DDHD - PFAM28P - GREMLIN Contacts

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DDHD - DDHD domain

PFAM:	PF02862	Sequences: LDFEVENFFALGSPLGLFLALRGIRIITVLPGLDGEDGQYGRPACKQLYNIFHPTDPVAYRLEPLIDPEYSSLKPVLIPHYKGGKEGLTRLGADLKQSVLLSSLSSWNRLTRESSAALAASSSSEERASEASIESEESGEEDSYTASSISSESLEEAEKKVGALNWNGRIDYVLQEGPLESEYLSALASHLSYWESEDVALFILRQIY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	208 (202)
Sequences:	1047 (750)
Seq/√Len:	52.8
META:	0.101

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_A	48_L	2.477	1.00
133_I	137_E	2.466	1.00
78_I	174_L	2.399	1.00
10_A	15_L	2.387	1.00
66_I	170_I	2.349	1.00
142_D	145_T	2.184	1.00
137_E	140_E	2.128	1.00
48_L	62_L	2.118	1.00
144_Y	147_S	2.113	1.00
126_E	131_A	2.107	1.00
143_S	146_A	2.101	1.00
132_S	139_G	2.086	1.00
141_E	145_T	2.085	1.00
114_S	117_A	2.073	1.00
63_E	169_R	2.000	1.00
118_L	121_S	1.959	1.00
112_R	119_A	1.952	1.00
120_A	123_S	1.939	1.00
158_E	161_V	1.932	1.00
80_H	84_G	1.888	0.99
13_S	79_P	1.810	0.99
126_E	135_S	1.801	0.99
132_S	136_E	1.783	0.99
51_I	78_I	1.783	0.99
31_P	34_D	1.771	0.99
50_N	54_P	1.739	0.99
139_G	142_D	1.732	0.99
61_R	64_P	1.721	0.99
132_S	135_S	1.715	0.99
135_S	139_G	1.689	0.99
52_F	175_Q	1.687	0.99
128_A	133_I	1.665	0.99
6_E	46_K	1.628	0.98
142_D	146_A	1.624	0.98
136_E	139_G	1.622	0.98
134_E	137_E	1.621	0.98
130_E	134_E	1.620	0.98
53_H	61_R	1.597	0.98
139_G	144_Y	1.584	0.98
134_E	140_E	1.574	0.98
157_A	161_V	1.574	0.98
144_Y	148_S	1.565	0.98
146_A	149_I	1.507	0.97
18_F	60_Y	1.499	0.97
133_I	136_E	1.495	0.97
190_H	193_Y	1.492	0.97
131_A	137_E	1.491	0.97
18_F	58_V	1.490	0.97
115_S	118_L	1.487	0.97
110_L	113_E	1.470	0.97
7_N	49_Y	1.463	0.97
122_S	126_E	1.436	0.96
130_E	135_S	1.430	0.96
129_S	133_I	1.426	0.96
129_S	136_E	1.368	0.95
117_A	120_A	1.366	0.95
65_L	169_R	1.365	0.95
127_R	135_S	1.359	0.95
114_S	118_L	1.333	0.94
61_R	169_R	1.325	0.94
1_L	4_E	1.323	0.94
134_E	139_G	1.318	0.94
148_S	151_S	1.315	0.94
179_L	182_E	1.300	0.93
129_S	135_S	1.295	0.93
138_S	144_Y	1.295	0.93
125_E	128_A	1.287	0.93
129_S	132_S	1.283	0.93
182_E	186_A	1.283	0.93
124_S	131_A	1.281	0.93
115_S	120_A	1.277	0.93
131_A	136_E	1.275	0.93
96_K	99_V	1.270	0.93
109_R	113_E	1.265	0.93
133_I	138_S	1.258	0.92
166_W	203_I	1.254	0.92
127_R	137_E	1.242	0.92
7_N	47_Q	1.240	0.92
28_T	31_P	1.234	0.92
129_S	137_E	1.232	0.92
179_L	186_A	1.219	0.91
100_L	105_S	1.217	0.91
147_S	150_S	1.199	0.90
132_S	137_E	1.195	0.90
135_S	138_S	1.189	0.90
124_S	130_E	1.183	0.90
111_T	118_L	1.177	0.90
8_F	48_L	1.168	0.89
179_L	191_L	1.163	0.89
131_A	134_E	1.140	0.88
134_E	138_S	1.132	0.88
140_E	144_Y	1.132	0.88
113_E	118_L	1.131	0.88
