Senescence - PFAM28P - GREMLIN Contacts

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Senescence - Senescence-associated protein

PFAM:	PF06911	Sequences: IVSGAGQISRGIVTGSDYTAKGLQSGAESLKKKTKPNEKPMTFSPATHKRLRRVKKLTKMAAKVSAKTVGGVGKVAGNVGASLANSKAGKKFKSLLPGEKAPKVLNASLDAFSTVADGLEQAGKNLLSSTSTATTTVVGHKYGEEAGEATRDALGAAGNVGLVAIDVFGVGRKAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	175 (173)
Sequences:	636 (459)
Seq/√Len:	34.9
META:	0.233

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_L	149_A	5.185	1.00
100_K	103_K	4.733	1.00
138_V	146_A	3.578	1.00
31_K	136_T	2.989	1.00
163_V	166_D	2.747	1.00
13_V	118_G	2.614	1.00
139_G	147_G	2.609	1.00
166_D	169_G	2.351	0.99
135_T	147_G	2.335	0.99
30_L	34_T	2.270	0.99
55_K	152_D	2.258	0.99
131_S	154_L	2.245	0.99
150_T	154_L	2.241	0.99
50_R	53_R	2.188	0.99
20_A	129_S	2.108	0.99
168_F	173_K	2.076	0.99
8_I	11_G	2.054	0.99
36_P	40_P	2.049	0.98
93_K	99_E	2.018	0.98
16_S	20_A	1.951	0.98
32_K	47_T	1.930	0.98
72_V	84_A	1.888	0.97
139_G	144_E	1.861	0.97
47_T	51_L	1.789	0.96
94_S	97_P	1.774	0.96
26_G	30_L	1.675	0.95
138_V	150_T	1.644	0.94
40_P	140_H	1.632	0.94
89_G	98_G	1.598	0.93
75_V	160_V	1.594	0.93
76_A	80_G	1.564	0.92
46_A	49_K	1.563	0.92
14_T	17_D	1.561	0.92
7_Q	175_L	1.552	0.92
164_A	169_G	1.532	0.92
93_K	97_P	1.512	0.91
48_H	145_E	1.478	0.90
163_V	169_G	1.459	0.90
85_N	88_A	1.455	0.89
94_S	99_E	1.450	0.89
51_L	156_A	1.449	0.89
149_A	157_A	1.417	0.88
122_A	154_L	1.383	0.87
107_A	110_D	1.344	0.85
94_S	98_G	1.338	0.85
31_K	122_A	1.334	0.85
51_L	157_A	1.332	0.85
127_L	130_T	1.316	0.84
44_S	47_T	1.308	0.84
31_K	140_H	1.307	0.84
162_L	173_K	1.278	0.82
45_P	49_K	1.269	0.82
17_D	79_V	1.259	0.81
156_A	159_N	1.253	0.81
95_L	98_G	1.252	0.81
93_K	96_L	1.243	0.80
49_K	115_V	1.217	0.79
106_N	119_L	1.200	0.78
5_A	147_G	1.191	0.77
5_A	9_S	1.181	0.77
149_A	152_D	1.179	0.77
17_D	120_E	1.172	0.76
37_N	41_M	1.163	0.76
58_T	152_D	1.161	0.76
92_F	95_L	1.157	0.75
40_P	43_F	1.154	0.75
50_R	112_F	1.152	0.75
8_I	50_R	1.122	0.73
90_K	100_K	1.098	0.71
161_G	170_V	1.097	0.71
71_G	74_K	1.082	0.70
29_S	119_L	1.075	0.70
76_A	111_A	1.054	0.68
120_E	124_K	1.032	0.67
9_S	164_A	1.027	0.66
67_K	122_A	1.020	0.66
24_Q	115_V	1.018	0.65
80_G	83_L	1.016	0.65
96_L	99_E	1.014	0.65
