46_L1.8991.00
216_C282_A1.8941.00
101_I106_L1.8861.00
278_L282_A1.8841.00
11_A14_S1.8541.00
76_T163_T1.7991.00
359_G364_E1.7971.00
206_A217_L1.7781.00
171_E176_L1.7631.00
167_M176_L1.7561.00
225_L229_R1.7501.00
10_D14_S1.7461.00
27_L70_L1.7401.00
239_V244_L1.7361.00
288_D291_P1.7171.00
12_L55_I1.7051.00
167_M171_E1.7051.00
258_L276_L1.6961.00
42_G140_L1.6921.00
262_G268_I1.6911.00
137_T148_Q1.6851.00
181_D356_G1.6791.00
219_L222_D1.6681.00
247_V258_L1.6271.00
40_Q232_D1.6231.00
79_L97_P1.6181.00
280_E284_T1.6070.99
179_A183_C1.6010.99
122_V130_L1.5990.99
44_I57_P1.5960.99
209_L213_Q1.5960.99
112_R125_Y1.5780.99
65_P68_A1.5720.99
177_P181_D1.5620.99
106_L110_C1.5480.99
227_K230_E1.5470.99
318_S321_H1.5170.99
112_R169_E1.5130.99
169_E172_A1.5130.99
20_R68_A1.4960.99
43_L57_P1.4940.99
126_S162_I1.4930.99
177_P180_L1.4900.99
86_L97_P1.4720.99
264_S268_I1.4650.99
285_L291_P1.4630.99
218_Q285_L1.4470.99
251_M283_Q1.4430.99
154_A157_W1.4420.99
64_S68_A1.4330.99
110_C173_S1.4320.99
279_V283_Q1.4230.99
236_N241_E1.4200.99
222_D226_R1.4180.99
265_G268_I1.4170.99
32_V140_L1.4020.99
212_R287_E1.3860.98
217_L244_L1.3810.98
19_V53_A1.3740.98
160_L164_A1.3650.98
317_V361_L1.3500.98
44_I66_L1.3450.98
359_G363_A1.3440.98
247_V263_L1.3390.98
33_R87_E1.3220.98
226_R230_E1.3180.98
227_K231_R1.3150.98
273_K277_A1.3110.98
42_G58_L1.3010.98
13_A65_P1.2850.97
125_Y162_I1.2830.97
168_V172_A1.2800.97
72_D75_I1.2780.97
67_K93_F1.2750.97
14_S17_E1.2750.97
314_I325_A1.2730.97
10_D13_A1.2720.97
219_L282_A1.2700.97
321_H361_L1.2620.97
52_L153_A1.2610.97
310_I334_I1.2540.97
277_A281_K1.2440.97
46_L66_L1.2390.97
213_Q251_M1.2370.97
35_R237_F1.2360.97
329_A362_M1.2300.97
215_A219_L1.2130.96
363_A367_H1.2120.96
258_L272_G1.2030.96
25_I69_I1.1980.96
52_L157_W1.1830.96
347_Q350_L1.1830.96
161_P164_A1.1790.96
30_E45_Q1.1700.96
72_D77_K1.1530.95
47_F157_W1.1490.95
287_E290_L1.1430.95
215_A291_P1.1370.95
202_D241_E1.1300.95
362_M366_L1.1210.94
279_V282_A1.1160.94
145_T148_Q1.1090.94
37_Y225_L1.1080.94
6_I12_L1.1020.94
252_P258_L1.1010.94
317_V321_H1.1000.94
219_L278_L1.0890.93
262_G267_E1.0880.93
109_F182_E1.0870.93
49_G164_A1.0820.93
15_L55_I1.0810.93
24_A160_L1.0800.93
265_G269_R1.0780.93
104_Q108_A1.0760.93
24_A164_A1.0750.93
266_S269_R1.0730.93
295_L298_M1.0730.93
113_P120_S1.0690.93
199_A221_A1.0630.93
314_I362_M1.0630.93
112_R124_E1.0600.92
274_T278_L1.0580.92
286_P291_P1.0550.92
54_L149_C1.0510.92
216_C283_Q1.0480.92
13_A17_E1.0480.92
278_L281_K1.0420.92
225_L235_V1.0370.92
