RteC - PFAM28P - GREMLIN Contacts

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RteC - RteC protein

PFAM:	PF09357	Sequences: HFFKEIKPKFLSKLIYYNKIYNIETKRPKGSKKAQKKYLEKELKKLKRFFDKNLDFYQYYRSGSTYLDEKYFLRGKFDIKLYLDSFYFEIDPEFSTSHDYKVAKILANELLQVYLEKELEKLENKNSKSSSSKPKSKLKWTGSKTALIELIYALHASGVINNGNADIKEIAEYFEKVFNIDLGDYYRTFLEIKNRKKSRTKFLDKLKESLLKRMDEDD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	218 (216)
Sequences:	1610 (1254)
Seq/√Len:	85.3
META:	0.775

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
204_D	207_K	4.312	1.00
142_G	159_V	4.260	1.00
198_S	204_D	3.915	1.00
153_A	206_L	3.829	1.00
199_R	214_M	3.757	1.00
159_V	202_F	3.445	1.00
142_G	146_A	2.965	1.00
151_I	171_A	2.950	1.00
171_A	185_Y	2.612	1.00
150_L	154_L	2.606	1.00
151_I	174_F	2.593	1.00
187_R	190_L	2.564	1.00
173_Y	177_V	2.516	1.00
200_T	204_D	2.511	1.00
141_T	161_N	2.471	1.00
27_R	118_E	2.466	1.00
199_R	215_D	2.367	1.00
53_N	101_K	2.189	1.00
165_A	170_I	2.169	1.00
193_K	217_D	2.099	1.00
7_K	99_D	2.072	1.00
145_T	188_T	2.012	1.00
167_I	186_Y	2.004	1.00
156_A	213_R	1.975	1.00
36_K	119_L	1.970	1.00
143_S	146_A	1.967	1.00
23_I	39_L	1.967	1.00
154_L	160_I	1.965	1.00
56_F	102_V	1.946	1.00
141_T	163_G	1.856	1.00
43_L	112_Q	1.823	1.00
47_K	51_D	1.818	1.00
24_E	27_R	1.815	1.00
197_K	201_K	1.779	1.00
210_L	214_M	1.775	1.00
199_R	211_L	1.764	1.00
27_R	35_Q	1.742	1.00
160_I	173_Y	1.733	1.00
23_I	115_L	1.728	1.00
15_I	107_A	1.728	1.00
138_L	165_A	1.682	1.00
118_E	121_K	1.674	1.00
2_F	7_K	1.664	1.00
138_L	160_I	1.578	1.00
160_I	170_I	1.569	1.00
148_I	188_T	1.562	1.00
175_E	181_D	1.523	1.00
154_L	202_F	1.521	1.00
3_F	74_R	1.513	1.00
182_L	185_Y	1.510	1.00
35_Q	39_L	1.507	1.00
60_Y	102_V	1.488	0.99
187_R	191_E	1.479	0.99
61_R	109_E	1.475	0.99
13_K	110_L	1.459	0.99
157_S	206_L	1.449	0.99
192_I	214_M	1.427	0.99
192_I	201_K	1.401	0.99
148_I	182_L	1.396	0.99
7_K	94_F	1.359	0.99
207_K	211_L	1.324	0.99
74_R	96_T	1.316	0.99
3_F	7_K	1.314	0.99
175_E	182_L	1.306	0.99
190_L	193_K	1.302	0.99
212_K	216_E	1.301	0.99
152_Y	189_F	1.279	0.98
147_L	182_L	1.276	0.98
74_R	91_D	1.261	0.98
172_E	175_E	1.253	0.98
67_L	70_K	1.242	0.98
149_E	195_R	1.233	0.98
2_F	94_F	1.206	0.98
189_F	217_D	1.172	0.97
71_Y	98_H	1.164	0.97
36_K	123_E	1.152	0.97
6_I	10_F	1.145	0.97
152_Y	186_Y	1.145	0.97
49_F	101_K	1.138	0.97
142_G	202_F	1.137	0.97
28_P	38_Y	1.131	0.96
34_A	44_K	1.128	0.96
193_K	214_M	1.125	0.96
139_K	179_N	1.125	0.96
208_E	212_K	1.120	0.96
175_E	183_G	1.116	0.96
20_I	114_Y	1.107	0.96
184_D	190_L	1.099	0.96
146_A	159_V	1.098	0.96
66_Y	71_Y	1.089	0.96
148_I	185_Y	1.079	0.95
84_D	101_K	1.070	0.95
11_L	103_A	1.068	0.95
12_S	106_L	1.062	0.95
42_E	45_K	1.053	0.95
151_I	170_I	1.053	0.95
94_F	99_D	1.047	0.94
138_L	170_I	1.033	0.94
213_R	217_D	1.030	0.94
150_L	153_A	1.022	0.94
