GREMLIN Database
RNH - Ribonuclease HI
UniProt: P0A7Y4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10860
Length: 155 (140)
Sequences: 3358 (2135)
Seq/√Len: 180.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
101_V105_Q3.9001.00
86_K108_D3.5671.00
72_Q76_Q3.4671.00
76_Q80_Q3.4591.00
66_I119_E3.4241.00
57_E106_R3.1701.00
126_G131_E2.8391.00
54_V57_E2.8381.00
52_A74_V2.6071.00
14_L138_R2.4691.00
7_I55_A2.4211.00
14_L142_M2.1981.00
14_L141_A2.1301.00
46_R102_D2.1041.00
64_E115_Q2.0051.00
84_N88_R1.9151.00
69_T75_R1.8651.00
57_E110_A1.8531.00
50_M54_V1.8521.00
110_A113_Q1.7611.00
34_T132_R1.7111.00
77_G104_W1.6961.00
27_R129_E1.6521.00
66_I117_K1.6311.00
68_S119_E1.5831.00
138_R141_A1.5721.00
4_Q64_E1.5551.00
25_I133_C1.5531.00
9_T51_A1.5181.00
4_Q66_I1.5091.00
52_A67_L1.4391.00
6_E66_I1.4201.00
24_A55_A1.3981.00
92_T98_V1.3901.00
36_S140_A1.3901.00
82_I108_D1.3571.00
27_R32_E1.3501.00
106_R110_A1.2991.00
12_S141_A1.2981.00
75_R79_T1.2941.00
20_G42_T1.2941.00
122_K125_A1.2931.00
125_A131_E1.2791.00
23_G140_A1.2581.00
88_R95_K1.2511.00
8_F127_H1.2501.00
111_L118_W1.2371.00
138_R142_M1.2081.00
6_E27_R1.2041.00
132_R135_E1.1961.00
12_S137_A1.1951.00
72_Q75_R1.1831.00
84_N87_K1.1501.00
53_I107_L1.1411.00
36_S139_A1.1341.00
6_E68_S1.1321.00
128_P132_R1.1311.00
39_Y46_R1.1261.00
8_F129_E1.1201.00
12_S138_R1.1071.00
127_H131_E1.0821.00
135_E139_A1.0811.00
23_G136_L1.0671.00
72_Q120_W1.0561.00
86_K112_G1.0451.00
133_C140_A1.0371.00
68_S127_H1.0371.00
24_A35_F1.0301.00
140_A143_N1.0160.99
22_Y54_V1.0080.99
36_S143_N1.0030.99
91_K97_P0.9950.99
8_F68_S0.9820.99
21_G141_A0.9800.99
92_T99_K0.9650.99
25_I129_E0.9570.99
139_A143_N0.9550.99
25_I132_R0.9510.99
28_Y63_C0.9280.99
78_I111_L0.9120.99
20_G47_M0.9080.99
136_L140_A0.9060.99
108_D112_G0.8900.99
53_I106_R0.8870.99
92_T96_K0.8850.99
38_G140_A0.8770.98
50_M106_R0.8700.98
83_H87_K0.8640.98
98_V101_V0.8350.98
120_W125_A0.8310.98
7_I65_V0.8260.98
74_V104_W0.8090.97
49_L107_L0.8020.97
79_T118_W0.7920.97
22_Y37_A0.7920.97
135_E138_R0.7850.97
10_D134_D0.7750.97
49_L74_V0.7680.96
78_I118_W0.7680.96
32_E129_E0.7640.96
26_L58_A0.7600.96
82_I98_V0.7600.96
8_F27_R0.7560.96
64_E117_K0.7510.96
38_G141_A0.7500.96
59_L65_V0.7480.96
42_T47_M0.7480.96
53_I110_A0.7470.96
64_E114_H0.7430.96
26_L33_K0.7410.96
15_G141_A0.7370.95
23_G133_C0.7370.95
