SMK-1 - PFAM28P - GREMLIN Contacts

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SMK-1 - Component of IIS longevity pathway SMK-1

PFAM:	PF04802	Sequences: NEDYIKKLLDLFHMCEDLENLEGLHRLCNIMKGIILLNDTSLFEILLSDECIMDVVGALEYDPDFPQPKANHREFLKETAKFKEVIPIKDPELLSKIHQTYRLQYLKDVVLPRVLDDNTFSTLNSLIFFNQVEIVSHLQEDEKFLKELFAQLKDPSTDDERRRDLVLFLQEFCALSKNLQPPARDALFKTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	191 (190)
Sequences:	581 (405)
Seq/√Len:	29.4
META:	0.25

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
100_T	130_N	4.620	1.00
57_G	73_R	4.446	1.00
20_N	23_G	4.125	1.00
60_E	73_R	3.654	1.00
13_H	54_D	3.102	1.00
105_Y	168_F	2.721	1.00
57_G	60_E	2.695	1.00
125_S	129_F	2.661	1.00
16_E	73_R	2.587	0.99
31_M	58_A	2.582	0.99
52_I	56_V	2.534	0.99
48_S	51_C	2.439	0.99
84_E	94_L	2.428	0.99
72_H	105_Y	2.222	0.98
9_L	55_V	2.190	0.98
107_K	116_D	2.128	0.98
107_K	117_D	2.126	0.98
28_C	31_M	2.039	0.97
15_C	23_G	2.038	0.97
83_K	164_D	1.958	0.96
16_E	57_G	1.946	0.96
49_D	102_R	1.923	0.96
74_E	78_E	1.902	0.96
12_F	16_E	1.896	0.96
43_F	126_L	1.801	0.94
96_K	100_T	1.801	0.94
128_F	132_V	1.794	0.94
28_C	63_P	1.777	0.94
47_L	52_I	1.724	0.93
105_Y	167_L	1.704	0.92
96_K	99_Q	1.652	0.91
125_S	180_Q	1.623	0.90
6_K	35_I	1.607	0.90
163_R	166_V	1.605	0.90
31_M	55_V	1.586	0.89
145_L	149_F	1.567	0.89
16_E	24_L	1.528	0.87
188_F	191_L	1.510	0.87
152_L	165_L	1.510	0.87
164_D	174_A	1.451	0.85
5_I	102_R	1.384	0.82
38_N	180_Q	1.368	0.81
138_L	172_F	1.365	0.81
101_Y	167_L	1.364	0.81
97_I	168_F	1.336	0.79
109_V	169_L	1.315	0.78
169_L	187_L	1.304	0.78
78_E	90_D	1.300	0.77
28_C	65_F	1.299	0.77
64_D	107_K	1.297	0.77
152_L	171_E	1.296	0.77
110_V	184_R	1.272	0.76
156_S	167_L	1.247	0.74
98_H	101_Y	1.228	0.73
14_M	17_D	1.215	0.72
62_D	113_R	1.200	0.71
110_V	124_N	1.188	0.71
21_L	25_H	1.187	0.71
21_L	33_G	1.171	0.69
58_A	165_L	1.163	0.69
121_S	168_F	1.153	0.68
153_K	156_S	1.149	0.68
82_F	98_H	1.120	0.66
56_V	76_L	1.120	0.66
80_A	117_D	1.115	0.66
36_L	58_A	1.112	0.65
107_K	115_L	1.106	0.65
28_C	62_D	1.104	0.65
52_I	102_R	1.101	0.65
85_V	135_V	1.100	0.65
32_K	36_L	1.099	0.64
154_D	158_D	1.098	0.64
60_E	72_H	1.098	0.64
25_H	63_P	1.083	0.63
108_D	111_L	1.078	0.63
75_F	78_E	1.063	0.62
59_L	66_P	1.062	0.62
18_L	23_G	1.054	0.61
65_F	113_R	1.053	0.61
185_D	188_F	1.050	0.61
96_K	152_L	1.046	0.61
26_R	30_I	1.044	0.60
75_F	80_A	1.042	0.60
10_D	22_E	1.042	0.60
32_K	62_D	1.026	0.59
177_K	183_A	1.024	0.59
47_L	165_L	1.021	0.59