54_P	173_V	1.120	0.87
127_R	132_S	1.119	0.87
27_I	178_P	1.114	0.87
129_S	138_S	1.113	0.87
52_F	61_R	1.109	0.87
123_S	126_E	1.104	0.86
132_S	138_S	1.103	0.86
133_I	142_D	1.095	0.86
136_E	142_D	1.094	0.86
120_A	125_E	1.077	0.85
126_E	132_S	1.069	0.84
125_E	129_S	1.062	0.84
66_I	165_N	1.047	0.83
116_A	121_S	1.044	0.83
128_A	131_A	1.034	0.82
140_E	143_S	1.018	0.81
138_S	142_D	1.017	0.81
132_S	142_D	1.016	0.81
122_S	125_E	1.015	0.81
27_I	203_I	1.004	0.81
113_E	120_A	1.002	0.80
134_E	146_A	1.001	0.80
192_S	195_E	0.991	0.80
19_L	200_A	0.978	0.79
136_E	140_E	0.978	0.79
47_Q	168_G	0.976	0.79
130_E	141_E	0.971	0.78
86_E	89_T	0.966	0.78
125_E	134_E	0.960	0.77
124_S	127_R	0.960	0.77
84_G	87_G	0.957	0.77
127_R	133_I	0.942	0.76
201_L	208_Y	0.940	0.76
144_Y	149_I	0.938	0.76
19_L	22_R	0.934	0.75
131_A	135_S	0.933	0.75
79_P	82_K	0.931	0.75
141_E	144_Y	0.927	0.75
81_Y	84_G	0.921	0.74
157_A	160_K	0.914	0.74
116_A	119_A	0.912	0.74
113_E	116_A	0.911	0.74
118_L	124_S	0.910	0.74
115_S	119_A	0.906	0.73
165_N	206_Q	0.904	0.73
135_S	145_T	0.902	0.73
130_E	136_E	0.896	0.72
137_E	146_A	0.895	0.72
60_Y	63_E	0.892	0.72
172_Y	203_I	0.891	0.72
138_S	141_E	0.881	0.71
2_D	53_H	0.879	0.71
7_N	17_L	0.877	0.71
128_A	136_E	0.877	0.71
121_S	130_E	0.872	0.70
5_V	16_G	0.867	0.70
141_E	147_S	0.856	0.69
135_S	148_S	0.853	0.69
87_G	92_G	0.849	0.68
163_A	170_I	0.845	0.68
140_E	147_S	0.843	0.68
130_E	137_E	0.843	0.68
124_S	135_S	0.833	0.67
111_T	123_S	0.822	0.66
125_E	131_A	0.822	0.66
137_E	141_E	0.820	0.66
133_I	141_E	0.818	0.65
126_E	133_I	0.810	0.65
23_G	175_Q	0.805	0.64
117_A	124_S	0.803	0.64
136_E	146_A	0.802	0.64
135_S	141_E	0.801	0.64
94_D	97_Q	0.799	0.64
121_S	124_S	0.798	0.63
53_H	175_Q	0.794	0.63
89_T	93_A	0.793	0.63
126_E	130_E	0.788	0.62
118_L	126_E	0.782	0.62
117_A	121_S	0.781	0.62
87_G	94_D	0.780	0.62
45_C	191_L	0.777	0.61
102_S	106_S	0.774	0.61
92_G	95_L	0.771	0.61
128_A	134_E	0.767	0.60
113_E	117_A	0.766	0.60
126_E	136_E	0.766	0.60
119_A	125_E	0.764	0.60
180_E	208_Y	0.764	0.60
127_R	131_A	0.763	0.60
145_T	148_S	0.762	0.60
1_L	34_D	0.762	0.60
26_I	168_G	0.757	0.59
73_L	177_G	0.752	0.59
138_S	146_A	0.749	0.59
61_R	65_L	0.748	0.58
140_E	146_A	0.747	0.58
139_G	147_S	0.745	0.58
183_Y	186_A	0.740	0.58
136_E	145_T	0.738	0.57
130_E	133_I	0.735	0.57
123_S	149_I	0.732	0.57
114_S	121_S	0.731	0.57
115_S	122_S	0.728	0.56
86_E	93_A	0.726	0.56
135_S	143_S	0.724	0.56
64_P	169_R	0.722	0.56
139_G	143_S	0.716	0.55
127_R	144_Y	0.714	0.55
110_L	118_L	0.714	0.55
90_R	95_L	0.704	0.54
31_P	37_D	0.704	0.54
102_S	105_S	0.703	0.54
54_P	61_R	0.698	0.53
81_Y	85_K	0.695	0.53
111_T	115_S	0.693	0.53
123_S	144_Y	0.693	0.53
