DUF947 - PFAM28P - GREMLIN Contacts

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DUF947 - Domain of unknown function (DUF947)

PFAM:	PF06102	Sequences: RSNKHAPMEMSSKKPVSRKREVVPVPKKKARDPRFDPLSGEFDEDKFRKNYSFLDDYREKEIKELKKQLKKTKDPEEKEELKRLLQRMESQLKARKRKEREREVLKEHKKEEREAVKQGKKPFYLKKSEKKKLLLVEKFEELKKSGKLDKAIEKKRKKNAGKEKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	165 (165)
Sequences:	647 (515)
Seq/√Len:	40.1
META:	0.243

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
62_I	85_L	4.590	1.00
112_E	120_K	3.611	1.00
46_K	50_N	3.554	1.00
111_E	115_A	2.790	1.00
48_R	99_E	2.517	1.00
107_E	111_E	2.499	1.00
114_E	118_Q	2.409	1.00
103_E	107_E	2.281	1.00
142_L	148_L	2.182	0.99
59_E	92_L	2.109	0.99
135_L	139_F	2.072	0.99
43_D	46_K	2.071	0.99
137_E	140_E	2.025	0.99
112_E	115_A	1.987	0.99
106_K	110_K	1.963	0.99
97_R	101_E	1.948	0.99
129_E	132_K	1.774	0.98
62_I	88_M	1.752	0.97
12_S	20_R	1.752	0.97
62_I	92_L	1.696	0.97
45_D	49_K	1.694	0.97
66_K	89_E	1.678	0.97
139_F	144_K	1.668	0.96
160_A	164_K	1.651	0.96
135_L	159_N	1.624	0.96
144_K	147_K	1.600	0.95
130_K	133_L	1.599	0.95
124_Y	133_L	1.594	0.95
142_L	147_K	1.576	0.95
40_G	47_F	1.565	0.95
42_F	47_F	1.559	0.95
134_L	154_K	1.508	0.94
27_K	70_K	1.502	0.94
126_K	129_E	1.500	0.94
3_N	6_A	1.496	0.93
68_Q	77_E	1.477	0.93
90_S	93_K	1.473	0.93
69_L	81_L	1.445	0.92
112_E	123_F	1.434	0.92
161_G	164_K	1.425	0.92
148_L	163_E	1.418	0.91
85_L	92_L	1.418	0.91
40_G	43_D	1.354	0.89
78_K	82_K	1.348	0.89
148_L	151_A	1.346	0.89
57_Y	60_K	1.341	0.89
18_R	112_E	1.323	0.88
9_E	13_K	1.321	0.88
159_N	165_K	1.313	0.88
22_V	25_V	1.293	0.87
135_L	142_L	1.260	0.86
151_A	155_K	1.259	0.86
48_R	95_R	1.251	0.85
55_D	99_E	1.248	0.85
19_K	66_K	1.241	0.85
96_K	100_R	1.237	0.85
138_K	151_A	1.233	0.84
39_S	42_F	1.220	0.84
55_D	58_R	1.215	0.84
69_L	85_L	1.191	0.82
78_K	110_K	1.186	0.82
80_E	84_L	1.172	0.81
52_S	76_E	1.168	0.81
100_R	137_E	1.164	0.81
120_K	158_K	1.142	0.80
139_F	156_R	1.141	0.80
79_E	83_R	1.135	0.79
129_E	133_L	1.124	0.78
104_V	134_L	1.118	0.78
2_S	6_A	1.113	0.78
6_A	62_I	1.104	0.77
64_E	68_Q	1.100	0.77
159_N	164_K	1.097	0.77
45_D	50_N	1.084	0.76
100_R	104_V	1.082	0.76
144_K	148_L	1.075	0.75
77_E	80_E	1.071	0.75
21_E	27_K	1.066	0.75
14_K	117_K	1.050	0.74
31_R	36_D	1.045	0.73
31_R	39_S	1.034	0.72
88_M	92_L	1.027	0.72
116_V	122_P	1.026	0.72
72_T	78_K	1.023	0.72
25_V	29_K	1.015	0.71
129_E	138_K	1.002	0.70
97_R	138_K	0.990	0.69
108_H	125_L	0.986	0.69
1_R	6_A	0.985	0.69
105_L	116_V	0.983	0.68
155_K	158_K	0.983	0.68
55_D	95_R	0.982	0.68
125_L	129_E	0.980	0.68
142_L	151_A	0.976	0.68
74_D	165_K	0.959	0.67
110_K	113_R	0.957	0.66
76_E	79_E	0.953	0.66
20_R	54_L	0.946	0.65
56_D	59_E	0.938	0.65
88_M	91_Q	0.934	0.64
7_P	11_S	0.929	0.64
83_R	87_R	0.928	0.64
58_R	95_R	0.925	0.64
155_K	161_G	0.919	0.63
56_D	64_E	0.915	0.63
108_H	130_K	0.911	0.63
123_F	126_K	0.903	0.62
82_K	86_Q	0.890	0.61
63_K	165_K	0.887	0.60
112_E	116_V	0.887	0.60
45_D	106_K	0.887	0.60
143_K	151_A	0.877	0.60
50_N	124_Y	0.876	0.59
35_F	81_L	0.875	0.59
119_G	122_P	0.870	0.59
15_P	18_R	0.856	0.58
104_V	108_H	0.854	0.57
1_R	15_P	0.854	0.57
70_K	160_A	0.854	0.57
136_V	139_F	0.852	0.57
86_Q	90_S	0.848	0.57
70_K	86_Q	0.847	0.57
94_A	98_K	0.846	0.57
68_Q	84_L	0.838	0.56
