GREMLIN Database
HR_lesion - HR-like lesion-inducing
PFAM: PF05514 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 138 (134)
Sequences: 850 (524)
Seq/√Len: 45.3
META: 0.759

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
94_F103_H4.6801.00
104_D107_N3.6171.00
24_L27_I3.4021.00
23_K73_E3.2241.00
73_E77_G2.7971.00
71_A75_I2.6561.00
117_K121_D2.6411.00
75_I79_L2.5341.00
20_G23_K2.5021.00
67_A70_I2.4041.00
73_E76_G2.1301.00
30_T33_I2.0931.00
99_T125_N2.0430.99
76_G79_L2.0410.99
29_A33_I2.0300.99
70_I73_E1.9520.99
98_A102_F1.9240.99
74_G77_G1.8750.99
74_G79_L1.8500.99
64_A68_A1.8430.99
92_I129_I1.7870.98
49_L52_M1.7200.98
35_A39_I1.7120.98
48_Q53_T1.6540.97
93_L97_A1.6040.97
76_G81_A1.5060.95
6_T10_V1.4840.95
18_Y22_T1.4630.95
62_A66_A1.4350.94
12_F131_A1.3950.93
77_G80_I1.3350.92
95_V128_I1.3250.91
129_I132_L1.3200.91
71_A76_G1.2930.90
73_E78_L1.2930.90
62_A65_L1.2880.90
53_T57_T1.2870.90
20_G24_L1.2800.90
29_A32_G1.2540.89
80_I83_G1.2450.88
110_P113_N1.2330.88
72_L76_G1.2310.88
48_Q55_M1.2290.88
66_A70_I1.2270.88
50_E55_M1.2090.87
48_Q51_T1.2010.87
49_L53_T1.1950.86
73_E80_I1.1860.86
87_F90_L1.1830.86
71_A74_G1.1780.85
34_A37_V1.1710.85
6_T14_V1.1630.85
31_A34_A1.1540.84
30_T34_A1.1500.84
36_K39_I1.1340.83
33_I36_K1.1090.82
61_Q65_L1.1050.82
31_A35_A1.1030.81
52_M55_M1.0850.80
19_S22_T1.0760.80
28_G32_G1.0750.80
61_Q64_A1.0700.79
103_H118_T1.0620.79
72_L79_L1.0530.78
55_M59_Q1.0530.78
72_L77_G1.0440.78
73_E79_L1.0330.77
65_L70_I1.0310.77
63_L71_A1.0250.76
111_P114_E1.0100.75
46_T50_E0.9680.72
36_K40_P0.9630.72
48_Q52_M0.9560.71
125_N130_G0.9530.71
7_F133_L0.9470.71
53_T59_Q0.9260.69
93_L96_A0.9230.69
50_E53_T0.9180.68
97_A100_F0.9160.68
89_I93_L0.9060.67
53_T60_L0.9020.67
71_A77_G0.8990.66
91_L95_V0.8910.66
78_L81_A0.8850.65
9_R16_F0.8750.64
74_G78_L0.8740.64
92_I132_L0.8670.64
54_G58_P0.8650.63
47_A103_H0.8650.63
100_F131_A0.8540.62
72_L90_L0.8400.61
91_L132_L0.8230.60
51_T56_P0.8200.59
98_A103_H0.8070.58
65_L68_A0.8020.58
69_A76_G0.7930.57
63_L66_A0.7890.56
77_G81_A0.7840.56
7_F92_I0.7720.55
28_G33_I0.7710.55
19_S23_K0.7700.55
32_G35_A0.7640.54
118_T121_D0.7470.52
93_L99_T0.7460.52
67_A73_E0.7380.51
47_A98_A0.7330.51
70_I74_G0.7320.51
57_T63_L0.7320.51
5_I90_L0.7320.51
107_N110_P0.7300.51
2_P5_I0.7300.51
79_L87_F0.7280.50
103_H106_W0.7260.50
33_I37_V0.7230.50
68_A73_E0.7210.50
20_G26_D0.7180.49
86_F100_F0.7100.49
70_I77_G0.7080.48
94_F128_I0.7060.48
12_F34_A0.7020.48
18_Y123_L0.7020.48
47_A51_T0.7020.48
45_Y48_Q0.6850.46
32_G38_V0.6710.45
84_A87_F0.6700.45
30_T39_I0.6670.44
65_L69_A0.6590.44
28_G35_A0.6560.43
81_A84_A0.6560.43
7_F83_G0.6520.43
96_A129_I0.6520.43
71_A81_A0.6500.43
78_L126_L0.6490.43
94_F98_A0.6490.43
98_A101_Y0.6480.43
86_F90_L0.6420.42
94_F124_K0.6420.42
30_T36_K0.6400.42
5_I13_A0.6380.42
89_I101_Y0.6360.42
65_L73_E0.6310.41
65_L71_A0.6290.41
131_A134_F0.6200.40
50_E56_P0.6190.40
3_A129_I0.6170.40
7_F12_F0.6130.39
43_A47_A0.6120.39
94_F106_W0.6080.39
12_F80_I0.6060.39
15_L121_D0.6060.39
41_A100_F0.6000.38
97_A122_A0.5980.38
76_G80_I0.5970.38
27_I31_A0.5970.38
56_P60_L0.5970.38
42_L47_A0.5940.38
40_P54_G0.5930.38
28_G31_A0.5930.38
95_V113_N0.5920.37
15_L87_F0.5910.37
72_L75_I0.5880.37
38_V43_A0.5860.37
48_Q56_P0.5850.37
76_G90_L0.5790.36
5_I25_F0.5750.36
38_V44_P0.5720.36
31_A36_K0.5700.35
51_T55_M0.5680.35
26_D29_A0.5680.35
23_K103_H0.5660.35
42_L46_T0.5640.35
38_V41_A0.5620.35
12_F86_F0.5600.35
37_V40_P0.5600.35
72_L80_I0.5590.34
12_F128_I0.5580.34
92_I120_I0.5550.34
67_A131_A0.5540.34
20_G102_F0.5510.34
57_T61_Q0.5490.34
93_L111_P0.5430.33
13_A31_A0.5430.33
51_T60_L0.5400.33
128_I132_L0.5400.33
17_I96_A0.5370.33
45_Y50_E0.5370.33
34_A39_I0.5280.32
120_I127_S0.5230.31
69_A73_E0.5220.31
67_A75_I0.5220.31
109_A113_N0.5190.31
5_I87_F0.5190.31
19_S117_K0.5160.31
70_I133_L0.5160.31
110_P115_F0.5120.30
97_A131_A0.5120.30
123_L130_G0.5060.30
25_F87_F0.5050.30
123_L126_L0.5030.30
46_T54_G0.5010.30
22_T25_F0.5000.29
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  
1zcdA 1 0.471 2.8 0.948 Contact Map
2mg1A 1 0.1449 1.7 0.954 Contact Map
4cbfA 7 0.3478 1.6 0.955 Contact Map
3j27A 7 0.3478 1.6 0.955 Contact Map
4cctA 7 0.3478 1.5 0.955 Contact Map
4tq3A 1 0.8913 1.4 0.957 Contact Map
1fftA 1 0.8478 1.3 0.957 Contact Map
4ymkA 1 0.6957 1.1 0.959 Contact Map
1ymmC 1 0.0797 0.9 0.962 Contact Map
3pblA 1 0.3768 0.8 0.962 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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