101_L	104_L	0.693	0.53
128_A	135_S	0.692	0.53
95_L	103_S	0.685	0.52
134_E	143_S	0.683	0.52
135_S	149_I	0.676	0.51
89_T	92_G	0.675	0.51
83_G	172_Y	0.674	0.51
191_L	196_S	0.670	0.50
118_L	123_S	0.669	0.50
112_R	116_A	0.669	0.50
111_T	117_A	0.668	0.50
28_T	39_Q	0.667	0.50
111_T	116_A	0.667	0.50
8_F	13_S	0.659	0.49
110_L	114_S	0.659	0.49
80_H	85_K	0.658	0.49
134_E	144_Y	0.658	0.49
119_A	122_S	0.658	0.49
110_L	119_A	0.657	0.49
55_T	194_W	0.656	0.49
167_N	182_E	0.656	0.49
45_C	179_L	0.652	0.48
80_H	175_Q	0.647	0.48
41_G	44_A	0.645	0.48
36_E	59_A	0.641	0.47
81_Y	199_V	0.640	0.47
134_E	141_E	0.640	0.47
135_S	140_E	0.640	0.47
116_A	120_A	0.639	0.47
194_W	201_L	0.638	0.47
134_E	142_D	0.636	0.47
1_L	5_V	0.633	0.46
23_G	54_P	0.633	0.46
126_E	129_S	0.632	0.46
145_T	150_S	0.630	0.46
27_I	46_K	0.629	0.46
182_E	189_S	0.629	0.46
183_Y	189_S	0.627	0.46
175_Q	198_D	0.624	0.45
162_G	165_N	0.619	0.45
3_F	12_G	0.614	0.44
131_A	140_E	0.613	0.44
182_E	185_S	0.611	0.44
54_P	174_L	0.605	0.43
121_S	126_E	0.605	0.43
136_E	144_Y	0.604	0.43
138_S	145_T	0.603	0.43
119_A	127_R	0.603	0.43
110_L	116_A	0.598	0.43
46_K	207_I	0.597	0.43
131_A	138_S	0.594	0.42
137_E	147_S	0.591	0.42
135_S	142_D	0.589	0.42
135_S	144_Y	0.589	0.42
146_A	150_S	0.589	0.42
18_F	54_P	0.584	0.41
97_Q	172_Y	0.577	0.41
88_L	93_A	0.572	0.40
16_G	23_G	0.569	0.40
43_P	65_L	0.562	0.39
116_A	122_S	0.562	0.39
20_A	47_Q	0.560	0.39
88_L	91_L	0.552	0.38
5_V	186_A	0.550	0.38
52_F	75_P	0.550	0.38
120_A	138_S	0.550	0.38
117_A	132_S	0.547	0.38
140_E	145_T	0.546	0.37
152_E	161_V	0.546	0.37
86_E	92_G	0.544	0.37
178_P	201_L	0.543	0.37
138_S	148_S	0.542	0.37
143_S	147_S	0.539	0.37
195_E	205_R	0.535	0.36
137_E	149_I	0.533	0.36
90_R	96_K	0.530	0.36
100_L	109_R	0.522	0.35
4_E	7_N	0.521	0.35
119_A	143_S	0.521	0.35
142_D	149_I	0.518	0.35
139_G	148_S	0.518	0.35
27_I	40_Y	0.516	0.35
73_L	79_P	0.516	0.35
16_G	207_I	0.514	0.34
101_L	105_S	0.512	0.34
138_S	143_S	0.510	0.34
115_S	137_E	0.510	0.34
92_G	96_K	0.509	0.34
116_A	124_S	0.505	0.34
114_S	119_A	0.505	0.34
165_N	176_E	0.502	0.33
115_S	121_S	0.502	0.33
64_P	196_S	0.500	0.33
120_A	137_E	0.500	0.33

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
3cwxA	2	0.3317	8.5	0.957	Contact Map
1f35A	2	0.4375	6.8	0.959	Contact Map
3fbiB	1	0.3029	3.6	0.964	Contact Map
4i9xA	2	0.3269	2.8	0.966	Contact Map
4hicA	1	0.2019	2.2	0.968	Contact Map
2zvmU	1	0.0625	2.1	0.968	Contact Map
3p3gA	1	0.2837	1.9	0.969	Contact Map
3uhmA	1	0.2837	1.9	0.969	Contact Map
2npmA	2	0.2837	1.8	0.969	Contact Map
4ogqE	1	0.1298	1.7	0.97	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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