33_K	37_K	1.009	0.93
13_K	17_Y	1.009	0.93
151_I	185_Y	1.007	0.93
189_F	214_M	1.006	0.93
12_S	15_I	1.003	0.93
157_S	209_S	0.993	0.93
50_F	57_Y	0.991	0.93
24_E	118_E	0.988	0.93
153_A	203_L	0.986	0.92
139_K	161_N	0.984	0.92
27_R	39_L	0.977	0.92
200_T	210_L	0.957	0.91
188_T	192_I	0.953	0.91
196_K	199_R	0.943	0.91
102_V	106_L	0.938	0.91
171_A	186_Y	0.936	0.90
32_K	122_L	0.935	0.90
209_S	212_K	0.927	0.90
155_H	213_R	0.913	0.89
203_L	206_L	0.910	0.89
170_I	178_F	0.908	0.89
12_S	110_L	0.906	0.89
47_K	57_Y	0.904	0.89
148_I	192_I	0.903	0.89
203_L	207_K	0.894	0.88
11_L	18_N	0.893	0.88
145_T	187_R	0.890	0.88
155_H	158_G	0.887	0.88
16_Y	20_I	0.871	0.87
184_D	187_R	0.848	0.85
57_Y	105_I	0.847	0.85
100_Y	104_K	0.836	0.85
168_K	186_Y	0.836	0.85
49_F	53_N	0.829	0.84
89_E	100_Y	0.829	0.84
89_E	95_S	0.824	0.84
166_D	186_Y	0.820	0.84
157_S	160_I	0.819	0.83
24_E	115_L	0.813	0.83
47_K	112_Q	0.811	0.83
173_Y	178_F	0.806	0.82
144_K	182_L	0.801	0.82
189_F	193_K	0.798	0.82
108_N	111_L	0.797	0.82
96_T	99_D	0.797	0.82
147_L	174_F	0.795	0.82
26_K	38_Y	0.791	0.81
23_I	111_L	0.786	0.81
170_I	173_Y	0.785	0.81
145_T	192_I	0.785	0.81
202_F	206_L	0.782	0.81
39_L	115_L	0.780	0.80
56_F	71_Y	0.771	0.80
10_F	184_D	0.768	0.79
2_F	99_D	0.768	0.79
3_F	91_D	0.767	0.79
204_D	211_L	0.764	0.79
127_S	131_S	0.762	0.79
108_N	114_Y	0.762	0.79
152_Y	167_I	0.762	0.79
71_Y	96_T	0.761	0.79
174_F	182_L	0.757	0.78
50_F	61_R	0.755	0.78
157_S	205_K	0.753	0.78
141_T	162_N	0.753	0.78
89_E	112_Q	0.742	0.77
19_K	111_L	0.741	0.77
142_G	157_S	0.740	0.77
211_L	214_M	0.738	0.77
142_G	158_G	0.737	0.76
205_K	209_S	0.737	0.76
31_S	34_A	0.733	0.76
91_D	96_T	0.731	0.76
139_K	164_N	0.726	0.75
12_S	103_A	0.717	0.74
161_N	179_N	0.716	0.74
140_W	147_L	0.715	0.74
4_K	65_T	0.713	0.74
167_I	191_E	0.711	0.74
189_F	213_R	0.710	0.74
187_R	217_D	0.710	0.74
147_L	151_I	0.708	0.74
138_L	173_Y	0.702	0.73
32_K	116_E	0.699	0.73
151_I	167_I	0.697	0.72
66_Y	108_N	0.694	0.72
140_W	159_V	0.691	0.72
174_F	177_V	0.691	0.72
25_T	92_P	0.691	0.72
19_K	102_V	0.687	0.71
185_Y	188_T	0.684	0.71
23_I	119_L	0.684	0.71
28_P	61_R	0.683	0.71
118_E	184_D	0.682	0.71
168_K	172_E	0.681	0.71
7_K	28_P	0.678	0.70
69_E	73_L	0.678	0.70
66_Y	70_K	0.675	0.70
156_A	209_S	0.672	0.70
148_I	180_I	0.671	0.70
186_Y	190_L	0.671	0.70
56_F	97_S	0.671	0.70
171_A	175_E	0.670	0.69
24_E	114_Y	0.669	0.69
148_I	171_A	0.668	0.69
170_I	174_F	0.668	0.69
194_N	197_K	0.662	0.68
118_E	122_L	0.662	0.68
193_K	210_L	0.661	0.68
144_K	153_A	0.659	0.68
46_L	108_N	0.652	0.67
120_E	123_E	0.651	0.67
109_E	113_V	0.651	0.67
53_N	199_R	0.639	0.66
191_E	201_K	0.632	0.65
160_I	178_F	0.630	0.65
42_E	46_L	0.624	0.64
187_R	192_I	0.624	0.64
117_K	121_K	0.619	0.63
40_E	121_K	0.615	0.63
164_N	194_N	0.614	0.63
3_F	96_T	0.613	0.63
25_T	52_K	0.612	0.62
