TIMELESS - PFAM28P - GREMLIN Contacts

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TIMELESS - Timeless protein

PFAM:	PF04821	Sequences: VYVLGDDCLECLKDLKRWLRRDDDDNRRDVARCLGEANLVQNDLLPILAQWKEDDKLALACLELLVNLTWPIELLFETDEHHRHYPQLQLALLGYKEAILDSKVLKALVRLLLPPLAKDREERTERDEGIIELVLYLFRNILAIPPPPANEKLSDDGAEDEILQSALIWALHEQGVLDLLLTLASNMGEDFEFQQWNLLVLEIIYLLFKGQDPEKLAKSSMDEQRSTSEKKADSDELSALLQKEKAMKRSYARKNAPTRHSRFGTTIWV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	269 (265)
Sequences:	529 (400)
Seq/√Len:	24.5
META:	0.153

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_Y	43_D	4.499	1.00
4_L	47_I	3.837	1.00
168_I	207_L	3.348	1.00
62_L	137_L	3.294	1.00
96_K	144_I	3.164	1.00
40_V	65_L	3.014	1.00
14_D	20_R	3.011	1.00
69_T	202_E	2.924	1.00
260_H	264_G	2.815	0.99
10_E	17_R	2.787	0.99
259_R	263_F	2.511	0.99
15_L	39_L	2.423	0.98
52_K	56_K	2.368	0.98
93_L	145_P	2.356	0.98
17_R	50_Q	2.249	0.97
48_L	58_A	2.227	0.97
11_C	14_D	2.159	0.97
237_L	244_E	2.084	0.96
16_K	63_E	2.061	0.95
14_D	18_W	2.020	0.95
69_T	140_N	1.994	0.95
67_N	132_E	1.994	0.95
35_G	91_A	1.965	0.94
59_L	133_L	1.961	0.94
37_A	185_S	1.917	0.93
80_E	141_I	1.909	0.93
26_N	209_K	1.858	0.92
69_T	139_R	1.794	0.91
239_A	242_Q	1.779	0.90
43_D	47_I	1.771	0.90
63_E	132_E	1.760	0.90
47_I	122_E	1.750	0.90
16_K	31_A	1.747	0.90
66_V	137_L	1.713	0.89
63_E	136_Y	1.708	0.88
246_A	250_S	1.686	0.88
135_L	181_L	1.669	0.87
17_R	46_P	1.668	0.87
13_K	201_L	1.661	0.87
259_R	264_G	1.658	0.87
115_P	202_E	1.654	0.87
63_E	67_N	1.647	0.86
238_S	242_Q	1.637	0.86
17_R	213_P	1.633	0.86
92_L	99_I	1.627	0.86
165_S	265_T	1.624	0.86
221_M	225_R	1.598	0.85
47_I	253_R	1.580	0.84
14_D	17_R	1.562	0.83
258_T	269_V	1.550	0.83
225_R	230_K	1.547	0.83
129_G	265_T	1.519	0.82
136_Y	199_L	1.518	0.82
85_Y	206_L	1.515	0.81
27_R	83_R	1.494	0.80
9_L	27_R	1.486	0.80
164_Q	196_W	1.475	0.80
203_I	269_V	1.455	0.79
67_N	136_Y	1.448	0.78
4_L	8_C	1.436	0.78
248_K	257_P	1.395	0.76
240_L	248_K	1.374	0.74
59_L	99_I	1.369	0.74
63_E	70_W	1.368	0.74
64_L	185_S	1.356	0.73
19_L	63_E	1.351	0.73
170_A	183_L	1.329	0.72
65_L	235_D	1.313	0.71
204_I	208_F	1.304	0.70
52_K	106_K	1.302	0.70
243_K	247_M	1.289	0.70
170_A	216_L	1.284	0.69
242_Q	246_A	1.283	0.69
12_L	16_K	1.267	0.68
180_L	200_V	1.260	0.68
138_F	176_V	1.259	0.68
143_A	206_L	1.255	0.67
138_F	199_L	1.250	0.67
8_C	23_D	1.245	0.67
40_V	68_L	1.241	0.67
111_L	133_L	1.233	0.66
45_L	220_S	1.222	0.65
141_I	167_L	1.222	0.65
19_L	35_G	1.218	0.65
62_L	65_L	1.214	0.65
88_L	124_T	1.214	0.65
