DUF3164 - PFAM28P - GREMLIN Contacts

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DUF3164 - Protein of unknown function (DUF3164)

PFAM:	PF11363	Sequences: YMKDAKGRLVPEELVKPIDKLRDELVREIVAKAKELSEQLARFKAHAFDDIAAFVELSAEEYGVKLGGKKGNVTLTSFDGRYKVQVAVADRITFDERLQAAKALIDECLNEWSEGARPELRALVNDAFQVDKEGNINTSRVLGLRRLEIDDERWQEAMEAIRDSIQVVGSKTYIRFYERDEDGKYQPIPLDIAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	194 (193)
Sequences:	2085 (1643)
Seq/√Len:	118.3
META:	0.771

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_D	8_R	4.919	1.00
34_K	178_E	4.690	1.00
111_E	153_R	4.019	1.00
145_R	162_R	3.825	1.00
32_K	46_H	3.375	1.00
107_E	153_R	3.173	1.00
102_K	106_D	2.981	1.00
108_C	112_W	2.727	1.00
180_D	183_G	2.549	1.00
30_V	188_I	2.348	1.00
36_L	40_L	2.145	1.00
156_E	159_E	2.066	1.00
178_E	186_Q	2.029	1.00
23_D	27_R	2.002	1.00
2_M	12_E	1.987	1.00
180_D	186_Q	1.912	1.00
29_I	176_F	1.845	1.00
36_L	39_Q	1.821	1.00
2_M	20_K	1.813	1.00
104_L	156_E	1.813	1.00
29_I	47_A	1.813	1.00
21_L	24_E	1.784	1.00
76_T	83_K	1.773	1.00
103_A	107_E	1.758	1.00
159_E	163_D	1.755	1.00
2_M	15_V	1.752	1.00
77_S	81_R	1.726	1.00
83_K	177_Y	1.720	1.00
35_E	39_Q	1.687	1.00
62_Y	163_D	1.656	1.00
33_A	176_F	1.655	1.00
22_R	96_E	1.654	1.00
15_V	20_K	1.637	1.00
70_K	90_D	1.626	1.00
13_E	118_P	1.598	1.00
136_I	141_V	1.590	1.00
33_A	43_F	1.536	1.00
36_L	43_F	1.491	1.00
19_D	22_R	1.484	1.00
111_E	151_D	1.473	1.00
27_R	82_Y	1.440	1.00
1_Y	9_L	1.433	1.00
126_D	146_R	1.422	1.00
49_D	53_A	1.413	1.00
109_L	123_L	1.407	1.00
83_K	185_Y	1.400	1.00
38_E	42_R	1.399	1.00
140_R	143_G	1.396	1.00
152_E	156_E	1.387	1.00
37_S	41_A	1.383	1.00
131_D	135_N	1.373	1.00
28_E	50_D	1.371	1.00
30_V	176_F	1.370	1.00
150_D	155_Q	1.354	1.00
85_Q	177_Y	1.342	1.00
12_E	20_K	1.335	1.00
81_R	178_E	1.333	1.00
8_R	14_L	1.321	1.00
177_Y	187_P	1.311	1.00
107_E	111_E	1.307	1.00
104_L	153_R	1.302	1.00
137_N	140_R	1.298	1.00
88_V	170_S	1.297	1.00
30_V	82_Y	1.289	1.00
87_A	175_R	1.263	0.99
155_Q	159_E	1.246	0.99
57_L	60_E	1.235	0.99
52_A	56_E	1.233	0.99
112_W	117_R	1.212	0.99
27_R	77_S	1.204	0.99
109_L	113_S	1.202	0.99
3_K	9_L	1.196	0.99
40_L	190_L	1.187	0.99
55_V	73_V	1.166	0.99
105_I	158_M	1.142	0.99
129_Q	140_R	1.139	0.99
21_L	57_L	1.137	0.99
91_R	171_K	1.121	0.99
179_R	185_Y	1.106	0.99
93_T	168_V	1.103	0.99
40_L	192_I	1.092	0.98
122_A	147_L	1.087	0.98
52_A	172_T	1.082	0.98
120_L	123_L	1.075	0.98
118_P	121_R	1.075	0.98
24_E	60_E	1.071	0.98
5_A	80_G	1.061	0.98
98_L	136_I	1.052	0.98
