DUF4400 - PFAM28P - GREMLIN Contacts

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DUF4400 - Domain of unknown function (DUF4400)

PFAM:	PF14348	Sequences: FWPEQGWEHSQAMLEAELGYLSEHFTRSLLLGEPAARTALRRADALYQWLFVKTGLLDWLQRASAPAAASGQGGAAEMASVNRGFRNWLGQLYVWLEDYLLAAMYVTLLFLVRLAILLLWLPLFLLAALVALVDGLVRRDLRRFGAGRESPFVYHRAKRLIIPLLVLPWVLYLALPVSLHPLLILLPFAVLLGLAVAITAASFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	204 (195)
Sequences:	1148 (801)
Seq/√Len:	57.4
META:	0.636

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_D	143_R	4.569	1.00
8_E	11_Q	4.053	1.00
133_V	137_V	3.382	1.00
132_L	200_A	3.216	1.00
48_Q	53_K	2.555	1.00
127_A	131_A	2.515	1.00
155_H	158_K	2.418	1.00
123_L	185_L	2.277	1.00
133_V	136_L	2.250	1.00
99_Y	102_A	2.202	1.00
131_A	193_G	2.183	1.00
140_D	144_F	2.099	1.00
2_W	5_Q	2.057	1.00
120_W	151_P	2.007	1.00
198_I	201_A	1.883	1.00
12_A	15_E	1.845	1.00
134_D	197_A	1.820	0.99
121_L	125_L	1.802	0.99
8_E	18_L	1.796	0.99
5_Q	12_A	1.714	0.99
141_L	145_G	1.713	0.99
195_A	198_I	1.695	0.99
47_Y	59_W	1.678	0.99
65_A	68_A	1.659	0.99
185_L	188_F	1.648	0.99
186_L	199_T	1.635	0.99
40_L	44_D	1.629	0.99
84_G	87_N	1.626	0.99
178_S	184_I	1.617	0.99
48_Q	52_V	1.591	0.99
71_G	74_G	1.581	0.98
4_E	8_E	1.580	0.98
186_L	195_A	1.545	0.98
28_S	34_P	1.542	0.98
147_G	154_Y	1.535	0.98
139_R	144_F	1.496	0.98
138_R	197_A	1.472	0.97
10_S	105_Y	1.456	0.97
52_V	55_G	1.456	0.97
122_P	150_S	1.447	0.97
152_F	203_F	1.420	0.97
43_A	108_L	1.410	0.97
152_F	156_R	1.391	0.96
41_R	45_A	1.385	0.96
142_R	150_S	1.379	0.96
142_R	149_E	1.369	0.96
116_I	203_F	1.369	0.96
145_G	179_L	1.365	0.96
69_A	72_Q	1.365	0.96
130_V	143_R	1.360	0.96
104_M	143_R	1.357	0.96
160_L	195_A	1.351	0.96
10_S	13_M	1.338	0.96
71_G	94_V	1.297	0.95
118_L	121_L	1.280	0.94
160_L	164_L	1.273	0.94
142_R	145_G	1.269	0.94
134_D	139_R	1.267	0.94
97_E	101_L	1.257	0.94
189_A	200_A	1.256	0.94
197_A	201_A	1.255	0.94
93_Y	97_E	1.254	0.94
58_D	114_L	1.253	0.94
99_Y	154_Y	1.252	0.94
67_A	70_S	1.246	0.94
74_G	179_L	1.226	0.93
64_S	93_Y	1.226	0.93
42_R	46_L	1.200	0.92
126_L	130_V	1.198	0.92
19_G	23_E	1.195	0.92
25_F	28_S	1.176	0.91
99_Y	139_R	1.176	0.91
180_H	183_L	1.173	0.91
108_L	142_R	1.171	0.91
149_E	155_H	1.169	0.91
51_F	104_M	1.163	0.91
154_Y	158_K	1.158	0.91
34_P	163_P	1.155	0.91
144_F	156_R	1.148	0.90
140_D	149_E	1.142	0.90
194_L	198_I	1.138	0.90
25_F	179_L	1.127	0.90
107_T	129_L	1.126	0.89
191_L	195_A	1.111	0.89
21_L	112_V	1.097	0.88
134_D	137_V	1.096	0.88
100_L	104_M	1.093	0.88
8_E	13_M	1.084	0.88
132_L	203_F	1.081	0.87