31_A	133_L	1.207	0.64
81_H	176_V	1.201	0.64
183_L	230_K	1.200	0.64
127_D	140_N	1.188	0.63
4_L	33_C	1.171	0.62
21_R	30_V	1.168	0.62
36_E	138_F	1.167	0.62
220_S	230_K	1.151	0.61
98_A	184_A	1.146	0.60
19_L	34_L	1.142	0.60
124_T	269_V	1.142	0.60
245_K	249_R	1.139	0.60
235_D	238_S	1.134	0.59
135_L	183_L	1.125	0.59
38_N	41_Q	1.123	0.59
138_F	152_K	1.122	0.59
260_H	263_F	1.122	0.59
146_P	164_Q	1.117	0.58
248_K	252_A	1.116	0.58
62_L	108_L	1.116	0.58
98_A	178_D	1.112	0.58
64_L	168_I	1.110	0.58
258_T	265_T	1.110	0.58
116_L	184_A	1.104	0.57
108_L	134_V	1.103	0.57
122_E	256_A	1.100	0.57
65_L	138_F	1.100	0.57
135_L	139_R	1.089	0.56
13_K	60_A	1.089	0.56
129_G	132_E	1.083	0.56
16_K	70_W	1.076	0.55
131_I	170_A	1.075	0.55
135_L	140_N	1.067	0.55
34_L	37_A	1.065	0.55
12_L	29_D	1.048	0.53
57_L	208_F	1.048	0.53
57_L	99_I	1.046	0.53
45_L	49_A	1.046	0.53
154_S	210_G	1.045	0.53
200_V	269_V	1.044	0.53
220_S	224_Q	1.042	0.53
59_L	207_L	1.034	0.52
177_L	180_L	1.032	0.52
221_M	224_Q	1.026	0.52
181_L	186_N	1.025	0.52
166_A	207_L	1.024	0.52
7_D	43_D	1.018	0.51
264_G	267_I	1.013	0.51
230_K	242_Q	1.012	0.51
224_Q	227_T	1.008	0.50
16_K	133_L	1.005	0.50
7_D	204_I	1.002	0.50
87_Q	178_D	0.997	0.50
66_V	133_L	0.997	0.50
186_N	202_E	0.997	0.50
5_G	14_D	0.996	0.50
8_C	130_I	0.995	0.50
2_Y	14_D	0.993	0.49
27_R	112_L	0.992	0.49
6_D	11_C	0.986	0.49
193_F	207_L	0.985	0.49
112_L	178_D	0.983	0.49
130_I	215_K	0.982	0.49
105_L	174_Q	0.982	0.49
4_L	54_D	0.981	0.49
37_A	82_H	0.981	0.49
169_W	173_E	0.978	0.48
13_K	26_N	0.976	0.48
230_K	249_R	0.975	0.48
17_R	20_R	0.974	0.48
65_L	204_I	0.971	0.48
23_D	63_E	0.965	0.47
11_C	43_D	0.962	0.47
6_D	127_D	0.955	0.47
4_L	39_L	0.951	0.46
35_G	145_P	0.948	0.46
115_P	187_M	0.938	0.45
13_K	41_Q	0.938	0.45
14_D	30_V	0.935	0.45
9_L	60_A	0.932	0.45
4_L	51_W	0.931	0.45
45_L	110_R	0.926	0.45
202_E	207_L	0.926	0.45
95_Y	172_H	0.925	0.45
142_L	211_Q	0.918	0.44
166_A	173_E	0.916	0.44
19_L	68_L	0.912	0.44
135_L	196_W	0.912	0.44
16_K	20_R	0.911	0.44
213_P	245_K	0.910	0.43
226_S	229_E	0.905	0.43
45_L	179_L	0.904	0.43
84_H	88_L	0.903	0.43
64_L	100_L	0.898	0.43
177_L	205_Y	0.896	0.43
175_G	178_D	0.888	0.42
265_T	268_W	0.884	0.42
125_E	266_T	0.881	0.41
6_D	72_I	0.877	0.41
23_D	62_L	0.875	0.41
10_E	20_R	0.874	0.41
226_S	230_K	0.873	0.41
60_A	116_L	0.870	0.41
17_R	115_P	0.865	0.40
186_N	207_L	0.862	0.40
72_I	231_K	0.858	0.40
233_D	236_E	0.853	0.40
234_S	239_A	0.847	0.39
76_F	141_I	0.845	0.39
20_R	128_E	0.845	0.39
90_L	269_V	0.844	0.39
106_K	131_I	0.840	0.39