62_A	65_S	1.011	0.65
71_G	75_V	1.008	0.65
162_L	169_G	1.002	0.64
15_G	22_G	0.994	0.64
28_E	98_G	0.992	0.63
5_A	20_A	0.990	0.63
58_T	115_V	0.979	0.62
17_D	125_N	0.969	0.62
169_G	172_R	0.953	0.60
114_T	118_G	0.953	0.60
110_D	130_T	0.953	0.60
110_D	122_A	0.944	0.60
12_I	118_G	0.943	0.59
158_G	162_L	0.929	0.58
51_L	125_N	0.926	0.58
38_E	141_K	0.916	0.57
35_K	132_T	0.916	0.57
123_G	130_T	0.912	0.57
165_I	169_G	0.911	0.57
20_A	157_A	0.906	0.56
3_S	122_A	0.893	0.55
29_S	32_K	0.892	0.55
86_S	97_P	0.882	0.54
166_D	173_K	0.870	0.53
118_G	122_A	0.868	0.53
95_L	99_E	0.867	0.53
152_D	175_L	0.860	0.52
115_V	135_T	0.852	0.52
91_K	94_S	0.851	0.52
164_A	172_R	0.847	0.51
33_K	140_H	0.845	0.51
162_L	166_D	0.843	0.51
104_V	116_A	0.843	0.51
86_S	90_K	0.842	0.51
158_G	169_G	0.837	0.51
28_E	61_A	0.836	0.50
5_A	115_V	0.836	0.50
9_S	68_T	0.833	0.50
80_G	84_A	0.833	0.50
73_G	120_E	0.825	0.49
108_S	113_S	0.824	0.49
10_R	108_S	0.824	0.49
12_I	23_L	0.821	0.49
65_S	72_V	0.817	0.49
4_G	20_A	0.815	0.49
135_T	139_G	0.812	0.48
3_S	7_Q	0.804	0.48
125_N	135_T	0.804	0.48
128_S	173_K	0.803	0.48
157_A	161_G	0.795	0.47
111_A	134_T	0.794	0.47
120_E	123_G	0.793	0.47
27_A	141_K	0.791	0.47
120_E	129_S	0.790	0.46
139_G	151_R	0.785	0.46
39_K	75_V	0.785	0.46
69_V	114_T	0.784	0.46
24_Q	148_E	0.780	0.46
33_K	134_T	0.780	0.46
43_F	146_A	0.779	0.46
166_D	172_R	0.775	0.45
57_L	130_T	0.772	0.45
142_Y	168_F	0.772	0.45
111_A	115_V	0.770	0.45
4_G	116_A	0.770	0.45
1_I	129_S	0.766	0.44
34_T	111_A	0.762	0.44
89_G	141_K	0.761	0.44
117_D	135_T	0.757	0.44
23_L	140_H	0.755	0.44
168_F	172_R	0.755	0.44
90_K	94_S	0.754	0.43
93_K	98_G	0.752	0.43
27_A	134_T	0.746	0.43
27_A	133_A	0.744	0.43
169_G	174_A	0.743	0.43
21_K	173_K	0.739	0.42
45_P	132_T	0.734	0.42
21_K	24_Q	0.734	0.42
109_L	112_F	0.733	0.42
76_A	116_A	0.732	0.42
23_L	132_T	0.731	0.42
34_T	43_F	0.728	0.41
49_K	53_R	0.726	0.41
36_P	140_H	0.724	0.41
58_T	159_N	0.724	0.41
56_K	109_L	0.720	0.41
45_P	54_V	0.719	0.41
59_K	123_G	0.717	0.40
47_T	50_R	0.712	0.40
34_T	140_H	0.705	0.39
40_P	160_V	0.704	0.39
37_N	115_V	0.697	0.39
15_G	123_G	0.697	0.39
20_A	118_G	0.695	0.39
32_K	125_N	0.687	0.38
90_K	144_E	0.685	0.38
3_S	24_Q	0.680	0.37
9_S	159_N	0.667	0.36
23_L	118_G	0.666	0.36
4_G	55_K	0.664	0.36
48_H	152_D	0.664	0.36