153_A	159_V	0.609	0.62
190_L	194_N	0.607	0.62
20_I	24_E	0.607	0.62
139_K	173_Y	0.606	0.62
183_G	191_E	0.605	0.62
111_L	115_L	0.605	0.62
19_K	108_N	0.604	0.61
7_K	114_Y	0.602	0.61
147_L	203_L	0.601	0.61
27_R	102_V	0.601	0.61
126_N	129_S	0.600	0.61
42_E	61_R	0.599	0.61
125_K	135_K	0.597	0.61
114_Y	118_E	0.594	0.60
183_G	193_K	0.593	0.60
186_Y	198_S	0.592	0.60
191_E	202_F	0.592	0.60
160_I	177_V	0.591	0.60
21_Y	89_E	0.591	0.60
134_P	137_K	0.590	0.60
134_P	138_L	0.590	0.60
144_K	180_I	0.589	0.59
148_I	202_F	0.589	0.59
7_K	95_S	0.587	0.59
137_K	169_E	0.585	0.59
136_S	176_K	0.584	0.59
182_L	188_T	0.583	0.59
198_S	201_K	0.583	0.59
5_E	40_E	0.582	0.59
155_H	170_I	0.581	0.58
56_F	98_H	0.580	0.58
70_K	90_I	0.580	0.58
21_Y	25_T	0.580	0.58
93_E	132_S	0.580	0.58
128_K	131_S	0.579	0.58
12_S	105_I	0.576	0.58
26_K	71_Y	0.574	0.58
11_L	39_L	0.574	0.58
16_Y	111_L	0.573	0.57
167_I	189_F	0.572	0.57
139_K	162_N	0.571	0.57
142_G	154_L	0.570	0.57
191_E	196_K	0.569	0.57
102_V	105_I	0.568	0.57
47_K	114_Y	0.567	0.57
166_D	183_G	0.566	0.56
193_K	213_R	0.565	0.56
3_F	99_D	0.564	0.56
148_I	152_Y	0.564	0.56
132_S	135_K	0.563	0.56
193_K	199_R	0.560	0.56
33_K	63_G	0.557	0.55
35_Q	122_L	0.557	0.55
126_N	130_S	0.556	0.55
78_D	81_L	0.554	0.55
198_S	205_K	0.548	0.54
121_K	125_K	0.548	0.54
137_K	179_N	0.548	0.54
130_S	176_K	0.547	0.54
159_V	170_I	0.546	0.54
66_Y	69_E	0.545	0.54
57_Y	60_Y	0.541	0.53
67_L	71_Y	0.540	0.53
22_N	101_K	0.536	0.53
15_I	108_N	0.536	0.53
20_I	111_L	0.534	0.52
62_S	101_K	0.531	0.52
41_K	119_L	0.531	0.52
73_L	81_L	0.528	0.51
23_I	27_R	0.528	0.51
38_Y	46_L	0.527	0.51
148_I	170_I	0.526	0.51
34_A	39_L	0.522	0.51
46_L	112_Q	0.522	0.51
184_D	197_K	0.521	0.51
140_W	144_K	0.519	0.50
50_F	108_N	0.518	0.50
12_S	161_N	0.516	0.50
8_P	12_S	0.514	0.50
30_G	50_F	0.513	0.49
3_F	94_F	0.513	0.49
30_G	61_R	0.513	0.49
55_D	71_Y	0.511	0.49
24_E	39_L	0.510	0.49
77_F	87_Y	0.510	0.49
31_S	35_Q	0.509	0.49
130_S	133_K	0.509	0.49
199_R	210_L	0.509	0.49
55_D	88_F	0.507	0.49
102_V	109_E	0.506	0.48
25_T	62_S	0.506	0.48
57_Y	112_Q	0.505	0.48
32_K	35_Q	0.505	0.48
22_N	31_S	0.505	0.48
99_D	191_E	0.504	0.48
151_I	187_R	0.502	0.48
77_F	98_H	0.502	0.48
154_L	159_V	0.501	0.48
95_S	99_D	0.501	0.48
143_S	188_T	0.501	0.48
186_Y	189_F	0.500	0.48

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
4ujpE	1	0.5229	34.5	0.946	Contact Map
4bpeC	1	0.5229	28.3	0.948	Contact Map
3zeyX	1	0.5183	25.1	0.95	Contact Map
4w23D	1	0.5275	22.5	0.951	Contact Map
3j7aD	1	0.3257	18.3	0.953	Contact Map
1iufA	1	0.3807	15.3	0.954	Contact Map
3wtsC	1	0.3716	9.1	0.959	Contact Map
3j20C	1	0.5046	8.5	0.959	Contact Map
2pmyA	4	0.3211	7.5	0.96	Contact Map
2g1pA	1	0.367	7.3	0.961	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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