GREMLIN Database
RNPH - Ribonuclease PH
UniProt: P28619 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 245 (209)
Sequences: 7733 (3604)
Seq/√Len: 249.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
194_G234_K3.6711.00
18_L139_I3.3281.00
39_C132_G3.2131.00
15_T31_T3.0461.00
31_T36_K2.8831.00
232_K235_E2.7421.00
41_A136_A2.6791.00
166_I214_D2.6281.00
190_V222_A2.5741.00
157_D195_S2.4771.00
174_L225_G2.4501.00
131_T229_L2.4051.00
157_D194_G2.3911.00
39_C114_I2.3611.00
22_S34_N2.3591.00
211_S214_D2.3331.00
17_D31_T2.2981.00
25_E68_R2.1941.00
225_G228_E2.1551.00
16_F30_I2.1461.00
19_D139_I2.1451.00
134_F158_F2.1341.00
231_D235_E2.0901.00
165_G176_L2.0181.00
177_N180_E1.9731.00
16_F135_L1.9711.00
212_R216_N1.9611.00
194_G231_D1.9461.00
192_M226_I1.8881.00
158_F234_K1.8541.00
172_I217_G1.7911.00
38_I119_I1.7651.00
166_I185_E1.7421.00
37_V118_V1.7381.00
165_G184_A1.7241.00
98_L133_A1.7071.00
21_I40_N1.6891.00
78_S83_I1.6681.00
224_K228_E1.6641.00
69_A74_T1.6481.00
168_K183_S1.6371.00
11_L174_L1.6101.00
57_G95_G1.6081.00
212_R223_E1.5911.00
138_A237_L1.5471.00
160_A226_I1.5181.00
220_G224_K1.5041.00
30_I128_A1.5011.00
16_F131_T1.4771.00
234_K238_G1.4591.00
167_D173_L1.4581.00
106_K152_T1.4471.00
14_I32_A1.4301.00
29_L36_K1.4221.00
172_I221_L1.4221.00
223_E227_Q1.4131.00
228_E231_D1.4101.00
158_F230_I1.3971.00
190_V219_L1.3841.00
166_I172_I1.3631.00
16_F236_V1.3321.00
157_D193_T1.3001.00
97_A200_E1.2931.00
174_L221_L1.2751.00
138_A155_I1.2721.00
227_Q231_D1.2681.00
114_I133_A1.2491.00
16_F232_K1.2131.00
179_E183_S1.2081.00
21_I24_P1.2061.00
214_D217_G1.2051.00
32_A128_A1.1991.00
74_T77_E1.1861.00
98_L137_M1.1831.00
228_E232_K1.1691.00
51_L56_K1.1651.00
122_D179_E1.1551.00
161_A191_I1.1491.00
226_I230_I1.1441.00
28_V135_L1.1431.00
130_I161_A1.1401.00
95_G99_R1.1361.00
213_E217_G1.1331.00
14_I229_L1.1241.00
116_C129_S1.1191.00
74_T84_S1.1191.00
64_S87_T1.1131.00
56_K105_E1.1121.00
230_I234_K1.1121.00
48_P54_G1.1091.00
41_A114_I1.1021.00
25_E152_T1.0941.00
138_A153_N1.0811.00
43_V110_R1.0741.00
216_N220_G1.0651.00
41_A140_A1.0611.00
30_I132_G1.0411.00
163_S187_D1.0281.00
102_V137_M1.0191.00
169_E185_E1.0081.00
172_I218_L1.0061.00
164_V222_A0.9931.00
45_D110_R0.9851.00
71_N74_T0.9851.00
101_V157_D0.9811.00
39_C133_A0.9801.00
84_S88_M0.9761.00
25_E42_S0.9601.00
167_D183_S0.9581.00
167_D170_Q0.9551.00
73_R76_R0.9511.00
192_M223_E0.9471.00
162_I174_L0.9451.00
97_A191_I0.9451.00
18_L236_V0.9401.00
191_I200_E0.9391.00
135_L236_V0.9261.00
134_F138_A0.9251.00
172_I214_D0.9231.00
48_P53_G0.9191.00
127_T161_A0.9141.00
231_D234_K0.9031.00
212_R220_G0.9001.00
64_S83_I0.9001.00
164_V221_L0.8851.00
61_A94_I0.8831.00
24_P42_S0.8801.00
193_T199_V0.8791.00
185_E208_A0.8741.00
44_E48_P0.8721.00
26_G41_A0.8700.99
35_T123_G0.8690.99
134_F155_I0.8640.99
164_V174_L0.8560.99
101_V193_T0.8550.99
77_E87_T0.8530.99
224_K227_Q0.8530.99
232_K236_V0.8490.99
130_I159_L0.8420.99
56_K104_L0.8390.99
33_G120_Q0.8330.99
173_L180_E0.8320.99
84_S87_T0.8290.99
134_F234_K0.8280.99
25_E43_V0.8280.99
67_P76_R0.8230.99
107_L154_P0.8170.99
83_I88_M0.8140.99
63_Y125_T0.8110.99
24_P40_N0.8050.99
18_L135_L0.8030.99
14_I232_K0.8000.99
126_R163_S0.7990.99
135_L233_Q0.7930.99
43_V106_K0.7890.99
101_V159_L0.7890.99
220_G223_E0.7860.99
155_I158_F0.7830.99
14_I131_T0.7830.99
131_T233_Q0.7820.99
12_R175_D0.7800.99
11_L228_E0.7780.99
205_G208_A0.7740.99
26_G136_A0.7740.99
17_D20_F0.7700.99
