HR_lesion - PFAM28P - GREMLIN Contacts

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HR_lesion - HR-like lesion-inducing

PFAM:	PF05514	Sequences: MPAFITFGRVLFAVLFIYSGATKLFDIGATAGIAAKVVIPALAPYTAQLETMTGMPTPQLQALALAAAAIALEGIGGLLIAFGARFFAILLILFVAAATFYFHDFWNQAPPDNEFAKTLIDALKNLSIIGALLFFIGM	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_F	103_H	4.680	1.00
104_D	107_N	3.617	1.00
24_L	27_I	3.402	1.00
23_K	73_E	3.224	1.00
73_E	77_G	2.797	1.00
71_A	75_I	2.656	1.00
117_K	121_D	2.641	1.00
75_I	79_L	2.534	1.00
20_G	23_K	2.502	1.00
67_A	70_I	2.404	1.00
73_E	76_G	2.130	1.00
30_T	33_I	2.093	1.00
99_T	125_N	2.043	0.99
76_G	79_L	2.041	0.99
29_A	33_I	2.030	0.99
70_I	73_E	1.952	0.99
98_A	102_F	1.924	0.99
74_G	77_G	1.875	0.99
74_G	79_L	1.850	0.99
64_A	68_A	1.843	0.99
92_I	129_I	1.787	0.98
49_L	52_M	1.720	0.98
35_A	39_I	1.712	0.98
48_Q	53_T	1.654	0.97
93_L	97_A	1.604	0.97
76_G	81_A	1.506	0.95
6_T	10_V	1.484	0.95
18_Y	22_T	1.463	0.95
62_A	66_A	1.435	0.94
12_F	131_A	1.395	0.93
77_G	80_I	1.335	0.92
95_V	128_I	1.325	0.91
129_I	132_L	1.320	0.91
71_A	76_G	1.293	0.90
73_E	78_L	1.293	0.90
62_A	65_L	1.288	0.90
53_T	57_T	1.287	0.90
20_G	24_L	1.280	0.90
29_A	32_G	1.254	0.89
80_I	83_G	1.245	0.88
110_P	113_N	1.233	0.88
72_L	76_G	1.231	0.88
48_Q	55_M	1.229	0.88
66_A	70_I	1.227	0.88
50_E	55_M	1.209	0.87
48_Q	51_T	1.201	0.87
49_L	53_T	1.195	0.86
73_E	80_I	1.186	0.86
87_F	90_L	1.183	0.86
71_A	74_G	1.178	0.85
34_A	37_V	1.171	0.85
6_T	14_V	1.163	0.85
31_A	34_A	1.154	0.84
30_T	34_A	1.150	0.84
36_K	39_I	1.134	0.83
33_I	36_K	1.109	0.82
61_Q	65_L	1.105	0.82
31_A	35_A	1.103	0.81
52_M	55_M	1.085	0.80
19_S	22_T	1.076	0.80
28_G	32_G	1.075	0.80
61_Q	64_A	1.070	0.79
103_H	118_T	1.062	0.79
72_L	79_L	1.053	0.78
55_M	59_Q	1.053	0.78
72_L	77_G	1.044	0.78
73_E	79_L	1.033	0.77
65_L	70_I	1.031	0.77
63_L	71_A	1.025	0.76
111_P	114_E	1.010	0.75
46_T	50_E	0.968	0.72
36_K	40_P	0.963	0.72
48_Q	52_M	0.956	0.71
125_N	130_G	0.953	0.71
7_F	133_L	0.947	0.71
53_T	59_Q	0.926	0.69
93_L	96_A	0.923	0.69
50_E	53_T	0.918	0.68
97_A	100_F	0.916	0.68
89_I	93_L	0.906	0.67
53_T	60_L	0.902	0.67
71_A	77_G	0.899	0.66
91_L	95_V	0.891	0.66
78_L	81_A	0.885	0.65
9_R	16_F	0.875	0.64
74_G	78_L	0.874	0.64
92_I	132_L	0.867	0.64
54_G	58_P	0.865	0.63
47_A	103_H	0.865	0.63
100_F	131_A	0.854	0.62
72_L	90_L	0.840	0.61
91_L	132_L	0.823	0.60
51_T	56_P	0.820	0.59
98_A	103_H	0.807	0.58
65_L	68_A	0.802	0.58
69_A	76_G	0.793	0.57
63_L	66_A	0.789	0.56
77_G	81_A	0.784	0.56