1_R	66_K	0.831	0.55
73_K	150_K	0.824	0.55
47_F	148_L	0.823	0.55
36_D	62_I	0.814	0.54
65_L	81_L	0.806	0.53
45_D	102_R	0.805	0.53
149_D	153_E	0.805	0.53
82_K	89_E	0.803	0.53
7_P	32_D	0.801	0.53
59_E	96_K	0.801	0.53
48_R	124_Y	0.798	0.52
24_P	27_K	0.798	0.52
153_E	156_R	0.795	0.52
74_D	78_K	0.794	0.52
148_L	152_I	0.794	0.52
22_V	106_K	0.790	0.52
133_L	136_V	0.789	0.52
32_D	35_F	0.784	0.51
146_G	163_E	0.783	0.51
147_K	151_A	0.782	0.51
159_N	163_E	0.780	0.51
98_K	101_E	0.776	0.50
84_L	87_R	0.776	0.50
28_K	76_E	0.773	0.50
4_K	7_P	0.770	0.50
108_H	112_E	0.763	0.49
44_E	48_R	0.763	0.49
71_K	107_E	0.759	0.49
101_E	134_L	0.754	0.48
112_E	121_K	0.745	0.48
68_Q	81_L	0.743	0.47
109_K	126_K	0.741	0.47
56_D	111_E	0.740	0.47
13_K	152_I	0.737	0.47
105_L	130_K	0.728	0.46
62_I	158_K	0.721	0.45
60_K	122_P	0.717	0.45
24_P	30_A	0.713	0.45
65_L	85_L	0.709	0.44
81_L	112_E	0.709	0.44
110_K	116_V	0.701	0.44
145_S	148_L	0.700	0.43
78_K	94_A	0.700	0.43
154_K	158_K	0.697	0.43
63_K	140_E	0.685	0.42
72_T	77_E	0.684	0.42
62_I	69_L	0.680	0.42
155_K	163_E	0.675	0.41
43_D	131_K	0.673	0.41
125_L	133_L	0.671	0.41
85_L	93_K	0.668	0.41
47_F	142_L	0.668	0.41
4_K	126_K	0.664	0.40
86_Q	93_K	0.660	0.40
150_K	153_E	0.650	0.39
125_L	132_K	0.648	0.39
18_R	23_V	0.641	0.38
6_A	92_L	0.639	0.38
44_E	64_E	0.637	0.38
154_K	161_G	0.637	0.38
99_E	103_E	0.633	0.38
18_R	57_Y	0.632	0.37
57_Y	87_R	0.632	0.37
120_K	123_F	0.630	0.37
62_I	102_R	0.630	0.37
146_G	151_A	0.628	0.37
102_R	107_E	0.625	0.37
3_N	8_M	0.624	0.37
82_K	93_K	0.618	0.36
52_S	56_D	0.616	0.36
107_E	137_E	0.614	0.36
151_A	163_E	0.610	0.36
61_E	155_K	0.610	0.36
37_P	140_E	0.599	0.35
18_R	65_L	0.599	0.35
82_K	115_A	0.596	0.34
41_E	105_L	0.595	0.34
86_Q	152_I	0.594	0.34
132_K	157_K	0.592	0.34
44_E	100_R	0.591	0.34
17_S	23_V	0.588	0.34
46_K	102_R	0.587	0.34
89_E	93_K	0.584	0.33
74_D	77_E	0.584	0.33
56_D	60_K	0.579	0.33
10_M	14_K	0.576	0.33
69_L	78_K	0.576	0.33
87_R	108_H	0.572	0.32
3_N	79_E	0.572	0.32
139_F	152_I	0.569	0.32
48_R	55_D	0.565	0.32
100_R	131_K	0.564	0.32
54_L	58_R	0.563	0.32
16_V	35_F	0.561	0.32
111_E	114_E	0.557	0.31
67_K	75_P	0.555	0.31
17_S	154_K	0.554	0.31
18_R	60_K	0.554	0.31
77_E	84_L	0.553	0.31
56_D	67_K	0.553	0.31
33_P	119_G	0.548	0.31
5_H	20_R	0.543	0.30
47_F	50_N	0.541	0.30
127_K	130_K	0.536	0.30
35_F	69_L	0.535	0.30
19_K	23_V	0.534	0.29
73_K	126_K	0.530	0.29
116_V	123_F	0.528	0.29
156_R	161_G	0.527	0.29
116_V	149_D	0.527	0.29
1_R	4_K	0.527	0.29
58_R	130_K	0.523	0.29
67_K	139_F	0.523	0.29
62_I	66_K	0.521	0.28
17_S	29_K	0.521	0.28
9_E	56_D	0.514	0.28
112_E	119_G	0.511	0.28
86_Q	138_K	0.510	0.28
87_R	90_S	0.508	0.28
66_K	133_L	0.508	0.28
108_H	133_L	0.505	0.27
67_K	83_R	0.503	0.27
135_L	156_R	0.501	0.27
105_L	125_L	0.500	0.27

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
3ziaJ	1	0.2182	5.6	0.95	Contact Map
4elyA	2	0.5515	4.8	0.952	Contact Map
2wujA	2	0.303	4.5	0.952	Contact Map
1uk5A	1	0.5939	3.2	0.956	Contact Map
2akfA	3	0.1939	2.7	0.957	Contact Map
3vp9A	3	0.4	2.5	0.958	Contact Map
4d2hA	5	0.2303	2.4	0.958	Contact Map
2a26A	4	0.297	2.2	0.959	Contact Map
1gmjA	2	0.3818	2.2	0.959	Contact Map
2rt6A	1	0.5818	2.1	0.96	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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