139_R	143_R	1.081	0.87
11_Q	15_E	1.079	0.87
142_R	146_A	1.076	0.87
136_L	149_E	1.068	0.87
185_L	195_A	1.064	0.87
197_A	200_A	1.064	0.87
111_L	115_A	1.058	0.86
142_R	151_P	1.055	0.86
123_L	144_F	1.055	0.86
116_I	155_H	1.052	0.86
19_G	32_G	1.048	0.86
8_E	22_S	1.036	0.85
177_V	197_A	1.033	0.85
87_N	91_Q	1.033	0.85
100_L	141_L	1.031	0.85
9_H	13_M	1.025	0.85
148_R	151_P	1.019	0.84
140_D	163_P	1.015	0.84
62_R	67_A	1.014	0.84
47_Y	54_T	1.013	0.84
124_F	173_L	1.013	0.84
54_T	66_P	0.995	0.83
172_Y	181_P	0.986	0.82
16_A	125_L	0.979	0.82
146_A	149_E	0.979	0.82
110_F	187_P	0.970	0.81
144_F	151_P	0.970	0.81
68_A	71_G	0.969	0.81
41_R	118_L	0.968	0.81
132_L	194_L	0.964	0.81
186_L	191_L	0.962	0.81
119_L	154_Y	0.957	0.80
13_M	184_I	0.953	0.80
32_G	38_T	0.947	0.80
122_P	181_P	0.940	0.79
172_Y	185_L	0.937	0.79
194_L	200_A	0.928	0.78
199_T	203_F	0.927	0.78
135_G	149_E	0.924	0.78
136_L	139_R	0.915	0.77
175_L	178_S	0.913	0.77
131_A	147_G	0.913	0.77
37_R	165_L	0.906	0.76
33_E	50_L	0.900	0.76
197_A	202_S	0.894	0.75
189_A	193_G	0.892	0.75
137_V	141_L	0.892	0.75
186_L	189_A	0.886	0.75
103_A	142_R	0.884	0.75
46_L	111_L	0.880	0.74
137_V	181_P	0.869	0.73
57_L	197_A	0.867	0.73
135_G	147_G	0.863	0.73
68_A	73_G	0.859	0.72
84_G	88_W	0.859	0.72
18_L	23_E	0.857	0.72
29_L	159_R	0.855	0.72
57_L	61_Q	0.852	0.72
21_L	97_E	0.850	0.72
104_M	114_L	0.846	0.71
33_E	37_R	0.845	0.71
136_L	187_P	0.843	0.71
144_F	147_G	0.841	0.71
32_G	35_A	0.825	0.69
153_V	169_W	0.823	0.69
139_R	162_I	0.819	0.69
23_E	26_T	0.817	0.69
58_D	62_R	0.814	0.68
16_A	19_G	0.806	0.68
39_A	133_V	0.805	0.68
19_G	92_L	0.803	0.67
47_Y	57_L	0.801	0.67
102_A	183_L	0.799	0.67
69_A	125_L	0.783	0.65
162_I	179_L	0.783	0.65
47_Y	104_M	0.778	0.65
156_R	159_R	0.778	0.65
133_V	139_R	0.775	0.65
92_L	96_L	0.774	0.64
41_R	54_T	0.766	0.64
39_A	119_L	0.765	0.64
130_V	168_P	0.764	0.63
49_W	190_V	0.763	0.63
123_L	127_A	0.762	0.63
128_A	196_V	0.759	0.63
108_L	158_K	0.759	0.63
129_L	132_L	0.749	0.62
52_V	57_L	0.743	0.61
3_P	7_W	0.742	0.61
156_R	165_L	0.741	0.61
112_V	115_A	0.736	0.61
69_A	73_G	0.733	0.60
122_P	131_A	0.733	0.60
3_P	16_A	0.732	0.60
198_I	202_S	0.732	0.60
173_L	203_F	0.731	0.60
185_L	189_A	0.731	0.60
83_R	87_N	0.725	0.59
87_N	90_G	0.725	0.59
83_R	86_R	0.725	0.59
14_L	112_V	0.724	0.59
140_D	172_Y	0.724	0.59
155_H	173_L	0.715	0.58
60_L	104_M	0.712	0.58
41_R	172_Y	0.711	0.58
139_R	154_Y	0.711	0.58
130_V	142_R	0.711	0.58
45_A	49_W	0.711	0.58
23_E	65_A	0.709	0.58
164_L	189_A	0.708	0.58
172_Y	187_P	0.707	0.57
93_Y	96_L	0.705	0.57
