GREMLIN Database
DNAD - DNA replication protein DnaD
UniProt: P39787 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 232 (200)
Sequences: 1257 (1046)
Seq/√Len: 73.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
15_S19_N6.0931.00
193_L199_A4.6471.00
194_K198_Q4.3641.00
23_T43_M4.3561.00
191_N202_H3.6821.00
193_L202_H3.2471.00
133_F167_L3.1081.00
139_R145_E3.0201.00
169_E203_S2.9481.00
166_A185_L2.9251.00
148_T182_D2.7421.00
30_L75_F2.6661.00
193_L198_Q2.5681.00
17_I39_L2.4601.00
165_H168_K2.3331.00
34_E74_M2.3231.00
37_L71_R2.1841.00
57_L68_C2.0451.00
152_W182_D2.0411.00
183_R186_F2.0301.00
41_I72_L2.0151.00
170_A181_I1.9491.00
55_N65_V1.9141.00
131_T134_E1.8021.00
30_L80_F1.7951.00
162_L199_A1.7731.00
130_Y141_L1.7621.00
145_E178_F1.7371.00
162_L193_L1.7331.00
162_L196_V1.7271.00
199_A203_S1.6581.00
132_I164_K1.6501.00
117_T120_R1.6471.00
134_E141_L1.5930.99
179_R182_D1.5840.99
165_H169_E1.5760.99
151_I155_Q1.5630.99
180_Y184_I1.5390.99
129_L167_L1.5360.99
31_N34_E1.5300.99
201_I204_Q1.5020.99
112_L116_Q1.4920.99
24_H27_Q1.4720.99
58_Q64_S1.4680.99
170_A184_I1.4200.99
99_L102_L1.3790.98
33_T67_E1.3400.98
57_L60_G1.3240.98
32_E35_L1.3190.98
44_H52_P1.3160.98
67_E70_N1.3100.98
153_Q163_I1.2930.98
17_I42_K1.2730.97
195_T198_Q1.2730.97
169_E184_I1.2690.97
166_A170_A1.2500.97
158_H189_K1.2390.97
34_E71_R1.2380.97
167_L181_I1.2360.97
130_Y154_D1.2290.97
58_Q65_V1.2110.96
29_G78_K1.1950.96
152_W184_I1.1910.96
182_D186_F1.1890.96
37_L41_I1.1840.96
133_F136_E1.1770.96
54_P72_L1.1710.96
94_F97_Y1.1700.95
197_E200_K1.1660.95
146_C150_A1.1650.95
61_M71_R1.1640.95
205_K208_R1.1620.95
198_Q201_I1.1520.95
58_Q68_C1.1470.95
37_L90_N1.1410.95
150_A154_D1.1410.95
175_K178_F1.1370.95
130_Y150_A1.1250.94
132_I136_E1.1240.94
98_S103_W1.1140.94
35_L63_I1.1140.94
187_E191_N1.1100.94
115_N118_Q1.1080.94
126_Q160_A1.1020.94
15_S43_M1.1000.94
73_R77_Q1.0820.93
132_I135_E1.0630.93
172_L182_D1.0490.92
32_E36_I1.0340.91
165_H200_K1.0330.91
44_H60_G1.0300.91
133_F145_E1.0150.91
159_D162_L1.0150.91
137_F171_V1.0150.91
99_L103_W1.0100.90
13_G19_N0.9970.90
148_T199_A0.9900.90
30_L35_L0.9710.89
19_N43_M0.9660.88
136_E171_V0.9550.88
133_F171_V0.9530.88
37_L61_M0.9460.87
76_I82_F0.9390.87
20_L24_H0.9380.87
129_L163_I0.9350.87
175_K183_R0.9200.86
114_Q118_Q0.9140.86
126_Q150_A0.9070.85
200_K204_Q0.9000.85
113_A120_R0.8960.84
15_S21_L0.8910.84
38_L61_M0.8910.84
133_F149_L0.8890.84
148_T183_R0.8880.84
144_L178_F0.8810.83
15_S22_L0.8780.83
162_L188_W0.8770.83
84_E98_S0.8670.82
192_G202_H0.8630.82
148_T178_F0.8600.82
133_F181_I0.8590.82
199_A206_F0.8560.82
137_F167_L0.8560.82
161_Q199_A0.8530.81
141_L178_F0.8520.81
104_G108_E0.8510.81
32_E62_S0.8490.81
196_V200_K0.8460.81
10_Q14_T0.8450.81
36_I74_M0.8400.80
169_E185_L0.8330.80
136_E169_E0.8240.79
115_N120_R0.8210.79
183_R187_E0.8140.78
156_D185_L0.8110.78
144_L177_S0.8090.78
115_N119_E0.8010.77
61_M158_H0.8000.77
136_E164_K0.7990.77
113_A116_Q0.7970.77
74_M78_K0.7960.77
142_S179_R0.7890.76
143_P147_E0.7870.76
54_P69_T0.7830.75
134_E138_A0.7790.75
38_L80_F0.7770.75
170_A185_L0.7760.75
34_E78_K0.7750.75
203_S206_F0.7710.74
37_L57_L0.7670.74
152_W163_I0.7650.74
96_K100_Q0.7590.73
146_C179_R0.7580.73
121_K125_E0.7500.72
112_L119_E0.7450.72
162_L165_H0.7440.72
30_L36_I0.7430.72