10_D124_H0.7360.95
62_H114_H0.7280.95
91_K95_K0.7170.95
96_K99_K0.7150.95
42_T46_R0.7140.95
75_R118_W0.7060.94
72_Q122_K0.7040.94
60_K114_H0.7020.94
7_I26_L0.6970.94
45_N100_N0.6960.94
13_C16_N0.6930.94
34_T136_L0.6930.94
59_L63_C0.6900.94
7_I67_L0.6830.93
5_V63_C0.6820.93
35_F58_A0.6820.93
32_E132_R0.6810.93
39_Y50_M0.6760.93
109_A112_G0.6750.93
49_L73_Y0.6740.93
10_D70_D0.6720.93
81_W85_W0.6720.93
9_T55_A0.6670.92
21_G140_A0.6670.92
105_Q109_A0.6670.92
7_I24_A0.6620.92
73_Y100_N0.6590.92
46_R103_L0.6550.92
124_H134_D0.6490.91
16_N44_N0.6420.91
38_G47_M0.6410.91
27_R127_H0.6380.91
70_D134_D0.6320.90
97_P101_V0.6300.90
9_T52_A0.6300.90
6_E127_H0.6300.90
53_I103_L0.6230.90
59_L114_H0.6200.89
5_V60_K0.6180.89
79_T117_K0.6170.89
82_I90_W0.6150.89
22_Y39_Y0.6110.89
60_K113_Q0.6080.88
75_R78_I0.6050.88
139_A142_M0.6040.88
28_Y61_E0.6040.88
25_I33_K0.5970.87
63_C114_H0.5930.87
137_A141_A0.5930.87
22_Y47_M0.5920.87
77_G82_I0.5910.87
33_K58_A0.5880.87
10_D48_E0.5870.87
21_G137_A0.5850.86
50_M103_L0.5770.86
15_G18_G0.5770.86
130_N134_D0.5760.86
83_H112_G0.5760.86
70_D130_N0.5750.85
92_T95_K0.5710.85
120_W123_G0.5700.85
121_V124_H0.5670.85
124_H130_N0.5660.85
52_A118_W0.5630.84
54_V58_A0.5620.84
121_V127_H0.5600.84
49_L77_G0.5560.84
78_I82_I0.5540.83
48_E124_H0.5540.83
70_D124_H0.5530.83
111_L116_I0.5530.83
18_G41_R0.5520.83
9_T69_T0.5520.83
52_A107_L0.5480.83
45_N92_T0.5450.82
88_R91_K0.5400.82
27_R30_G0.5380.81
37_A54_V0.5340.81
46_R50_M0.5330.81
88_R93_A0.5300.81
9_T67_L0.5290.80
59_L62_H0.5250.80
45_N99_K0.5240.80
28_Y31_R0.5220.80
44_N70_D0.5210.79
55_A65_V0.5210.79
12_S15_G0.5200.79
26_L55_A0.5170.79
10_D130_N0.5160.79
85_W88_R0.5160.79
17_P42_T0.5130.78
30_G33_K0.5120.78
7_I52_A0.5110.78
65_V114_H0.5090.78
90_W98_V0.5060.77
41_R50_M0.5060.77
54_V106_R0.5060.77
86_K105_Q0.5000.77
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  
1jl1A 1 0.9806 100 0.233 Contact Map
3h08A 1 0.9097 100 0.262 Contact Map
2e4lA 1 0.9871 100 0.272 Contact Map
2qkbA 1 0.929 100 0.276 Contact Map
1rilA 1 0.9419 100 0.281 Contact Map
2lsnA 1 0.9355 100 0.293 Contact Map
4mh8A 1 0 100 0.312 Contact Map
4ibnA 1 0.9935 100 0.32 Contact Map
3qioA 1 0.8194 100 0.324 Contact Map
3p1gA 1 0.8774 100 0.41 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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