168_P	180_H	0.702	0.57
61_Q	65_A	0.699	0.57
150_S	168_P	0.694	0.56
131_A	197_A	0.693	0.56
135_G	172_Y	0.692	0.56
49_W	53_K	0.690	0.56
2_W	9_H	0.690	0.56
27_R	32_G	0.684	0.55
51_F	54_T	0.683	0.55
66_P	69_A	0.675	0.54
147_G	155_H	0.674	0.54
112_V	142_R	0.670	0.53
3_P	90_G	0.669	0.53
101_L	109_L	0.664	0.53
166_V	175_L	0.650	0.51
24_H	99_Y	0.647	0.51
62_R	68_A	0.644	0.51
120_W	149_E	0.644	0.51
21_L	26_T	0.644	0.51
51_F	55_G	0.644	0.51
63_A	69_A	0.640	0.50
75_A	125_L	0.640	0.50
20_Y	159_R	0.639	0.50
102_A	156_R	0.638	0.50
70_S	73_G	0.636	0.50
102_A	143_R	0.636	0.50
198_I	204_K	0.632	0.49
150_S	159_R	0.630	0.49
117_L	169_W	0.630	0.49
13_M	109_L	0.627	0.49
128_A	192_L	0.624	0.48
3_P	12_A	0.624	0.48
37_R	137_V	0.623	0.48
63_A	94_V	0.622	0.48
51_F	57_L	0.622	0.48
4_E	7_W	0.618	0.48
149_E	172_Y	0.618	0.48
126_L	180_H	0.610	0.47
109_L	123_L	0.608	0.47
188_F	193_G	0.608	0.47
68_A	72_Q	0.605	0.46
7_W	12_A	0.605	0.46
57_L	65_A	0.602	0.46
141_L	184_I	0.602	0.46
102_A	122_P	0.596	0.45
47_Y	51_F	0.591	0.45
156_R	173_L	0.589	0.45
136_L	140_D	0.588	0.44
148_R	180_H	0.587	0.44
6_G	10_S	0.584	0.44
39_A	71_G	0.582	0.44
48_Q	58_D	0.581	0.44
16_A	175_L	0.580	0.44
39_A	137_V	0.579	0.44
145_G	159_R	0.578	0.43
157_A	163_P	0.574	0.43
53_K	127_A	0.573	0.43
55_G	62_R	0.570	0.43
101_L	125_L	0.569	0.42
123_L	188_F	0.564	0.42
115_A	178_S	0.564	0.42
59_W	62_R	0.563	0.42
122_P	126_L	0.562	0.42
187_P	198_I	0.560	0.41
155_H	168_P	0.550	0.40
88_W	129_L	0.550	0.40
126_L	154_Y	0.543	0.40
46_L	62_R	0.540	0.39
30_L	164_L	0.539	0.39
27_R	126_L	0.538	0.39
53_K	125_L	0.536	0.39
57_L	139_R	0.533	0.39
85_F	89_L	0.532	0.39
51_F	66_P	0.532	0.39
131_A	140_D	0.530	0.38
117_L	122_P	0.529	0.38
16_A	20_Y	0.524	0.38
38_T	111_L	0.522	0.37
28_S	138_R	0.519	0.37
164_L	168_P	0.519	0.37
3_P	8_E	0.515	0.37
20_Y	164_L	0.509	0.36
45_A	48_Q	0.505	0.36
66_P	90_G	0.503	0.36
108_L	120_W	0.502	0.35
66_P	93_Y	0.501	0.35
104_M	139_R	0.501	0.35
46_L	50_L	0.501	0.35
59_W	129_L	0.500	0.35
92_L	95_W	0.500	0.35
7_W	11_Q	0.500	0.35

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
5ajiA	3	0.4902	39.3	0.922	Contact Map
4hw9A	3	0.4412	24.2	0.93	Contact Map
3udcA	3	0.4706	9.5	0.942	Contact Map
4p02A	1	0.25	3.4	0.953	Contact Map
4a2nB	1	0.4412	2.8	0.955	Contact Map
2xq2A	2	0.5637	2.2	0.957	Contact Map
2onkC	2	0.1912	2	0.959	Contact Map
4m7cA	2	0.5245	1.9	0.959	Contact Map
4r7jA	3	0.3088	1.4	0.962	Contact Map
2q32A	1	0.2745	1.3	0.963	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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