44_E	180_Q	1.013	0.58
65_F	112_P	1.008	0.58
98_H	102_R	1.007	0.58
42_L	48_S	1.005	0.57
3_D	146_K	1.004	0.57
113_R	116_D	1.002	0.57
98_H	130_N	1.001	0.57
84_E	100_T	1.001	0.57
138_L	144_F	1.000	0.57
17_D	23_G	0.995	0.57
162_R	170_Q	0.992	0.56
167_L	187_L	0.991	0.56
99_Q	130_N	0.975	0.55
97_I	102_R	0.974	0.55
142_E	159_D	0.949	0.53
177_K	181_P	0.947	0.53
78_E	91_P	0.947	0.53
7_K	30_I	0.944	0.53
107_K	177_K	0.942	0.53
19_E	88_I	0.940	0.52
36_L	111_L	0.937	0.52
22_E	158_D	0.936	0.52
151_Q	168_F	0.935	0.52
154_D	161_R	0.931	0.52
56_V	106_L	0.924	0.51
59_L	73_R	0.922	0.51
65_F	70_A	0.913	0.50
152_L	162_R	0.912	0.50
22_E	42_L	0.912	0.50
115_L	120_F	0.905	0.50
84_E	87_P	0.904	0.50
30_I	184_R	0.904	0.50
114_V	123_L	0.901	0.49
37_L	87_P	0.898	0.49
9_L	58_A	0.888	0.48
47_L	172_F	0.887	0.48
116_D	119_T	0.886	0.48
59_L	145_L	0.883	0.48
149_F	180_Q	0.881	0.48
24_L	27_L	0.880	0.48
116_D	177_K	0.874	0.47
168_F	179_L	0.868	0.47
105_Y	110_V	0.865	0.46
44_E	157_T	0.864	0.46
71_N	74_E	0.859	0.46
113_R	117_D	0.856	0.46
115_L	118_N	0.854	0.46
10_D	17_D	0.850	0.45
14_M	187_L	0.848	0.45
83_K	158_D	0.848	0.45
32_K	137_H	0.844	0.45
39_D	180_Q	0.837	0.44
34_I	72_H	0.837	0.44
133_E	157_T	0.834	0.44
12_F	46_L	0.832	0.44
5_I	9_L	0.831	0.44
107_K	113_R	0.829	0.44
5_I	51_C	0.824	0.43
26_R	123_L	0.823	0.43
141_D	165_L	0.820	0.43
182_P	189_K	0.816	0.43
113_R	119_T	0.807	0.42
143_K	154_D	0.803	0.42
128_F	134_I	0.788	0.41
86_I	161_R	0.787	0.40
7_K	25_H	0.780	0.40
15_C	45_I	0.779	0.40
29_N	124_N	0.778	0.40
5_I	10_D	0.776	0.40
103_L	165_L	0.773	0.39
39_D	93_L	0.771	0.39
176_S	179_L	0.769	0.39
181_P	185_D	0.767	0.39
37_L	56_V	0.750	0.38
2_E	6_K	0.745	0.37
79_T	184_R	0.745	0.37
43_F	122_T	0.740	0.37
78_E	183_A	0.739	0.37
181_P	186_A	0.738	0.37
89_K	136_S	0.737	0.37
89_K	92_E	0.737	0.37
126_L	131_Q	0.731	0.36
155_P	160_E	0.729	0.36
24_L	76_L	0.728	0.36
49_D	96_K	0.726	0.36
168_F	171_E	0.720	0.36
77_K	124_N	0.717	0.35
97_I	100_T	0.712	0.35
141_D	149_F	0.706	0.35
62_D	108_D	0.703	0.34
176_S	181_P	0.702	0.34
107_K	111_L	0.701	0.34
54_D	123_L	0.698	0.34
43_F	150_A	0.695	0.34
159_D	186_A	0.692	0.34
115_L	119_T	0.692	0.34
132_V	180_Q	0.687	0.33
9_L	13_H	0.686	0.33
65_F	90_D	0.676	0.32
75_F	101_Y	0.676	0.32
153_K	157_T	0.676	0.32
53_M	59_L	0.674	0.32
153_K	167_L	0.671	0.32
103_L	171_E	0.670	0.32
51_C	167_L	0.670	0.32
4_Y	164_D	0.667	0.32
138_L	150_A	0.667	0.32
83_K	162_R	0.664	0.32
100_T	104_Q	0.661	0.31
35_I	90_D	0.660	0.31