106_L166_L1.0360.92
271_H274_T1.0330.92
180_L184_R1.0220.91
22_F50_E1.0170.91
9_D62_D1.0160.91
169_E173_S1.0030.90
263_L268_I1.0010.90
25_I73_P0.9900.90
107_A166_L0.9890.90
28_D151_Y0.9850.89
262_G265_G0.9840.89
6_I11_A0.9820.89
314_I318_S0.9800.89
227_K271_H0.9760.89
353_L356_G0.9750.89
307_F334_I0.9710.89
196_P199_A0.9710.89
125_Y165_K0.9680.89
71_R95_E0.9650.88
32_V42_G0.9620.88
316_D320_T0.9620.88
168_V171_E0.9620.88
209_L249_R0.9520.88
186_M189_R0.9520.88
9_D60_I0.9490.88
72_D98_Q0.9490.88
288_D292_Q0.9480.88
110_C166_L0.9480.88
66_L70_L0.9470.88
208_Q249_R0.9420.87
17_E20_R0.9360.87
28_D45_Q0.9300.87
198_D201_R0.9260.86
263_L269_R0.9260.86
85_D151_Y0.9230.86
318_S323_I0.9160.86
272_G276_L0.9090.85
12_L60_I0.9050.85
41_L88_V0.9030.85
37_Y235_V0.9020.85
116_W120_S0.8980.85
6_I55_I0.8970.85
119_A129_T0.8940.84
340_W348_N0.8930.84
312_S316_D0.8920.84
108_A116_W0.8920.84
134_E147_R0.8920.84
123_E127_G0.8900.84
264_S267_E0.8860.84
251_M279_V0.8830.84
29_T88_V0.8830.84
253_G283_Q0.8820.84
211_T287_E0.8810.83
6_I15_L0.8780.83
85_D132_K0.8750.83
81_A154_A0.8720.83
81_A115_S0.8710.83
85_D155_D0.8700.83
78_F164_A0.8700.83
84_E136_R0.8680.83
134_E148_Q0.8670.82
215_A290_L0.8660.82
106_L318_S0.8610.82
332_R336_Q0.8550.82
105_I186_M0.8550.82
40_Q140_L0.8550.82
18_A53_A0.8540.82
216_C220_L0.8400.80
151_Y155_D0.8380.80
31_F148_Q0.8370.80
109_F179_A0.8360.80
68_A71_R0.8350.80
274_T277_A0.8320.80
165_K169_E0.8310.80
69_I75_I0.8250.79
31_F156_V0.8240.79
361_L365_A0.8230.79
246_S250_Y0.8210.79
28_D85_D0.8210.79
43_L54_L0.8130.78
81_A88_V0.8130.78
364_E367_H0.8120.78
314_I328_L0.8070.78
54_L153_A0.8060.78
354_I367_H0.8030.77
9_D61_T0.8010.77
259_D272_G0.7960.77
215_A285_L0.7950.77
268_I272_G0.7930.76
333_Q352_E0.7910.76
16_C69_I0.7910.76
360_E364_E0.7870.76
182_E185_L0.7870.76
209_L245_W0.7860.76
304_R311_K0.7810.75
43_L152_A0.7780.75
213_Q249_R0.7750.75
83_S135_S0.7750.75
19_V46_L0.7740.75
277_A280_E0.7740.75
236_N240_R0.7720.75
122_V162_I0.7710.74
22_F48_D0.7680.74
211_T215_A0.7680.74
30_E151_Y0.7680.74
210_R213_Q0.7620.74
81_A135_S0.7610.73
90_L96_L0.7580.73
347_Q351_P0.7570.73
125_Y166_L0.7570.73
110_C169_E0.7550.73
252_P276_L0.7540.73
80_H106_L0.7510.72
86_L201_R0.7510.72
255_L276_L0.7490.72
219_L285_L0.7480.72
104_Q116_W0.7450.72
54_L86_L0.7420.72
171_E174_G0.7410.71
100_L187_Q0.7400.71
15_L46_L0.7390.71
80_H159_L0.7390.71
132_K151_Y0.7360.71
134_E153_A0.7340.71
31_F84_E0.7310.70
150_E154_A0.7300.70
83_S186_M0.7290.70
353_L359_G0.7290.70
231_R271_H0.7270.70