91_R	170_S	1.049	0.98
126_D	129_Q	1.047	0.98
17_P	61_E	1.044	0.98
51_I	75_L	1.035	0.98
180_D	184_K	1.022	0.98
45_A	49_D	1.018	0.98
11_P	14_L	1.014	0.97
47_A	174_I	1.012	0.97
125_N	130_V	1.002	0.97
37_S	40_L	0.991	0.97
42_R	46_H	0.989	0.97
81_R	185_Y	0.985	0.97
18_I	97_R	0.984	0.97
50_D	53_A	0.982	0.97
41_A	45_A	0.969	0.97
27_R	79_D	0.964	0.97
94_F	98_L	0.964	0.97
58_S	96_E	0.960	0.96
22_R	54_F	0.957	0.96
92_I	165_I	0.956	0.96
16_K	148_E	0.953	0.96
3_K	81_R	0.951	0.96
34_K	38_E	0.947	0.96
12_E	15_V	0.946	0.96
15_V	78_F	0.945	0.96
126_D	147_L	0.936	0.96
126_D	140_R	0.929	0.96
18_I	58_S	0.923	0.96
112_W	119_E	0.905	0.95
100_A	103_A	0.900	0.95
131_D	137_N	0.897	0.95
178_E	188_I	0.878	0.94
26_V	75_L	0.874	0.94
11_P	122_A	0.872	0.94
61_E	97_R	0.871	0.94
18_I	22_R	0.869	0.94
50_D	60_E	0.868	0.94
6_K	90_D	0.864	0.94
30_V	84_V	0.858	0.94
32_K	39_Q	0.855	0.93
129_Q	137_N	0.852	0.93
186_Q	189_P	0.845	0.93
22_R	97_R	0.842	0.93
25_L	29_I	0.840	0.93
142_L	145_R	0.836	0.93
115_G	118_P	0.835	0.93
2_M	27_R	0.832	0.92
82_Y	178_E	0.828	0.92
28_E	32_K	0.819	0.92
105_I	108_C	0.819	0.92
59_A	66_L	0.818	0.92
102_K	130_V	0.817	0.92
121_R	125_N	0.809	0.91
29_I	84_V	0.803	0.91
48_F	172_T	0.798	0.91
17_P	20_K	0.797	0.91
81_R	181_E	0.796	0.91
77_S	80_G	0.792	0.90
85_Q	133_E	0.791	0.90
51_I	86_V	0.791	0.90
21_L	25_L	0.790	0.90
23_D	78_F	0.787	0.90
89_A	170_S	0.781	0.90
8_R	11_P	0.777	0.90
24_E	57_L	0.773	0.89
64_V	103_A	0.771	0.89
127_A	130_V	0.766	0.89
55_V	75_L	0.764	0.89
10_V	78_F	0.760	0.89
53_A	60_E	0.753	0.88
32_K	35_E	0.743	0.87
84_V	176_F	0.743	0.87
154_W	158_M	0.742	0.87
22_R	95_D	0.738	0.87
104_L	160_A	0.735	0.87
38_E	41_A	0.723	0.86
43_F	47_A	0.723	0.86
152_E	155_Q	0.723	0.86
95_D	166_Q	0.720	0.86
109_L	153_R	0.719	0.86
145_R	158_M	0.719	0.86
113_S	120_L	0.718	0.86
58_S	95_D	0.713	0.85
162_R	165_I	0.709	0.85
114_E	117_R	0.708	0.85
86_V	172_T	0.708	0.85
119_E	151_D	0.705	0.85
104_L	108_C	0.696	0.84
142_L	165_I	0.694	0.84
58_S	97_R	0.693	0.84
76_T	185_Y	0.689	0.83
123_L	129_Q	0.684	0.83
28_E	60_E	0.682	0.83
64_V	100_A	0.679	0.82
25_L	51_I	0.678	0.82
17_P	148_E	0.677	0.82
62_Y	95_D	0.677	0.82
112_W	151_D	0.677	0.82
138_T	142_L	0.676	0.82
32_K	50_D	0.676	0.82
77_S	82_Y	0.674	0.82
108_C	119_E	0.673	0.82
48_F	174_I	0.670	0.81
110_N	125_N	0.668	0.81
146_R	166_Q	0.668	0.81
88_V	172_T	0.667	0.81
119_E	149_I	0.666	0.81
46_H	50_D	0.666	0.81
39_Q	46_H	0.662	0.81
42_R	45_A	0.659	0.80
159_E	162_R	0.659	0.80
124_V	127_A	0.659	0.80
189_P	192_I	0.656	0.80