223_E	232_A	0.839	0.39
7_D	112_L	0.834	0.38
252_A	255_N	0.831	0.38
105_L	217_A	0.830	0.38
45_L	124_T	0.829	0.38
232_A	250_S	0.828	0.38
112_L	115_P	0.828	0.38
180_L	262_R	0.822	0.37
18_W	33_C	0.820	0.37
29_D	39_L	0.819	0.37
249_R	252_A	0.817	0.37
39_L	183_L	0.813	0.37
159_E	168_I	0.812	0.37
49_A	91_A	0.809	0.37
240_L	243_K	0.807	0.36
11_C	16_K	0.807	0.36
162_I	190_D	0.803	0.36
44_L	98_A	0.794	0.36
24_D	63_E	0.794	0.36
10_E	14_D	0.793	0.35
52_K	199_L	0.793	0.35
96_K	165_S	0.793	0.35
111_L	130_I	0.791	0.35
5_G	11_C	0.791	0.35
37_A	46_P	0.789	0.35
223_E	228_S	0.788	0.35
178_D	249_R	0.779	0.35
108_L	125_E	0.774	0.34
216_L	221_M	0.773	0.34
15_L	197_N	0.773	0.34
221_M	226_S	0.769	0.34
62_L	196_W	0.769	0.34
184_A	246_A	0.768	0.34
13_K	46_P	0.765	0.34
18_W	30_V	0.762	0.33
184_A	200_V	0.761	0.33
65_L	137_L	0.757	0.33
153_L	157_G	0.752	0.33
166_A	169_W	0.750	0.33
31_A	67_N	0.748	0.33
5_G	123_R	0.746	0.32
19_L	25_D	0.746	0.32
137_L	231_K	0.741	0.32
233_D	239_A	0.740	0.32
37_A	144_I	0.740	0.32
2_Y	20_R	0.740	0.32
48_L	240_L	0.739	0.32
230_K	233_D	0.734	0.32
62_L	138_F	0.732	0.32
121_E	240_L	0.731	0.32
77_E	80_E	0.731	0.32
114_P	117_A	0.730	0.31
251_Y	256_A	0.728	0.31
67_N	70_W	0.727	0.31
21_R	45_L	0.722	0.31
123_R	202_E	0.721	0.31
4_L	16_K	0.720	0.31
117_A	213_P	0.720	0.31
247_M	251_Y	0.720	0.31
60_A	196_W	0.719	0.31
59_L	132_E	0.719	0.31
70_W	126_R	0.718	0.31
21_R	25_D	0.717	0.31
102_S	207_L	0.716	0.31
9_L	59_L	0.706	0.30
225_R	228_S	0.705	0.30
222_D	240_L	0.705	0.30
109_V	176_V	0.701	0.30
178_D	184_A	0.697	0.29
235_D	239_A	0.693	0.29
234_S	241_L	0.692	0.29
118_K	208_F	0.691	0.29
70_W	136_Y	0.690	0.29
138_F	169_W	0.688	0.29
29_D	33_C	0.687	0.29
46_P	203_I	0.687	0.29
130_I	214_E	0.685	0.29
8_C	18_W	0.684	0.29
183_L	212_D	0.681	0.28
31_A	165_S	0.681	0.28
17_R	30_V	0.679	0.28
141_I	162_I	0.678	0.28
154_S	160_D	0.678	0.28
212_D	224_Q	0.677	0.28
158_A	200_V	0.673	0.28
167_L	178_D	0.672	0.28
10_E	21_R	0.667	0.28
51_W	98_A	0.661	0.27
19_L	137_L	0.660	0.27
59_L	127_D	0.660	0.27
126_R	198_L	0.657	0.27
62_L	210_G	0.655	0.27
223_E	226_S	0.655	0.27
64_L	212_D	0.653	0.27
133_L	186_N	0.653	0.27
54_D	68_L	0.650	0.27
12_L	174_Q	0.648	0.27
62_L	132_E	0.648	0.27
129_G	182_T	0.647	0.27
49_A	89_Q	0.647	0.27
94_G	104_V	0.642	0.26
13_K	125_E	0.641	0.26
8_C	63_E	0.641	0.26
43_D	88_L	0.637	0.26
183_L	200_V	0.637	0.26
102_S	146_P	0.633	0.26
87_Q	217_A	0.633	0.26
171_L	176_V	0.632	0.26
20_R	161_E	0.631	0.26
151_E	155_D	0.630	0.26
242_Q	245_K	0.626	0.25
39_L	198_L	0.623	0.25