47_T	68_T	0.663	0.36
22_G	26_G	0.663	0.36
128_S	141_K	0.662	0.36
3_S	21_K	0.661	0.36
113_S	171_G	0.657	0.36
121_Q	124_K	0.654	0.35
4_G	72_V	0.652	0.35
33_K	142_Y	0.647	0.35
61_A	66_A	0.644	0.35
122_A	151_R	0.643	0.34
31_K	34_T	0.642	0.34
66_A	161_G	0.642	0.34
90_K	93_K	0.637	0.34
37_N	119_L	0.637	0.34
83_L	147_G	0.635	0.34
15_G	19_T	0.635	0.34
82_S	122_A	0.634	0.34
113_S	117_D	0.634	0.34
5_A	142_Y	0.626	0.33
165_I	174_A	0.623	0.33
111_A	133_A	0.617	0.32
108_S	111_A	0.616	0.32
81_A	145_E	0.614	0.32
99_E	141_K	0.613	0.32
34_T	175_L	0.608	0.32
82_S	125_N	0.604	0.31
121_Q	129_S	0.604	0.31
6_G	11_G	0.604	0.31
161_G	164_A	0.604	0.31
95_L	157_A	0.603	0.31
32_K	36_P	0.602	0.31
113_S	119_L	0.597	0.31
9_S	118_G	0.596	0.31
111_A	116_A	0.592	0.31
106_N	170_V	0.587	0.30
32_K	175_L	0.581	0.30
69_V	83_L	0.573	0.29
62_A	158_G	0.572	0.29
133_A	136_T	0.571	0.29
124_K	162_L	0.571	0.29
15_G	62_A	0.569	0.29
67_K	71_G	0.566	0.29
65_S	70_G	0.565	0.29
4_G	34_T	0.565	0.29
1_I	104_V	0.563	0.29
23_L	128_S	0.561	0.28
113_S	116_A	0.561	0.28
115_V	160_V	0.555	0.28
65_S	127_L	0.555	0.28
70_G	150_T	0.552	0.28
4_G	7_Q	0.550	0.28
162_L	168_F	0.549	0.28
163_V	170_V	0.544	0.27
24_Q	140_H	0.542	0.27
105_L	161_G	0.542	0.27
16_S	42_T	0.538	0.27
74_K	150_T	0.536	0.27
48_H	149_A	0.535	0.27
165_I	172_R	0.530	0.26
86_S	89_G	0.530	0.26
24_Q	126_L	0.529	0.26
104_V	108_S	0.526	0.26
91_K	96_L	0.522	0.26
131_S	135_T	0.520	0.26
54_V	77_G	0.516	0.25
14_T	29_S	0.515	0.25
18_Y	22_G	0.514	0.25
41_M	56_K	0.512	0.25
27_A	70_G	0.512	0.25
59_K	150_T	0.511	0.25
141_K	173_K	0.510	0.25
2_V	107_A	0.508	0.25
68_T	163_V	0.508	0.25
8_I	82_S	0.506	0.25
18_Y	156_A	0.503	0.25
60_M	63_K	0.503	0.25
73_G	136_T	0.502	0.24
52_R	152_D	0.501	0.24
31_K	38_E	0.500	0.24

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
3b5nC	1	0.1829	3.8	0.94	Contact Map
1un8A	2	0.6114	2.3	0.946	Contact Map
3pnlB	1	0.6971	2.2	0.946	Contact Map
2k6oA	1	0.2114	1.6	0.951	Contact Map
2p58B	1	0.2171	1.3	0.953	Contact Map
2cx0A	1	0.4171	1.3	0.953	Contact Map
2i88A	1	0.28	1.2	0.955	Contact Map
2ca5A	1	0.3829	1.1	0.955	Contact Map
1n7sC	1	0.2457	1.1	0.956	Contact Map
1l4aC	1	0.2286	1.1	0.956	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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