7_F	92_I	0.772	0.55
28_G	33_I	0.771	0.55
19_S	23_K	0.770	0.55
32_G	35_A	0.764	0.54
118_T	121_D	0.747	0.52
93_L	99_T	0.746	0.52
67_A	73_E	0.738	0.51
47_A	98_A	0.733	0.51
70_I	74_G	0.732	0.51
57_T	63_L	0.732	0.51
5_I	90_L	0.732	0.51
107_N	110_P	0.730	0.51
2_P	5_I	0.730	0.51
79_L	87_F	0.728	0.50
103_H	106_W	0.726	0.50
33_I	37_V	0.723	0.50
68_A	73_E	0.721	0.50
20_G	26_D	0.718	0.49
86_F	100_F	0.710	0.49
70_I	77_G	0.708	0.48
94_F	128_I	0.706	0.48
12_F	34_A	0.702	0.48
18_Y	123_L	0.702	0.48
47_A	51_T	0.702	0.48
45_Y	48_Q	0.685	0.46
32_G	38_V	0.671	0.45
84_A	87_F	0.670	0.45
30_T	39_I	0.667	0.44
65_L	69_A	0.659	0.44
28_G	35_A	0.656	0.43
81_A	84_A	0.656	0.43
7_F	83_G	0.652	0.43
96_A	129_I	0.652	0.43
71_A	81_A	0.650	0.43
78_L	126_L	0.649	0.43
94_F	98_A	0.649	0.43
98_A	101_Y	0.648	0.43
86_F	90_L	0.642	0.42
94_F	124_K	0.642	0.42
30_T	36_K	0.640	0.42
5_I	13_A	0.638	0.42
89_I	101_Y	0.636	0.42
65_L	73_E	0.631	0.41
65_L	71_A	0.629	0.41
131_A	134_F	0.620	0.40
50_E	56_P	0.619	0.40
3_A	129_I	0.617	0.40
7_F	12_F	0.613	0.39
43_A	47_A	0.612	0.39
94_F	106_W	0.608	0.39
12_F	80_I	0.606	0.39
15_L	121_D	0.606	0.39
41_A	100_F	0.600	0.38
97_A	122_A	0.598	0.38
76_G	80_I	0.597	0.38
27_I	31_A	0.597	0.38
56_P	60_L	0.597	0.38
42_L	47_A	0.594	0.38
40_P	54_G	0.593	0.38
28_G	31_A	0.593	0.38
95_V	113_N	0.592	0.37
15_L	87_F	0.591	0.37
72_L	75_I	0.588	0.37
38_V	43_A	0.586	0.37
48_Q	56_P	0.585	0.37
76_G	90_L	0.579	0.36
5_I	25_F	0.575	0.36
38_V	44_P	0.572	0.36
31_A	36_K	0.570	0.35
51_T	55_M	0.568	0.35
26_D	29_A	0.568	0.35
23_K	103_H	0.566	0.35
42_L	46_T	0.564	0.35
38_V	41_A	0.562	0.35
12_F	86_F	0.560	0.35
37_V	40_P	0.560	0.35
72_L	80_I	0.559	0.34
12_F	128_I	0.558	0.34
92_I	120_I	0.555	0.34
67_A	131_A	0.554	0.34
20_G	102_F	0.551	0.34
57_T	61_Q	0.549	0.34
93_L	111_P	0.543	0.33
13_A	31_A	0.543	0.33
51_T	60_L	0.540	0.33
128_I	132_L	0.540	0.33
17_I	96_A	0.537	0.33
45_Y	50_E	0.537	0.33
34_A	39_I	0.528	0.32
120_I	127_S	0.523	0.31
69_A	73_E	0.522	0.31
67_A	75_I	0.522	0.31
109_A	113_N	0.519	0.31
5_I	87_F	0.519	0.31
19_S	117_K	0.516	0.31
70_I	133_L	0.516	0.31
110_P	115_F	0.512	0.30
97_A	131_A	0.512	0.30
123_L	130_G	0.506	0.30
25_F	87_F	0.505	0.30
123_L	126_L	0.503	0.30
46_T	54_G	0.501	0.30
22_T	25_F	0.500	0.29

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

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

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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