47_I	210_G	0.622	0.25
83_R	171_L	0.621	0.25
21_R	27_R	0.619	0.25
99_I	186_N	0.616	0.25
113_L	117_A	0.616	0.25
137_L	215_K	0.613	0.25
41_Q	72_I	0.613	0.25
246_A	249_R	0.612	0.25
100_L	108_L	0.611	0.25
35_G	199_L	0.611	0.25
191_F	194_Q	0.606	0.24
63_E	265_T	0.604	0.24
4_L	11_C	0.604	0.24
39_L	130_I	0.603	0.24
47_I	88_L	0.603	0.24
206_L	209_K	0.596	0.24
26_N	168_I	0.596	0.24
83_R	248_K	0.596	0.24
152_K	155_D	0.593	0.24
58_A	107_A	0.590	0.23
179_L	252_A	0.587	0.23
61_C	131_I	0.585	0.23
64_L	128_E	0.584	0.23
167_L	197_N	0.583	0.23
247_M	252_A	0.580	0.23
46_P	102_S	0.579	0.23
40_V	148_P	0.578	0.23
187_M	200_V	0.578	0.23
5_G	127_D	0.576	0.23
178_D	213_P	0.576	0.23
144_I	171_L	0.574	0.23
66_V	132_E	0.573	0.23
98_A	131_I	0.568	0.22
127_D	135_L	0.567	0.22
18_W	29_D	0.562	0.22
44_L	68_L	0.561	0.22
37_A	90_L	0.559	0.22
33_C	37_A	0.559	0.22
146_P	167_L	0.558	0.22
15_L	261_S	0.558	0.22
11_C	18_W	0.556	0.22
226_S	232_A	0.552	0.22
120_R	203_I	0.551	0.22
182_T	185_S	0.551	0.22
121_E	241_L	0.550	0.21
64_L	178_D	0.549	0.21
70_W	182_T	0.546	0.21
213_P	224_Q	0.546	0.21
2_Y	118_K	0.544	0.21
92_L	165_S	0.544	0.21
63_E	133_L	0.543	0.21
129_G	136_Y	0.541	0.21
68_L	85_Y	0.539	0.21
116_L	217_A	0.539	0.21
188_G	193_F	0.537	0.21
45_L	230_K	0.537	0.21
105_L	138_F	0.536	0.21
18_W	36_E	0.536	0.21
115_P	134_V	0.535	0.21
15_L	96_K	0.533	0.21
138_F	142_L	0.531	0.21
177_L	203_I	0.529	0.20
38_N	42_N	0.528	0.20
230_K	245_K	0.527	0.20
48_L	171_L	0.527	0.20
46_P	71_P	0.526	0.20
238_S	241_L	0.525	0.20
227_T	250_S	0.523	0.20
41_Q	94_G	0.523	0.20
29_D	127_D	0.522	0.20
258_T	264_G	0.522	0.20
108_L	112_L	0.518	0.20
147_P	181_L	0.518	0.20
194_Q	198_L	0.517	0.20
227_T	248_K	0.515	0.20
99_I	137_L	0.514	0.20
200_V	233_D	0.512	0.20
232_A	245_K	0.512	0.20
58_A	70_W	0.509	0.20
67_N	164_Q	0.508	0.20
69_T	127_D	0.507	0.19
132_E	198_L	0.506	0.19
19_L	136_Y	0.503	0.19
63_E	68_L	0.503	0.19
40_V	231_K	0.501	0.19
148_P	216_L	0.501	0.19
168_I	266_T	0.500	0.19
61_C	126_R	0.500	0.19

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
4db6A	1	0.6914	58.3	0.946	Contact Map
4uaeA	1	0.5836	40	0.951	Contact Map
4cb9A	1	0.803	30.9	0.954	Contact Map
3opbA	2	0.6617	27.4	0.955	Contact Map
3nmzA	2	0.7286	25.3	0.956	Contact Map
4mfuA	2	0.8364	20.4	0.958	Contact Map
1xqrA	1	0.5985	17.2	0.959	Contact Map
4yc7B	1	0.5874	16.6	0.96	Contact Map
4b8jA	1	0.6877	14.8	0.961	Contact Map
3nmwA	1	0.6543	13.7	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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