GREMLIN Database
Rep_1 - Replication protein
PFAM: PF01446 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 237 (203)
Sequences: 875 (680)
Seq/√Len: 47.7
META: 0.782

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
51_N55_K3.8141.00
52_R117_K3.7241.00
113_Q121_D3.6181.00
56_R114_K3.3101.00
58_K107_E3.1691.00
22_R128_A2.9931.00
109_V121_D2.8841.00
45_H49_A2.8321.00
66_W185_G2.7671.00
26_L89_L2.7321.00
46_M85_F2.7091.00
31_K120_Y2.6861.00
44_D179_R2.4091.00
192_H196_K2.3431.00
40_R179_R2.2721.00
109_V123_I2.2611.00
198_D203_G2.2141.00
33_C42_T2.1871.00
56_R115_A2.1751.00
31_K122_P2.1671.00
30_V42_T2.1481.00
26_L108_W2.0321.00
105_Q109_V2.0291.00
74_Y79_G2.0190.99
48_K51_N1.9610.99
54_T59_F1.9160.99
176_L181_L1.8950.99
49_A116_L1.8240.99
118_V122_P1.8060.99
50_F87_V1.7920.99
103_I107_E1.7830.99
146_E149_K1.7500.99
48_K52_R1.7260.98
49_A118_V1.7100.98
104_K107_E1.6980.98
105_Q124_V1.6950.98
23_F188_L1.6630.98
66_W183_A1.6530.98
42_T46_M1.6370.98
64_K92_P1.6360.98
171_E175_A1.6330.98
47_N85_F1.6220.98
43_L70_L1.6200.98
13_E16_K1.5960.97
24_L126_I1.5780.97
23_F90_A1.5300.96
43_L47_N1.5190.96
24_L89_L1.5180.96
21_A90_A1.4920.96
57_K61_K1.4680.96
56_R59_F1.4610.95
105_Q123_I1.4540.95
42_T45_H1.4460.95
68_R183_A1.4300.95
180_R183_A1.4140.95
89_L108_W1.3660.93
75_N80_T1.3540.93
47_N68_R1.3470.93
97_K100_D1.3360.93
187_I190_E1.3190.92
52_R115_A1.3090.92
116_L120_Y1.3010.92
109_V122_P1.2900.91
74_Y168_V1.2820.91
105_Q121_D1.2750.91
31_K119_D1.2730.91
107_E111_L1.2680.91
53_L108_W1.2490.90
191_I194_E1.1940.88
13_E17_R1.1890.87
20_K93_P1.1880.87
34_E37_E1.1800.87
108_W126_I1.1760.87
107_E110_E1.1730.87
21_A64_K1.1660.86
70_L85_F1.1590.86
200_V203_G1.1500.86
22_R93_P1.1410.85
72_V176_L1.1370.85
52_R55_K1.1270.84
51_N54_T1.1220.84
90_A188_L1.1220.84
204_D207_H1.1170.84
118_V121_D1.1160.84
59_F111_L1.1080.83
109_V120_Y1.1030.83
75_N78_D1.0860.82
81_Y157_Y1.0820.82
30_V82_H1.0810.82
70_L181_L1.0730.81
48_K55_K1.0660.81
170_K174_K1.0630.81
30_V33_C1.0610.81
116_L122_P1.0540.80
50_F66_W1.0520.80
45_H52_R1.0500.80
199_D203_G1.0430.80
47_N70_L1.0340.79
22_R96_F1.0170.78
31_K118_V1.0110.77
62_A101_N1.0060.77
50_F54_T1.0040.77
129_V143_A0.9940.76
74_Y80_T0.9830.75
141_Q145_A0.9810.75
60_K186_G0.9780.75
26_L126_I0.9740.75
124_V127_R0.9630.74
19_P90_A0.9590.74
31_K109_V0.9500.73
203_G206_I0.9460.73
50_F53_L0.9400.72
67_F70_L0.9380.72
63_V89_L0.9260.71
131_P142_A0.9210.70
192_H197_L0.9210.70
168_V171_E0.9160.70
12_D15_V0.9130.70
147_T208_V0.9080.69
91_V96_F0.8970.68
190_E194_E0.8970.68
161_D165_N0.8870.68
94_S97_K0.8820.67
36_G171_E0.8620.65
45_H116_L0.8610.65
36_G81_Y0.8570.65
106_A110_E0.8540.65
66_W188_L0.8510.64
30_V46_M0.8460.64
30_V116_L0.8440.64
25_F147_T0.8430.64
121_D124_V0.8420.64
50_F183_A0.8400.63
88_L129_V0.8320.63
57_K114_K0.8260.62
62_A89_L0.8230.62
176_L179_R0.8140.61
17_R194_E0.8120.61
74_Y173_D0.8110.61
161_D164_E0.8100.60
30_V83_P0.8100.60
157_Y160_L0.8100.60
184_F200_V0.8090.60
58_K103_I0.8060.60
47_N171_E0.8050.60
39_L175_A0.8040.60
189_K192_H0.8010.60
188_L192_H0.7950.59
143_A147_T0.7920.59
109_V118_V0.7880.58
180_R189_K0.7850.58
58_K111_L0.7850.58
55_K60_K0.7800.58
109_V125_D0.7730.57
108_W111_L0.7720.57
109_V124_V0.7660.56
31_K116_L0.7540.55
119_D122_P0.7490.55
160_L165_N0.7470.54
26_L87_V0.7460.54
