PDCD2_C - PFAM28P - GREMLIN Contacts

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PDCD2_C - Programmed cell death protein 2, C-terminal putative domain

PFAM:	PF04194	Sequences: FPEYEIVVEEEPEEDEVDPDSSEDPDNEEIELSDYEELSEQEEEGADGEDDESEEEELEKYEKSLDKTFQKFKKRIAANPEQVLRYSRGGKPLWISENIPSEESDIPNCSNCGAKRVFEFQLMPQLLNYLEVDSLDWGTLAVYTCSKSCWDSGGVGYVEEFVWVQD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	166 (166)
Sequences:	868 (697)
Seq/√Len:	54.1
META:	0.156

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
114_A	146_S	4.120	1.00
95_I	138_G	3.982	1.00
94_W	141_A	3.477	1.00
145_C	149_C	3.139	1.00
6_I	83_V	3.129	1.00
109_C	112_C	2.956	1.00
140_L	162_V	2.759	1.00
95_I	139_T	2.552	1.00
90_G	118_F	2.478	1.00
31_E	35_Y	2.449	1.00
111_N	158_V	2.416	1.00
109_C	145_C	2.365	1.00
112_C	145_C	2.326	1.00
112_C	149_C	2.228	1.00
82_Q	123_M	2.212	1.00
115_K	146_S	2.191	1.00
109_C	149_C	2.181	1.00
27_N	31_E	2.157	1.00
28_E	31_E	2.116	1.00
72_F	124_P	2.116	1.00
66_D	69_F	2.067	1.00
110_S	159_E	2.031	1.00
75_R	78_A	1.973	1.00
82_Q	85_R	1.927	1.00
88_R	144_T	1.922	1.00
56_E	61_Y	1.916	1.00
84_L	148_S	1.870	0.99
57_E	61_Y	1.861	0.99
58_L	61_Y	1.700	0.99
108_N	115_K	1.668	0.99
113_G	116_R	1.665	0.99
107_P	161_F	1.636	0.98
32_L	35_Y	1.524	0.98
4_Y	8_V	1.522	0.98
114_A	147_K	1.506	0.97
89_G	117_V	1.499	0.97
125_Q	157_Y	1.482	0.97
107_P	116_R	1.463	0.97
120_F	142_V	1.431	0.96
99_I	103_E	1.414	0.96
79_N	94_W	1.328	0.95
87_S	90_G	1.317	0.94
125_Q	128_N	1.298	0.94
125_Q	129_Y	1.283	0.93
96_S	116_R	1.271	0.93
3_E	122_L	1.268	0.93
74_K	90_G	1.259	0.93
123_M	139_T	1.258	0.93
71_K	135_L	1.206	0.91
22_S	25_P	1.198	0.91
95_I	123_M	1.181	0.90
41_Q	44_E	1.173	0.90
37_E	40_E	1.165	0.90
28_E	32_L	1.160	0.89
42_E	45_G	1.155	0.89
116_R	161_F	1.143	0.89
5_E	120_F	1.118	0.88
18_D	21_S	1.112	0.87
127_L	164_V	1.112	0.87
56_E	83_V	1.105	0.87
3_E	9_E	1.098	0.87
20_D	23_E	1.096	0.87
143_Y	161_F	1.095	0.87
72_F	82_Q	1.089	0.86
23_E	27_N	1.086	0.86
11_E	75_R	1.078	0.86
24_D	27_N	1.077	0.86
27_N	30_I	1.077	0.86
76_I	123_M	1.071	0.85
34_D	83_V	1.064	0.85
127_L	140_L	1.058	0.85
96_S	130_L	1.042	0.84
49_E	53_S	1.041	0.84
88_R	148_S	1.030	0.83
59_E	74_K	1.025	0.83
76_I	142_V	0.997	0.81
122_L	140_L	0.987	0.80
17_V	20_D	0.973	0.79
14_E	18_D	0.972	0.79
106_I	161_F	0.971	0.79
27_N	32_L	0.966	0.79
41_Q	46_A	0.965	0.79
54_E	58_L	0.949	0.78
69_F	92_P	0.938	0.77
20_D	24_D	0.937	0.77
158_V	162_V	0.935	0.76
95_I	164_V	0.934	0.76
49_E	52_E	0.918	0.75
29_E	32_L	0.913	0.75
134_S	137_W	0.911	0.75
88_R	95_I	0.901	0.74
87_S	143_Y	0.891	0.73
54_E	61_Y	0.891	0.73
30_I	34_D	0.889	0.73
139_T	159_E	0.888	0.73
70_Q	74_K	0.885	0.72
9_E	96_S	0.882	0.72
130_L	138_G	0.866	0.71
71_K	75_R	0.863	0.71
82_Q	93_L	0.863	0.71
31_E	34_D	0.851	0.69
34_D	39_S	0.848	0.69
67_K	80_P	0.843	0.69
140_L	164_V	0.836	0.68
88_R	136_D	0.836	0.68
57_E	60_K	0.823	0.67
106_I	116_R	0.823	0.67
67_K	73_K	0.822	0.67
71_K	74_K	0.821	0.67
36_E	39_S	0.819	0.66
79_N	127_L	0.811	0.66
147_K	150_W	0.804	0.65
77_A	132_V	0.804	0.65
19_P	27_N	0.795	0.64
69_F	96_S	0.793	0.64
29_E	52_E	0.791	0.64
52_E	135_L	0.791	0.64
127_L	163_W	0.790	0.64
1_F	154_G	0.786	0.63
123_M	137_W	0.785	0.63
69_F	80_P	0.785	0.63
35_Y	38_L	0.783	0.63
85_R	93_L	0.782	0.63
120_F	140_L	0.782	0.63
26_D	30_I	0.777	0.62
