GREMLIN Database
PDDEXK_7 - PD-(D/E)XK nuclease superfamily
PFAM: PF04411 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 165 (160)
Sequences: 2166 (1711)
Seq/√Len: 135.3
META: 0.847

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
66_T82_R4.6491.00
7_C159_L4.4161.00
11_L85_I4.1831.00
61_L87_L3.6201.00
127_K130_D3.4551.00
130_D133_K3.0851.00
132_N136_R2.5401.00
88_E98_H2.4321.00
66_T80_P2.4011.00
81_Q136_R2.2841.00
4_E64_N2.2601.00
135_H139_D2.2141.00
30_K39_T2.2061.00
67_F98_H2.1951.00
106_R129_D2.1291.00
60_E88_E2.1121.00
100_H153_V2.0741.00
86_V98_H2.0711.00
62_S65_R1.8941.00
134_M156_A1.8461.00
60_E90_W1.7991.00
64_N82_R1.7971.00
106_R130_D1.7591.00
58_R90_W1.7291.00
22_E51_E1.7191.00
128_R132_N1.6411.00
4_E63_Y1.6251.00
15_L18_L1.6111.00
67_F86_V1.6031.00
49_V58_R1.5751.00
135_H140_A1.5471.00
57_L91_P1.4911.00
133_K136_R1.4591.00
47_R60_E1.4491.00
119_D122_G1.4351.00
138_R156_A1.4201.00
10_K13_R1.4181.00
81_Q132_N1.4171.00
115_G118_D1.4151.00
122_G126_P1.4111.00
11_L61_L1.3661.00
120_E124_P1.2581.00
121_D125_G1.2361.00
65_R86_V1.2261.00
79_V132_N1.2151.00
117_D121_D1.1911.00
130_D134_M1.1890.99
3_Y6_W1.1880.99
12_L61_L1.1880.99
22_E25_S1.1780.99
147_G150_E1.1690.99
8_F12_L1.1370.99
120_E123_D1.1270.99
91_P94_G1.0920.99
90_W94_G1.0700.99
64_N103_A1.0650.99
43_G46_S1.0580.99
11_L101_F1.0570.99
78_T135_H1.0540.99
101_F134_M1.0520.99
79_V131_I1.0520.99
83_P104_K1.0510.99
59_I89_I1.0500.99
108_D127_K1.0460.99
116_E119_D1.0460.99
114_F118_D1.0420.99
12_L16_K1.0380.99
152_R157_Y1.0360.99
9_L13_R1.0360.99
84_D137_Y1.0260.99
110_L113_G1.0250.98
105_Y157_Y1.0200.98
69_G73_Y1.0150.98
32_T35_G0.9980.98
78_T136_R0.9980.98
100_H141_I0.9970.98
85_I159_L0.9950.98
12_L50_F0.9900.98
14_I18_L0.9880.98
71_K74_P0.9870.98
81_Q128_R0.9820.98
62_S98_H0.9810.98
121_D126_P0.9810.98
118_D121_D0.9800.98
42_K82_R0.9790.98
69_G75_G0.9770.98
4_E104_K0.9680.98
51_E56_G0.9600.98
31_V44_K0.9540.98
117_D122_G0.9450.97
99_Y155_G0.9440.97
106_R155_G0.9340.97
127_K133_K0.9290.97
122_G125_G0.9250.97
97_V154_F0.9170.97
108_D128_R0.9120.97
76_S135_H0.9100.97
61_L85_I0.9060.97
118_D122_G0.9000.97
134_M162_G0.8960.96
9_L85_I0.8960.96
84_D102_D0.8940.96
5_Y63_Y0.8800.96
87_L101_F0.8730.96
83_P137_Y0.8730.96
84_D104_K0.8680.96
29_I38_V0.8670.96
151_R155_G0.8610.96
8_F64_N0.8600.96
133_K162_G0.8550.95
98_H153_V0.8470.95
81_Q106_R0.8320.95
102_D106_R0.8250.94
31_V36_L0.8200.94
1_T42_K0.8120.94
18_L59_I0.8100.94
35_G38_V0.8070.94
7_C15_L0.8020.94
7_C103_A0.7990.93
4_E84_D0.7980.93
26_Q30_K0.7980.93
49_V87_L0.7910.93
135_H138_R0.7870.93
13_R101_F0.7830.93
137_Y140_A0.7780.93
103_A129_D0.7780.93
103_A155_G0.7760.92