82_F	97_I	0.660	0.31
54_D	105_Y	0.659	0.31
51_C	90_D	0.656	0.31
116_D	175_L	0.656	0.31
67_Q	169_L	0.655	0.31
28_C	113_R	0.651	0.31
89_K	141_D	0.649	0.31
4_Y	139_Q	0.644	0.30
3_D	6_K	0.642	0.30
111_L	169_L	0.638	0.30
101_Y	163_R	0.636	0.30
158_D	188_F	0.634	0.30
92_E	155_P	0.631	0.29
169_L	173_C	0.628	0.29
151_Q	165_L	0.625	0.29
96_K	130_N	0.623	0.29
36_L	172_F	0.622	0.29
49_D	162_R	0.620	0.29
38_N	179_L	0.620	0.29
65_F	69_K	0.618	0.29
37_L	63_P	0.611	0.28
144_F	165_L	0.609	0.28
6_K	51_C	0.609	0.28
102_R	176_S	0.609	0.28
42_L	95_S	0.606	0.28
138_L	179_L	0.602	0.28
30_I	92_E	0.601	0.27
20_N	62_D	0.600	0.27
27_L	58_A	0.595	0.27
55_V	133_E	0.595	0.27
129_F	180_Q	0.592	0.27
51_C	95_S	0.592	0.27
79_T	95_S	0.591	0.27
40_T	129_F	0.589	0.27
66_P	119_T	0.589	0.27
5_I	34_I	0.588	0.27
2_E	11_L	0.587	0.27
159_D	166_V	0.587	0.27
61_Y	177_K	0.586	0.27
5_I	8_L	0.585	0.26
5_I	56_V	0.583	0.26
64_D	120_F	0.580	0.26
47_L	144_F	0.578	0.26
25_H	96_K	0.576	0.26
155_P	158_D	0.570	0.26
45_I	82_F	0.568	0.25
14_M	18_L	0.565	0.25
37_L	173_C	0.556	0.25
93_L	175_L	0.553	0.25
113_R	177_K	0.553	0.25
76_L	98_H	0.552	0.25
101_Y	174_A	0.551	0.24
9_L	51_C	0.549	0.24
63_P	99_Q	0.548	0.24
48_S	58_A	0.547	0.24
131_Q	170_Q	0.546	0.24
10_D	14_M	0.541	0.24
117_D	178_N	0.539	0.24
46_L	55_V	0.538	0.24
125_S	133_E	0.537	0.24
44_E	62_D	0.537	0.24
48_S	88_I	0.536	0.24
5_I	158_D	0.535	0.24
87_P	138_L	0.532	0.23
3_D	156_S	0.526	0.23
16_E	60_E	0.525	0.23
96_K	139_Q	0.523	0.23
29_N	127_I	0.523	0.23
31_M	65_F	0.521	0.23
107_K	119_T	0.519	0.23
39_D	126_L	0.519	0.23
165_L	175_L	0.518	0.23
178_N	184_R	0.517	0.23
39_D	116_D	0.517	0.23
120_F	137_H	0.515	0.22
120_F	131_Q	0.515	0.22
103_L	162_R	0.515	0.22
72_H	75_F	0.512	0.22
38_N	121_S	0.510	0.22
21_L	160_E	0.508	0.22
146_K	166_V	0.507	0.22
24_L	57_G	0.507	0.22
14_M	44_E	0.505	0.22
49_D	108_D	0.503	0.22
112_P	165_L	0.502	0.22
11_L	174_A	0.502	0.22
60_E	106_L	0.501	0.22
2_E	5_I	0.500	0.22

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
3fgaB	2	0.8325	28.9	0.939	Contact Map
2nppB	1	0.8325	23.1	0.942	Contact Map
2jakA	1	0.8063	9.4	0.951	Contact Map
1w9cA	2	0.4398	8.6	0.952	Contact Map
3ibvA	1	0.3927	8.2	0.953	Contact Map
3u0rA	1	0.8796	7.7	0.953	Contact Map
4eswA	2	0.445	6.9	0.954	Contact Map
3e3rA	2	0.5079	4.3	0.958	Contact Map
3qh6A	2	0.2723	3.7	0.96	Contact Map
4f7zA	1	0.801	3.6	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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