8_V	81_E	0.776	0.62
88_R	117_V	0.775	0.62
88_R	127_L	0.775	0.62
84_L	138_G	0.774	0.62
64_S	162_V	0.763	0.61
55_E	61_Y	0.763	0.61
98_N	101_S	0.760	0.61
42_E	51_D	0.759	0.61
72_F	138_G	0.756	0.60
15_D	108_N	0.751	0.60
66_D	95_I	0.749	0.60
86_Y	119_E	0.749	0.60
42_E	49_E	0.748	0.59
73_K	130_L	0.743	0.59
62_E	87_S	0.743	0.59
18_D	22_S	0.742	0.59
59_E	117_V	0.736	0.58
1_F	126_L	0.735	0.58
63_K	130_L	0.734	0.58
126_L	143_Y	0.734	0.58
110_S	116_R	0.729	0.57
106_I	143_Y	0.728	0.57
31_E	36_E	0.728	0.57
93_L	147_K	0.721	0.57
124_P	161_F	0.721	0.57
94_W	127_L	0.718	0.56
160_E	165_Q	0.714	0.56
76_I	82_Q	0.712	0.56
137_W	163_W	0.710	0.55
38_L	44_E	0.709	0.55
127_L	166_D	0.703	0.55
69_F	138_G	0.702	0.55
113_G	149_C	0.701	0.55
135_L	166_D	0.699	0.54
4_Y	17_V	0.698	0.54
83_V	138_G	0.691	0.53
140_L	155_V	0.687	0.53
124_P	135_L	0.686	0.53
100_P	115_K	0.685	0.53
45_G	49_E	0.683	0.53
61_Y	64_S	0.682	0.52
29_E	33_S	0.680	0.52
9_E	13_E	0.676	0.52
69_F	117_V	0.673	0.52
155_V	162_V	0.672	0.51
109_C	113_G	0.667	0.51
18_D	103_E	0.663	0.50
79_N	148_S	0.659	0.50
65_L	127_L	0.658	0.50
101_S	105_D	0.654	0.50
87_S	118_F	0.650	0.49
54_E	57_E	0.643	0.48
126_L	148_S	0.643	0.48
155_V	158_V	0.642	0.48
25_P	29_E	0.641	0.48
95_I	125_Q	0.638	0.48
80_P	94_W	0.638	0.48
87_S	144_T	0.637	0.48
82_Q	106_I	0.636	0.48
95_I	135_L	0.633	0.47
6_I	91_K	0.633	0.47
100_P	105_D	0.626	0.47
113_G	145_C	0.624	0.46
41_Q	45_G	0.624	0.46
144_T	157_Y	0.620	0.46
7_V	95_I	0.618	0.46
88_R	134_S	0.617	0.46
127_L	134_S	0.614	0.45
55_E	71_K	0.613	0.45
42_E	46_A	0.612	0.45
27_N	33_S	0.612	0.45
88_R	125_Q	0.611	0.45
70_Q	73_K	0.609	0.45
136_D	150_W	0.607	0.45
47_D	53_S	0.606	0.44
48_G	55_E	0.606	0.44
98_N	137_W	0.600	0.44
5_E	125_Q	0.599	0.44
85_R	121_Q	0.599	0.44
100_P	114_A	0.597	0.43
22_S	27_N	0.596	0.43
75_R	159_E	0.586	0.42
22_S	26_D	0.578	0.41
43_E	49_E	0.575	0.41
11_E	84_L	0.575	0.41
61_Y	65_L	0.574	0.41
25_P	28_E	0.567	0.40
107_P	124_P	0.564	0.40
29_E	35_Y	0.563	0.40
61_Y	140_L	0.562	0.40
63_K	153_G	0.558	0.39
34_D	37_E	0.555	0.39
85_R	119_E	0.555	0.39
149_C	160_E	0.551	0.39
29_E	76_I	0.551	0.39
84_L	125_Q	0.551	0.39
96_S	118_F	0.550	0.39
64_S	111_N	0.549	0.39
124_P	148_S	0.548	0.38
8_V	95_I	0.542	0.38
44_E	49_E	0.541	0.38
70_Q	129_Y	0.538	0.37
19_P	22_S	0.536	0.37
17_V	21_S	0.536	0.37
25_P	30_I	0.530	0.37
16_E	21_S	0.530	0.37
73_K	79_N	0.524	0.36
11_E	85_R	0.523	0.36
57_E	158_V	0.522	0.36
37_E	45_G	0.518	0.35
62_E	81_E	0.517	0.35
35_Y	39_S	0.516	0.35
59_E	100_P	0.516	0.35
56_E	122_L	0.513	0.35
79_N	157_Y	0.512	0.35
68_T	123_M	0.510	0.35
21_S	24_D	0.510	0.35
59_E	63_K	0.506	0.34
35_Y	44_E	0.503	0.34
139_T	165_Q	0.502	0.34
132_V	135_L	0.502	0.34
63_K	151_D	0.501	0.34
30_I	35_Y	0.501	0.34
69_F	73_K	0.500	0.34

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
1qypA	1	0.3434	43.6	0.931	Contact Map
4e2xA	1	0.3614	32.1	0.936	Contact Map
4rv9A	1	0.3795	28.1	0.938	Contact Map
4h9dA	3	0.5301	19.4	0.943	Contact Map
1tfiA	1	0.3012	18.4	0.943	Contact Map
2f4mA	2	0.6687	15.7	0.945	Contact Map
2k5cA	1	0.3072	11.6	0.948	Contact Map
1pv5A	1	0.6386	10.2	0.949	Contact Map
2dj8A	1	0.3554	9.3	0.95	Contact Map
3o9xA	2	0.3313	8.9	0.95	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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