253_G257_E0.7270.70
84_E87_E0.7260.70
110_C315_T0.7240.70
30_E43_L0.7240.70
45_Q151_Y0.7190.69
84_E241_E0.7190.69
285_L288_D0.7170.69
30_E85_D0.7160.69
5_M54_L0.7130.69
214_L291_P0.7130.69
5_M149_C0.7110.68
215_A282_A0.7100.68
101_I166_L0.7100.68
28_D155_D0.7100.68
69_I77_K0.7060.68
31_F104_Q0.7030.67
185_L188_M0.7020.67
255_L259_D0.7020.67
209_L248_A0.7020.67
356_G360_E0.7000.67
67_K92_V0.6970.67
82_G186_M0.6880.66
34_T234_A0.6880.66
195_A198_D0.6870.66
233_L238_V0.6860.66
86_L96_L0.6860.66
157_W311_K0.6860.66
29_T117_G0.6840.65
330_S333_Q0.6840.65
33_R163_T0.6830.65
107_A116_W0.6810.65
223_W275_L0.6780.65
55_I122_V0.6730.64
33_R84_E0.6730.64
12_L16_C0.6720.64
60_I63_W0.6690.64
14_S168_V0.6680.64
227_K274_T0.6670.63
45_Q85_D0.6670.63
28_D132_K0.6670.63
227_K238_V0.6670.63
69_I218_Q0.6660.63
331_R334_I0.6610.63
167_M180_L0.6600.63
226_R273_K0.6590.62
136_R248_A0.6570.62
39_P92_V0.6570.62
247_V251_M0.6570.62
31_F87_E0.6570.62
107_A111_G0.6550.62
247_V264_S0.6550.62
170_T179_A0.6540.62
281_K284_T0.6540.62
361_L364_E0.6520.62
139_W152_A0.6520.62
80_H156_V0.6500.61
313_L317_V0.6480.61
56_D102_D0.6470.61
20_R75_I0.6460.61
263_L266_S0.6460.61
248_A279_V0.6460.61
103_T159_L0.6440.61
197_E226_R0.6430.61
120_S124_E0.6410.60
139_W155_D0.6410.60
30_E155_D0.6410.60
171_E320_T0.6360.60
252_P257_E0.6360.60
200_W221_A0.6350.60
87_E104_Q0.6350.60
79_L82_G0.6340.59
9_D65_P0.6340.59
14_S18_A0.6330.59
28_D43_L0.6320.59
168_V197_E0.6320.59
356_G363_A0.6300.59
194_V238_V0.6290.59
318_S325_A0.6290.59
83_S189_R0.6290.59
34_T236_N0.6280.59
66_L89_F0.6260.59
268_I271_H0.6250.58
296_N339_N0.6240.58
320_T365_A0.6220.58
359_G367_H0.6210.58
289_A292_Q0.6200.58
31_F39_P0.6180.58
104_Q358_R0.6170.57
45_Q155_D0.6160.57
264_S269_R0.6140.57
19_V48_D0.6130.57
161_P165_K0.6120.57
45_Q152_A0.6110.57
254_S260_S0.6090.56
118_F157_W0.6090.56
174_G245_W0.6080.56
34_T237_F0.6080.56
259_D276_L0.6080.56
78_F167_M0.6060.56
47_F156_V0.6040.56
33_R235_V0.6040.56
117_G198_D0.6030.56
137_T156_V0.6030.56
33_R38_Y0.5990.55
197_E218_Q0.5990.55
246_S249_R0.5980.55
29_T39_P0.5970.55
23_P181_D0.5970.55
223_W274_T0.5940.55
254_S276_L0.5930.54
280_E283_Q0.5900.54
33_R104_Q0.5890.54
34_T42_G0.5890.54
104_Q115_S0.5890.54
69_I72_D0.5880.54
315_T319_E0.5860.54
20_R62_D0.5860.54
211_T290_L0.5840.53
262_G266_S0.5830.53
117_G121_M0.5830.53
118_F234_A0.5830.53
50_E244_L0.5820.53
33_R39_P0.5810.53
203_I245_W0.5810.53
101_I163_T0.5800.53
126_S161_P0.5800.53
282_A286_P0.5780.53
323_I329_A0.5770.52
32_V40_Q0.5770.52
