DUF2259 - PFAM28P - GREMLIN Contacts

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DUF2259 - Predicted secreted protein (DUF2259)

PFAM:	PF10016	Sequences: AFEQYGVQDGSGFPYAEIYVVDVATNNFVPGGPIRYTDEGQDGSGARYRLLAKAAPLLERYGIEFLNQGQPLYISLDGDPPPPDGGETIEFRDFESGASYRCELVPTIEGSGQNVRSFRLELTSRDGGGKTYTVHEDKGLPQSRGCPLSYRIKRVLIDPGGSSLIFVIEMKRQGFEGPDIRYMVETLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	188 (187)
Sequences:	1238 (964)
Seq/√Len:	70.5
META:	0.867

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_Q	17_E	7.189	1.00
165_I	186_T	5.175	1.00
138_K	141_P	3.912	1.00
172_R	179_D	3.602	1.00
8_Q	13_F	3.123	1.00
174_G	179_D	3.064	1.00
8_Q	11_S	2.861	1.00
167_V	184_V	2.638	1.00
109_E	143_S	2.500	1.00
153_K	182_Y	2.346	1.00
119_R	136_E	2.342	1.00
3_E	16_A	2.255	1.00
20_V	29_V	2.231	1.00
34_I	54_A	2.166	1.00
4_Q	19_Y	2.165	1.00
141_P	144_R	2.051	1.00
34_I	57_L	2.043	1.00
169_E	180_I	1.906	1.00
7_V	14_P	1.894	1.00
23_V	186_T	1.818	1.00
139_G	142_Q	1.815	1.00
23_V	163_S	1.803	1.00
65_F	71_P	1.768	1.00
174_G	177_G	1.734	1.00
93_D	149_S	1.696	1.00
119_R	133_T	1.692	1.00
17_E	35_R	1.656	0.99
49_R	53_K	1.621	0.99
164_L	186_T	1.619	0.99
58_L	63_I	1.619	0.99
129_G	132_Y	1.618	0.99
118_F	122_L	1.598	0.99
166_F	187_L	1.574	0.99
137_D	140_L	1.554	0.99
170_M	183_M	1.495	0.99
152_I	168_I	1.495	0.99
94_F	136_E	1.492	0.99
159_P	163_S	1.435	0.99
16_A	47_R	1.434	0.99
110_G	116_R	1.433	0.99
14_P	41_Q	1.428	0.98
21_V	184_V	1.424	0.98
19_Y	28_F	1.408	0.98
41_Q	46_A	1.392	0.98
126_D	134_V	1.369	0.98
3_E	47_R	1.365	0.98
134_V	137_D	1.359	0.98
12_G	15_Y	1.354	0.98
108_I	111_S	1.352	0.98
118_F	127_G	1.351	0.98
16_A	43_G	1.337	0.98
34_I	50_L	1.312	0.97
171_K	180_I	1.299	0.97
75_S	78_G	1.296	0.97
133_T	136_E	1.285	0.97
6_G	15_Y	1.283	0.97
102_C	146_C	1.265	0.97
26_N	32_G	1.259	0.97
9_D	12_G	1.257	0.97
18_I	54_A	1.248	0.96
124_S	129_G	1.237	0.96
157_I	164_L	1.232	0.96
158_D	162_S	1.230	0.96
144_R	150_Y	1.208	0.96
166_F	186_T	1.204	0.96
72_L	154_R	1.195	0.95
47_R	51_L	1.182	0.95
16_A	50_L	1.180	0.95
3_E	50_L	1.179	0.95
138_K	142_Q	1.173	0.95
23_V	26_N	1.169	0.95
115_V	148_L	1.167	0.95
111_S	176_E	1.154	0.94
14_P	46_A	1.139	0.94
95_E	116_R	1.129	0.94
169_E	182_Y	1.128	0.94
22_D	25_T	1.122	0.94
10_G	176_E	1.121	0.94
36_Y	50_L	1.097	0.93
137_D	144_R	1.048	0.91
44_S	48_Y	1.035	0.90
120_L	134_V	1.018	0.90
15_Y	181_R	1.008	0.89
129_G	134_V	0.989	0.88
2_F	5_Y	0.982	0.88