116_A	121_R	0.653	0.80
94_F	141_V	0.643	0.79
129_Q	143_G	0.640	0.78
19_D	164_S	0.637	0.78
54_F	58_S	0.636	0.78
123_L	127_A	0.635	0.78
101_A	161_I	0.629	0.77
55_V	59_A	0.629	0.77
39_Q	42_R	0.628	0.77
132_K	137_N	0.627	0.77
37_S	189_P	0.624	0.77
145_R	165_I	0.624	0.77
2_M	8_R	0.623	0.77
33_A	47_A	0.619	0.76
89_A	173_Y	0.618	0.76
59_A	100_A	0.616	0.76
164_S	168_V	0.615	0.76
10_V	14_L	0.612	0.75
17_P	21_L	0.612	0.75
93_T	165_I	0.611	0.75
91_R	169_G	0.609	0.75
32_K	42_R	0.606	0.75
25_L	53_A	0.599	0.74
68_G	71_G	0.599	0.74
14_L	119_E	0.598	0.74
22_R	66_L	0.598	0.74
2_M	23_D	0.597	0.74
177_Y	185_Y	0.597	0.74
74_T	83_K	0.596	0.73
110_N	121_R	0.592	0.73
28_E	46_H	0.591	0.73
120_L	124_V	0.591	0.73
98_L	102_K	0.590	0.73
31_A	34_K	0.590	0.73
126_D	143_G	0.589	0.73
52_A	86_V	0.587	0.72
22_R	58_S	0.587	0.72
54_F	66_L	0.587	0.72
98_L	138_T	0.584	0.72
35_E	38_E	0.580	0.71
105_I	161_I	0.580	0.71
51_I	73_V	0.576	0.71
182_D	186_Q	0.576	0.71
73_V	86_V	0.575	0.71
100_A	160_A	0.574	0.71
19_D	97_R	0.574	0.71
129_Q	132_K	0.572	0.70
123_L	147_L	0.572	0.70
111_E	114_E	0.572	0.70
86_V	174_I	0.567	0.70
76_T	80_G	0.566	0.70
145_R	161_I	0.563	0.69
4_D	146_R	0.563	0.69
82_Y	176_F	0.561	0.69
98_L	101_A	0.558	0.68
2_M	24_E	0.551	0.68
4_D	10_V	0.551	0.68
25_L	54_F	0.551	0.68
110_N	126_D	0.547	0.67
30_V	178_E	0.547	0.67
105_I	141_V	0.544	0.67
109_L	125_N	0.541	0.66
141_V	161_I	0.540	0.66
2_M	6_K	0.539	0.66
56_E	60_E	0.539	0.66
53_A	61_E	0.535	0.65
22_R	166_Q	0.530	0.65
65_K	107_E	0.529	0.64
105_I	157_A	0.528	0.64
122_A	148_E	0.525	0.64
122_A	125_N	0.525	0.64
32_K	43_F	0.524	0.64
34_K	37_S	0.521	0.63
118_P	150_D	0.518	0.63
41_A	46_H	0.517	0.63
29_I	51_I	0.511	0.62
28_E	61_E	0.511	0.62
18_I	95_D	0.511	0.62
15_V	27_R	0.510	0.62
58_S	100_A	0.510	0.62
109_L	115_G	0.509	0.61
30_V	33_A	0.509	0.61
138_T	141_V	0.505	0.61
1_Y	6_K	0.505	0.61
27_R	31_A	0.503	0.61
143_G	147_L	0.502	0.60
52_A	73_V	0.501	0.60
174_I	192_I	0.500	0.60
16_K	19_D	0.500	0.60

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
2wnyA	1	0.5206	24.4	0.939	Contact Map
4rbnA	3	0.4485	9.9	0.949	Contact Map
1j7nA	2	0.9021	9	0.95	Contact Map
1cl8A	2	0.5	8.7	0.95	Contact Map
1t6sA	4	0.4175	5.4	0.955	Contact Map
2julA	1	0.6289	5	0.956	Contact Map
3zpnA	2	0.2887	4.9	0.956	Contact Map
3o0lA	2	0.2423	4.6	0.956	Contact Map
4d0pA	1	0.8041	4.5	0.957	Contact Map
1pcfA	2	0.201	4.1	0.957	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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