25_I72_D0.5760.52
140_L153_A0.5750.52
76_T100_L0.5750.52
299_D303_Y0.5750.52
14_S21_A0.5740.52
172_A230_E0.5730.52
72_D99_P0.5710.52
31_F358_R0.5710.52
6_I17_E0.5700.52
351_P356_G0.5700.52
30_E132_K0.5690.51
39_P88_V0.5670.51
331_R335_N0.5670.51
212_R293_P0.5670.51
239_V275_L0.5670.51
220_L277_A0.5660.51
354_I365_A0.5650.51
33_R36_T0.5640.51
113_P240_R0.5620.51
118_F241_E0.5590.50
36_T237_F0.5590.50
32_V136_R0.5590.50
239_V243_H0.5570.50
118_F122_V0.5560.50
351_P354_I0.5560.50
353_L364_E0.5550.50
243_H262_G0.5540.50
238_V267_E0.5520.49
237_F240_R0.5510.49
10_D168_V0.5500.49
56_D143_P0.5500.49
55_I325_A0.5490.49
317_V323_I0.5490.49
102_D142_R0.5490.49
67_K71_R0.5490.49
349_N352_E0.5480.49
9_D63_W0.5470.49
90_L232_D0.5450.48
89_F117_G0.5450.48
312_S318_S0.5450.48
104_Q156_V0.5450.48
25_I75_I0.5440.48
314_I323_I0.5440.48
83_S105_I0.5440.48
102_D159_L0.5440.48
355_S364_E0.5430.48
55_I347_Q0.5430.48
330_S335_N0.5410.48
20_R244_L0.5410.48
75_I86_L0.5410.48
314_I317_V0.5400.48
90_L93_F0.5400.48
7_T59_G0.5400.48
333_Q363_A0.5390.48
17_E21_A0.5390.48
247_V333_Q0.5390.48
352_E356_G0.5390.48
197_E222_D0.5390.48
103_T106_L0.5380.48
31_F34_T0.5370.47
236_N326_E0.5370.47
325_A333_Q0.5360.47
21_A281_K0.5330.47
45_Q132_K0.5310.47
178_A181_D0.5290.46
119_A131_D0.5270.46
20_R25_I0.5260.46
329_A334_I0.5260.46
313_L365_A0.5250.46
12_L65_P0.5240.46
18_A113_P0.5230.46
177_P212_R0.5220.46
348_N351_P0.5220.46
38_Y86_L0.5220.46
31_F36_T0.5220.46
311_K319_E0.5190.45
138_D232_D0.5190.45
258_L275_L0.5190.45
212_R285_L0.5190.45
26_A78_F0.5180.45
39_P84_E0.5170.45
235_V241_E0.5170.45
303_Y306_A0.5150.45
138_D141_A0.5150.45
6_I14_S0.5140.45
31_F41_L0.5130.45
218_Q282_A0.5130.45
31_F88_V0.5120.44
6_I9_D0.5100.44
35_R233_L0.5100.44
315_T321_H0.5090.44
33_R88_V0.5090.44
175_W202_D0.5080.44
259_D264_S0.5070.44
36_T87_E0.5060.44
126_S164_A0.5050.44
91_N96_L0.5040.43
326_E331_R0.5030.43
148_Q358_R0.5020.43
347_Q363_A0.5010.43
29_T38_Y0.5000.43
246_S261_L0.5000.43
203_I221_A0.5000.43
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  
1yt3A 1 1 100 0.31 Contact Map
3cymA 1 0.9653 100 0.378 Contact Map
5c0xK 1 0.6907 100 0.41 Contact Map
2hbjA 1 0.7707 100 0.436 Contact Map
4oo1J 1 0.9813 100 0.439 Contact Map
4nlcA 1 0.7547 100 0.44 Contact Map
3safA 1 0.7813 100 0.468 Contact Map
1vk0A 3 0.44 100 0.655 Contact Map
2e6mA 1 0.4507 100 0.661 Contact Map
4yfuA 1 0.8853 100 0.724 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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