183_M	186_T	0.981	0.88
109_E	112_G	0.980	0.88
26_N	33_P	0.966	0.87
91_F	94_F	0.964	0.87
34_I	53_K	0.963	0.87
75_S	79_D	0.954	0.87
10_G	175_F	0.949	0.86
9_D	13_F	0.945	0.86
120_L	125_R	0.943	0.86
76_L	81_P	0.941	0.86
177_G	181_R	0.941	0.86
9_D	175_F	0.940	0.86
118_F	185_E	0.920	0.84
89_I	94_F	0.919	0.84
20_V	28_F	0.916	0.84
180_I	183_M	0.915	0.84
181_R	184_V	0.912	0.84
36_Y	53_K	0.912	0.84
20_V	183_M	0.911	0.84
54_A	58_L	0.911	0.84
14_P	157_I	0.908	0.84
135_H	186_T	0.905	0.83
7_V	12_G	0.903	0.83
117_S	168_I	0.889	0.82
158_D	161_G	0.881	0.82
174_G	178_P	0.878	0.82
8_Q	14_P	0.877	0.82
99_S	103_E	0.876	0.81
170_M	182_Y	0.872	0.81
3_E	8_Q	0.869	0.81
18_I	50_L	0.866	0.81
127_G	131_T	0.862	0.80
149_S	154_R	0.862	0.80
128_G	131_T	0.859	0.80
49_R	52_A	0.858	0.80
55_A	59_E	0.853	0.80
6_G	181_R	0.851	0.80
154_R	157_I	0.846	0.79
11_S	176_E	0.844	0.79
58_L	61_Y	0.843	0.79
12_G	175_F	0.840	0.79
156_L	165_I	0.833	0.78
126_D	130_K	0.827	0.78
118_F	135_H	0.823	0.77
61_Y	179_D	0.821	0.77
72_L	75_S	0.818	0.77
8_Q	12_G	0.817	0.77
108_I	143_S	0.817	0.77
156_L	167_V	0.812	0.76
26_N	117_S	0.810	0.76
48_Y	52_A	0.807	0.76
145_G	173_Q	0.803	0.75
161_G	164_L	0.800	0.75
133_T	137_D	0.796	0.75
26_N	143_S	0.796	0.75
46_A	59_E	0.790	0.74
148_L	178_P	0.788	0.74
71_P	74_I	0.786	0.74
13_F	33_P	0.781	0.73
160_G	163_S	0.779	0.73
109_E	113_Q	0.779	0.73
64_E	69_G	0.776	0.73
28_F	147_P	0.769	0.72
5_Y	31_G	0.766	0.72
3_E	25_T	0.765	0.72
127_G	130_K	0.764	0.72
73_Y	79_D	0.764	0.72
23_V	187_L	0.763	0.72
67_N	79_D	0.759	0.71
41_Q	45_G	0.752	0.71
2_F	6_G	0.735	0.69
10_G	13_F	0.735	0.69
15_Y	35_R	0.734	0.69
81_P	151_R	0.733	0.69
11_S	174_G	0.732	0.68
33_P	36_Y	0.729	0.68
145_G	172_R	0.728	0.68
110_G	114_N	0.725	0.68
108_I	112_G	0.722	0.67
20_V	60_R	0.722	0.67
46_A	66_L	0.721	0.67
64_E	67_N	0.719	0.67
49_R	131_T	0.716	0.67
158_D	169_E	0.716	0.67
66_L	69_G	0.712	0.66
125_R	131_T	0.707	0.66
33_P	54_A	0.703	0.65
4_Q	181_R	0.702	0.65
2_F	21_V	0.690	0.64
25_T	38_D	0.689	0.64
147_P	172_R	0.687	0.64
45_G	48_Y	0.686	0.63
111_S	114_N	0.680	0.63
28_F	33_P	0.679	0.63
121_E	131_T	0.678	0.63
146_C	175_F	0.674	0.62
40_G	44_S	0.672	0.62
118_F	121_E	0.671	0.62
51_L	63_I	0.670	0.62
43_G	46_A	0.665	0.61
74_I	77_D	0.663	0.61
96_S	117_S	0.661	0.61
102_C	166_F	0.659	0.60
79_D	82_P	0.659	0.60
82_P	98_A	0.656	0.60
108_I	173_Q	0.648	0.59
42_D	169_E	0.647	0.59
6_G	141_P	0.646	0.59
16_A	100_Y	0.646	0.59
108_I	176_E	0.645	0.59