163_I175_K0.7390.71
25_Y32_E0.7390.71
55_N59_E0.7360.71
204_Q208_R0.7360.71
30_L38_L0.7350.71
22_L43_M0.7340.71
156_D170_A0.7250.70
197_E201_I0.7210.69
126_Q163_I0.7200.69
165_H203_S0.7190.69
166_A169_E0.7140.69
36_I40_K0.7130.68
172_L179_R0.7110.68
134_E146_C0.7100.68
148_T165_H0.7010.67
95_E98_S0.6990.67
69_T90_N0.6980.67
49_S56_Q0.6970.67
30_L74_M0.6960.67
37_L75_F0.6940.66
91_G94_F0.6940.66
40_K61_M0.6940.66
133_F169_E0.6850.65
22_L26_K0.6840.65
114_Q117_T0.6830.65
130_Y149_L0.6760.64
142_S181_I0.6730.64
24_H46_E0.6690.63
116_Q119_E0.6680.63
137_F145_E0.6680.63
92_I95_E0.6670.63
112_L118_Q0.6670.63
9_M20_L0.6600.62
67_E74_M0.6560.62
176_L200_K0.6560.62
140_P186_F0.6540.62
145_E183_R0.6470.61
33_T63_I0.6430.60
52_P57_L0.6410.60
137_F148_T0.6410.60
51_F83_I0.6400.60
96_K99_L0.6370.60
166_A188_W0.6340.59
91_G96_K0.6330.59
32_E71_R0.6330.59
141_L148_T0.6330.59
91_G102_L0.6310.59
113_A118_Q0.6300.59
119_E127_K0.6270.59
26_K38_L0.6250.58
73_R192_G0.6240.58
81_L89_Q0.6220.58
129_L164_K0.6180.57
162_L198_Q0.6170.57
158_H163_I0.6170.57
136_E168_K0.6160.57
191_N205_K0.6150.57
12_Q20_L0.6130.57
61_M74_M0.6110.57
15_S42_K0.6110.57
201_I205_K0.6090.56
32_E63_I0.6080.56
71_R74_M0.6030.56
18_P22_L0.6020.55
136_E142_S0.6020.55
174_G187_E0.6020.55
137_F140_P0.5980.55
133_F142_S0.5970.55
36_I39_L0.5970.55
73_R76_I0.5960.55
36_I75_F0.5960.55
30_L37_L0.5940.54
53_T56_Q0.5940.54
203_S207_R0.5890.54
133_F137_F0.5880.54
173_S203_S0.5860.53
129_L133_F0.5850.53
31_N54_P0.5790.53
34_E62_S0.5790.53
34_E37_L0.5790.53
10_Q20_L0.5710.52
15_S39_L0.5700.51
178_F182_D0.5690.51
144_L185_L0.5690.51
110_I116_Q0.5670.51
167_L171_V0.5650.51
149_L152_W0.5630.51
136_E172_L0.5630.51
128_S152_W0.5630.51
141_L145_E0.5630.51
101_P106_L0.5620.50
135_E191_N0.5590.50
16_T19_N0.5590.50
48_G72_L0.5570.50
175_K184_I0.5560.50
141_L160_A0.5540.49
26_K36_I0.5540.49
64_S67_E0.5530.49
114_Q120_R0.5490.49
118_Q123_E0.5480.49
134_E188_W0.5480.49
144_L147_E0.5470.49
13_G16_T0.5440.48
25_Y30_L0.5420.48
24_H63_I0.5420.48
83_I95_E0.5410.48
153_Q158_H0.5400.48
159_D194_K0.5380.47
128_S177_S0.5380.47
57_L61_M0.5370.47
164_K177_S0.5360.47
138_A178_F0.5330.47
41_I81_L0.5330.47
17_I114_Q0.5330.47
165_H199_A0.5320.47
200_K203_S0.5320.47
156_D169_E0.5320.47
64_S70_N0.5270.46
112_L117_T0.5250.46
94_F98_S0.5230.46
160_A177_S0.5220.46
170_A175_K0.5210.45
37_L68_C0.5210.45
176_L192_G0.5210.45
196_V199_A0.5200.45
21_L26_K0.5200.45
168_K177_S0.5190.45
149_L160_A0.5190.45
21_L35_L0.5190.45
136_E167_L0.5180.45
31_N74_M0.5180.45
27_Q68_C0.5170.45
48_G58_Q0.5150.45
199_A202_H0.5150.45
30_L61_M0.5150.45
88_D94_F0.5150.45
133_F170_A0.5140.45
158_H185_L0.5110.44
155_Q189_K0.5070.44
129_L149_L0.5060.44
18_P75_F0.5030.43
35_L39_L0.5000.43
180_Y188_W0.5000.43
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  
2zc2A 1 0.3233 99.8 0.601 Contact Map
2i5uA 1 0.3017 99.8 0.635 Contact Map
2v79A 4 0.5043 99.5 0.708 Contact Map
2vn2A 4 0.4741 99 0.769 Contact Map
4ptaD 3 0.4612 97.9 0.832 Contact Map
4pt7A 3 0.5086 97.8 0.836 Contact Map
3bjaA 2 0.5948 96.4 0.868 Contact Map
3broA 2 0.5991 96.4 0.869 Contact Map
3kp7A 2 0.5862 96.3 0.869 Contact Map
3jw4A 2 0.5431 96.2 0.87 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.

Page generated in 0.0078 seconds.