101_V134_F0.7700.99
10_E13_P0.7690.99
78_S84_S0.7670.99
170_Q180_E0.7630.99
164_V172_I0.7630.99
90_I124_G0.7620.99
164_V188_M0.7610.99
63_Y129_S0.7600.99
77_E84_S0.7580.99
198_F219_L0.7560.99
229_L233_Q0.7510.99
30_I131_T0.7490.98
194_G230_I0.7470.98
103_D106_K0.7470.98
94_I116_C0.7440.98
92_R99_R0.7430.98
37_V129_S0.7420.98
234_K237_L0.7390.98
162_I225_G0.7360.98
20_F36_K0.7330.98
44_E113_W0.7320.98
32_A127_T0.7310.98
131_T161_A0.7280.98
235_E238_G0.7250.98
104_L107_L0.7170.98
19_D26_G0.7150.98
57_G104_L0.7140.98
179_E182_S0.7110.98
164_V190_V0.7110.98
160_A229_L0.7080.98
59_I102_V0.7060.98
186_V210_F0.7040.98
102_V112_I0.7020.98
62_E115_D0.7020.98
221_L225_G0.6960.98
43_V140_A0.6950.98
88_M91_Q0.6950.98
21_I38_I0.6920.97
34_N122_D0.6890.97
126_R189_N0.6790.97
138_A234_K0.6770.97
37_V128_A0.6770.97
181_D187_D0.6760.97
43_V152_T0.6740.97
170_Q217_G0.6670.97
57_G107_L0.6650.97
21_I28_V0.6550.96
131_T160_A0.6510.96
116_C133_A0.6440.96
42_S113_W0.6420.96
29_L117_D0.6420.96
17_D29_L0.6410.96
64_S115_D0.6380.96
28_V132_G0.6380.96
185_E214_D0.6380.96
217_G220_G0.6370.96
92_R95_G0.6360.96
20_F29_L0.6360.96
205_G209_T0.6340.96
32_A123_G0.6320.96
27_S40_N0.6300.96
112_I137_M0.6300.96
31_T34_N0.6280.96
216_N223_E0.6270.96
90_I126_R0.6260.95
75_I113_W0.6210.95
54_G107_L0.6210.95
26_G139_I0.6210.95
46_R110_R0.6200.95
39_C116_C0.6190.95
33_G123_G0.6160.95
193_T230_I0.6140.95
162_I226_I0.6130.95
43_V108_G0.6110.95
86_R90_I0.6110.95
103_D107_L0.6110.95
119_I125_T0.6110.95
114_I137_M0.6100.95
54_G57_G0.6060.95
124_G181_D0.6020.94
188_M203_G0.5970.94
18_L28_V0.5960.94
15_T29_L0.5960.94
186_V205_G0.5930.94
134_F157_D0.5910.94
27_S38_I0.5900.94
34_N120_Q0.5870.94
28_V139_I0.5870.94
210_F214_D0.5850.94
57_G110_R0.5830.93
32_A131_T0.5830.93
53_G56_K0.5820.93
235_E239_D0.5790.93
164_V218_L0.5790.93
45_D108_G0.5780.93
39_C61_A0.5760.93
138_A158_F0.5740.93
24_P27_S0.5730.93
37_V132_G0.5720.93
208_A214_D0.5670.92
163_S189_N0.5610.92
101_V156_T0.5610.92
121_A178_Y0.5590.92
168_K185_E0.5580.92
20_F40_N0.5580.92
70_T121_A0.5550.92
215_L219_L0.5540.92
57_G112_I0.5520.91
127_T189_N0.5510.91
208_A211_S0.5500.91
217_G221_L0.5490.91
44_E110_R0.5490.91
58_W99_R0.5490.91
30_I37_V0.5480.91
35_T128_A0.5460.91
53_G109_E0.5460.91
57_G92_R0.5450.91
118_V129_S0.5430.91
43_V153_N0.5420.91
158_F194_G0.5370.90
32_A162_I0.5360.90
23_H71_N0.5350.90
178_Y181_D0.5350.90
127_T130_I0.5330.90
94_I130_I0.5310.90
175_D180_E0.5290.90
92_R96_R0.5280.90
40_N117_D0.5250.89
227_Q230_I0.5240.89
173_L177_N0.5240.89
177_N183_S0.5230.89
120_Q123_G0.5210.89
23_H34_N0.5210.89
75_I78_S0.5200.89
131_T135_L0.5190.89
44_E75_I0.5180.89
55_G109_E0.5150.88
170_Q213_E0.5150.88
196_G223_E0.5110.88
101_V155_I0.5110.88
124_G128_A0.5100.88
196_G201_L0.5100.88
121_A125_T0.5090.88
74_T78_S0.5070.88
63_Y87_T0.5050.87
119_I123_G0.5050.87
42_S115_D0.5040.87
64_S74_T0.5030.87
64_S67_P0.5000.87
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  
1oysA 2 0.8694 100 0.132 Contact Map
1udnA 5 0.9918 100 0.143 Contact Map
3m7nD 1 0.9184 100 0.154 Contact Map
3dd6A 3 0.9878 100 0.156 Contact Map
2je6B 2 0.9061 100 0.16 Contact Map
2wnrB 1 0.8939 100 0.163 Contact Map
1r6lA 3 0.9592 100 0.163 Contact Map
3b4tA 3 0.9714 100 0.165 Contact Map
2nn6B 1 0.9224 100 0.169 Contact Map
2po1A 1 0.9184 100 0.171 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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