85_G	89_I	0.642	0.58
71_P	88_T	0.639	0.58
143_S	146_C	0.638	0.58
22_D	92_R	0.634	0.57
43_G	47_R	0.634	0.57
96_S	115_V	0.630	0.57
6_G	19_Y	0.626	0.56
38_D	41_Q	0.625	0.56
28_F	32_G	0.625	0.56
118_F	124_S	0.623	0.56
15_Y	40_G	0.622	0.56
53_K	113_Q	0.620	0.56
74_I	89_I	0.620	0.56
137_D	141_P	0.618	0.56
92_R	119_R	0.617	0.55
111_S	123_T	0.616	0.55
53_K	122_L	0.615	0.55
42_D	50_L	0.615	0.55
129_G	162_S	0.615	0.55
120_L	127_G	0.613	0.55
141_P	146_C	0.613	0.55
124_S	188_R	0.604	0.54
11_S	146_C	0.603	0.54
28_F	150_Y	0.594	0.53
45_G	99_S	0.593	0.52
5_Y	47_R	0.585	0.52
22_D	26_N	0.582	0.51
140_L	147_P	0.582	0.51
123_T	134_V	0.578	0.51
87_E	90_E	0.578	0.51
122_L	164_L	0.575	0.50
93_D	167_V	0.574	0.50
75_S	81_P	0.573	0.50
84_D	89_I	0.573	0.50
68_Q	74_I	0.572	0.50
115_V	173_Q	0.567	0.49
44_S	57_L	0.566	0.49
155_V	166_F	0.566	0.49
79_D	168_I	0.565	0.49
5_Y	183_M	0.565	0.49
29_V	32_G	0.565	0.49
138_K	159_P	0.563	0.49
113_Q	116_R	0.561	0.49
40_G	46_A	0.559	0.48
36_Y	46_A	0.559	0.48
69_G	73_Y	0.557	0.48
71_P	179_D	0.552	0.48
117_S	147_P	0.549	0.47
19_Y	32_G	0.549	0.47
77_D	80_P	0.546	0.47
102_C	106_P	0.545	0.47
89_I	102_C	0.545	0.47
26_N	135_H	0.544	0.47
57_L	61_Y	0.542	0.46
109_E	116_R	0.541	0.46
63_I	115_V	0.540	0.46
44_S	58_L	0.540	0.46
123_T	130_K	0.539	0.46
36_Y	39_E	0.538	0.46
26_N	36_Y	0.537	0.46
100_Y	147_P	0.535	0.45
42_D	152_I	0.534	0.45
127_G	132_Y	0.531	0.45
110_G	177_G	0.529	0.45
135_H	139_G	0.527	0.44
163_S	188_R	0.525	0.44
35_R	156_L	0.524	0.44
128_G	134_V	0.522	0.44
69_G	93_D	0.519	0.44
146_C	177_G	0.519	0.44
18_I	47_R	0.518	0.43
14_P	179_D	0.514	0.43
48_Y	51_L	0.513	0.43
63_I	90_E	0.513	0.43
50_L	154_R	0.513	0.43
10_G	120_L	0.513	0.43
164_L	187_L	0.511	0.43
115_V	146_C	0.509	0.42
10_G	131_T	0.506	0.42
11_S	175_F	0.505	0.42
8_Q	35_R	0.503	0.42
152_I	164_L	0.502	0.42
56_P	60_R	0.500	0.41
122_L	134_V	0.500	0.41
22_D	28_F	0.500	0.41

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
3odgA	3	0.3245	7.2	0.951	Contact Map
2b94A	4	0.2713	5.1	0.954	Contact Map
1zd0A	1	0.2553	4.6	0.955	Contact Map
4gqcA	4	0.3032	4.4	0.956	Contact Map
4nawD	1	0.0372	4.1	0.956	Contact Map
3fucA	3	0.3351	3.9	0.957	Contact Map
4uc0A	3	0.2819	3.7	0.957	Contact Map
3fq3A	6	0.4894	3.6	0.958	Contact Map
3brcA	4	0.2926	3.2	0.959	Contact Map
1vmkA	3	0.2979	3	0.959	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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