175_A179_R0.7450.54
62_A103_I0.7440.54
49_A53_L0.7370.53
44_D51_N0.7330.53
192_H195_L0.7300.53
66_W90_A0.7200.52
189_K193_K0.7190.52
28_L89_L0.7160.51
81_Y192_H0.7150.51
117_K190_E0.7070.50
98_G101_N0.7070.50
25_F88_L0.7040.50
91_V95_Y0.7030.50
40_R44_D0.7020.50
94_S101_N0.7000.50
124_V172_L0.6990.50
44_D48_K0.6990.50
92_P101_N0.6970.49
182_I188_L0.6950.49
145_A151_A0.6950.49
30_V85_F0.6920.49
41_E48_K0.6830.48
47_N179_R0.6770.47
68_R179_R0.6740.47
53_L111_L0.6740.47
90_A187_I0.6730.47
30_V118_V0.6720.47
158_L166_L0.6720.47
139_A143_A0.6590.46
122_P125_D0.6580.45
106_A121_D0.6550.45
165_N169_V0.6490.45
169_V178_G0.6480.44
50_F185_G0.6450.44
140_L147_T0.6430.44
77_K80_T0.6420.44
69_A151_A0.6390.44
56_R66_W0.6390.44
110_E114_K0.6370.43
148_A184_F0.6330.43
170_K177_H0.6320.43
59_F103_I0.6280.42
69_A182_I0.6260.42
74_Y83_P0.6260.42
29_T82_H0.6250.42
64_K93_P0.6250.42
126_I131_P0.6230.42
205_L209_D0.6210.42
94_S99_S0.6160.41
201_E205_L0.6110.41
145_A179_R0.6090.41
109_V116_L0.6080.41
78_D116_L0.6080.41
116_L185_G0.6060.40
111_L114_K0.6040.40
182_I191_I0.6040.40
40_R175_A0.6040.40
94_S98_G0.6040.40
23_F67_F0.5970.39
23_F88_L0.5960.39
33_C83_P0.5950.39
14_A18_E0.5940.39
173_D182_I0.5900.39
200_V205_L0.5850.38
11_L16_K0.5850.38
23_F92_P0.5820.38
129_V159_T0.5790.38
67_F147_T0.5770.38
124_V128_A0.5760.37
70_L184_F0.5760.37
72_V208_V0.5750.37
30_V190_E0.5750.37
46_M185_G0.5740.37
43_L53_L0.5720.37
133_K139_A0.5710.37
207_H212_D0.5710.37
151_A154_D0.5710.37
131_P134_K0.5700.37
70_L176_L0.5690.37
150_Y153_K0.5680.37
18_E21_A0.5670.37
134_K211_E0.5670.37
195_L205_L0.5650.36
81_Y171_E0.5650.36
22_R130_K0.5640.36
165_N173_D0.5640.36
110_E113_Q0.5640.36
195_L204_D0.5630.36
58_K61_K0.5620.36
49_A98_G0.5610.36
66_W155_S0.5600.36
95_Y102_Y0.5600.36
14_A17_R0.5600.36
157_Y165_N0.5590.36
164_E168_V0.5590.36
193_K196_K0.5590.36
183_A189_K0.5560.36
199_D202_D0.5540.35
34_E38_E0.5520.35
56_R60_K0.5520.35
47_N175_A0.5510.35
81_Y168_V0.5500.35
23_F65_G0.5500.35
44_D49_A0.5490.35
171_E174_K0.5490.35
33_C154_D0.5490.35
67_F115_A0.5480.35
72_V175_A0.5470.35
38_E41_E0.5440.35
27_T86_H0.5400.34
74_Y78_D0.5390.34
152_V156_D0.5360.34
152_V193_K0.5350.34
151_A181_L0.5350.34
162_D168_V0.5330.34
49_A60_K0.5320.33
196_K200_V0.5310.33
167_E170_K0.5300.33
37_E199_D0.5290.33
142_A145_A0.5270.33
23_F173_D0.5250.33
46_M116_L0.5230.33
62_A92_P0.5220.33
43_L72_V0.5220.33
111_L115_A0.5220.33
177_H195_L0.5210.32
63_V103_I0.5200.32
88_L191_I0.5170.32
133_K136_G0.5170.32
62_A91_V0.5150.32
70_L179_R0.5140.32
144_V207_H0.5130.32
100_D104_K0.5110.32
179_R187_I0.5110.32
157_Y168_V0.5100.32
61_K143_A0.5090.31
53_L59_F0.5090.31
131_P144_V0.5080.31
33_C178_G0.5070.31
164_E167_E0.5050.31
75_N181_L0.5030.31
129_V147_T0.5020.31
202_D205_L0.5000.31
36_G175_A0.5000.31
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  
1l2mA 1 0.4937 50.3 0.955 Contact Map
2qsjA 2 0.2152 48.9 0.956 Contact Map
2qgzA 1 0.2447 24.8 0.962 Contact Map
1vhtA 1 0.2616 21.6 0.963 Contact Map
3douA 1 0.27 19.7 0.964 Contact Map
3lccA 1 0.3165 19.1 0.964 Contact Map
4ag4A 1 0.3207 17.4 0.965 Contact Map
4gmoA 1 0.2489 17 0.965 Contact Map
4a6dA 2 0.2911 16.4 0.965 Contact Map
2gpyA 2 0.2321 15.9 0.965 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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