40_L43_G0.7750.92
131_I134_M0.7660.92
7_C85_I0.7610.92
46_S50_F0.7570.91
85_I153_V0.7490.91
53_P56_G0.7460.91
2_L6_W0.7390.90
79_V115_G0.7350.90
79_V128_R0.7330.90
123_D126_P0.7260.90
101_F158_V0.7250.90
126_P159_L0.7250.90
15_L80_P0.7230.90
89_I105_Y0.7190.89
112_E115_G0.7160.89
12_L48_V0.7050.88
9_L63_Y0.7050.88
5_Y8_F0.7020.88
22_E26_Q0.6990.88
81_Q133_K0.6970.88
9_L81_Q0.6950.88
23_L31_V0.6950.88
130_D136_R0.6950.88
111_D124_P0.6940.88
64_N133_K0.6840.87
78_T158_V0.6810.87
15_L61_L0.6800.86
86_V100_H0.6760.86
77_W149_L0.6730.86
146_D150_E0.6730.86
121_D124_P0.6730.86
102_D137_Y0.6700.86
18_L23_L0.6680.85
83_P102_D0.6650.85
28_L38_V0.6650.85
24_D51_E0.6570.85
27_D111_D0.6540.84
9_L127_K0.6530.84
149_L157_Y0.6530.84
134_M137_Y0.6530.84
104_K137_Y0.6520.84
114_F120_E0.6510.84
41_K44_K0.6470.84
116_E120_E0.6440.83
33_R39_T0.6430.83
77_W136_R0.6420.83
79_V108_D0.6340.82
100_H156_A0.6330.82
136_R139_D0.6310.82
116_E126_P0.6310.82
47_R50_F0.6290.82
49_V60_E0.6280.82
9_L105_Y0.6260.82
1_T63_Y0.6220.81
85_I98_H0.6200.81
146_D149_L0.6200.81
7_C151_R0.6170.81
136_R160_Y0.6170.81
41_K45_E0.6140.80
42_K64_N0.6120.80
35_G44_K0.6120.80
22_E53_P0.6080.80
55_R67_F0.6080.80
106_R136_R0.6070.80
158_V161_P0.6050.79
77_W81_Q0.6040.79
129_D154_F0.6040.79
107_I157_Y0.6000.79
101_F133_K0.6000.79
21_Y25_S0.5990.79
6_W105_Y0.5920.78
7_C156_A0.5900.78
43_G64_N0.5860.77
5_Y38_V0.5840.77
117_D124_P0.5830.77
24_D28_L0.5820.77
8_F29_I0.5780.76
11_L100_H0.5610.74
101_F130_D0.5590.74
1_T12_L0.5580.74
115_G121_D0.5560.73
137_Y141_I0.5520.73
115_G126_P0.5510.73
18_L60_E0.5500.73
118_D126_P0.5490.73
72_G92_P0.5420.72
50_F53_P0.5420.72
62_S88_E0.5400.71
32_T37_G0.5390.71
117_D120_E0.5370.71
38_V42_K0.5320.70
5_Y15_L0.5310.70
52_R55_R0.5290.70
91_P99_Y0.5260.69
4_E8_F0.5260.69
25_S28_L0.5250.69
93_G116_E0.5230.69
43_G48_V0.5210.69
68_S80_P0.5210.69
7_C11_L0.5190.68
13_R16_K0.5160.68
78_T139_D0.5150.68
32_T41_K0.5140.68
116_E123_D0.5140.68
23_L26_Q0.5110.67
103_A106_R0.5110.67
4_E83_P0.5060.66
98_H152_R0.5050.66
65_R88_E0.5050.66
75_G100_H0.5040.66
46_S53_P0.5040.66
134_M157_Y0.5030.66
91_P100_H0.5000.65
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  
2w00A 1 0.7091 5.4 0.944 Contact Map
3kskA 3 0.6121 5.2 0.945 Contact Map
3pviA 2 0.6303 5.2 0.945 Contact Map
4uu3A 2 0.8364 3.7 0.949 Contact Map
4bl0B 1 0.1455 2.4 0.953 Contact Map
3iacA 3 0.8303 2.2 0.954 Contact Map
3riiA 2 0.3273 2.1 0.955 Contact Map
3dxpA 2 0.3333 2.1 0.955 Contact Map
1mw7A 1 0.3818 2 0.955 Contact Map
2x4wB 1 0.0727 1.7 0.957 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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