DUF3090 - PFAM28P - GREMLIN Contacts

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DUF3090 - Protein of unknown function (DUF3090)

PFAM:	PF11290	Sequences: YEFDPPDRFTAGTVGEPGQRTFYLQARQGGRVVSVALEKQQVAALAERLEELLDELARRGGAEVPAAAPDPLEDDMPLEEPVEPEFRVGTLGLGYDEDRDRVVLEAQELVEEEEDEEEDPDDDPEGPDVLRVRLTRAQARAFARRAAEVVAAGRPPCPLCGQPLDPEGHFC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	171 (168)
Sequences:	4792 (3042)
Seq/√Len:	234.7
META:	0.925

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_D	136_R	3.797	1.00
35_V	88_V	3.539	1.00
134_L	139_A	3.419	1.00
16_E	19_Q	3.205	1.00
3_F	33_V	3.088	1.00
36_A	87_R	3.020	1.00
11_A	42_V	2.941	1.00
21_T	36_A	2.936	1.00
91_L	106_A	2.787	1.00
27_R	79_E	2.705	1.00
42_V	146_A	2.654	1.00
8_R	79_E	2.614	1.00
108_E	128_D	2.196	1.00
156_P	164_L	2.178	1.00
40_Q	43_A	2.068	1.00
37_L	42_V	2.061	1.00
89_G	109_L	2.044	1.00
28_Q	31_R	2.036	1.00
26_A	132_V	2.005	1.00
27_R	32_V	1.973	1.00
9_F	142_F	1.961	1.00
49_L	139_A	1.952	1.00
35_V	130_L	1.930	1.00
4_D	99_R	1.902	1.00
88_V	106_A	1.877	1.00
50_E	147_A	1.868	1.00
94_G	103_V	1.864	1.00
7_D	28_Q	1.863	1.00
135_T	138_Q	1.827	1.00
9_F	134_L	1.821	1.00
143_A	147_A	1.709	1.00
78_L	82_V	1.677	1.00
110_V	127_P	1.625	1.00
142_F	146_A	1.581	1.00
165_D	168_G	1.517	1.00
115_D	118_E	1.485	1.00
157_C	160_C	1.473	1.00
46_A	146_A	1.464	1.00
102_V	139_A	1.461	1.00
11_A	146_A	1.454	1.00
95_Y	100_D	1.454	1.00
2_E	131_R	1.441	1.00
90_T	107_Q	1.420	1.00
78_L	81_P	1.408	1.00
47_E	147_A	1.387	1.00
6_P	9_F	1.370	1.00
43_A	150_V	1.362	1.00
10_T	76_M	1.356	1.00
6_P	28_Q	1.308	1.00
92_G	107_Q	1.306	1.00
49_L	143_A	1.295	1.00
52_L	102_V	1.256	1.00
92_G	131_R	1.256	1.00
144_R	147_A	1.238	1.00
95_Y	136_R	1.230	1.00
18_G	39_K	1.214	1.00
36_A	84_P	1.209	1.00
37_L	88_V	1.198	1.00
50_E	143_A	1.189	1.00
5_P	101_R	1.177	1.00
107_Q	129_V	1.174	1.00
23_Y	36_A	1.152	1.00
24_L	142_F	1.122	1.00
99_R	133_R	1.105	1.00
7_D	29_G	1.054	1.00
33_V	130_L	1.052	1.00
119_D	122_D	1.044	1.00
145_R	149_V	1.036	1.00
96_D	99_R	1.033	1.00
149_V	152_A	1.033	1.00
72_L	75_D	1.027	1.00
74_D	77_P	1.010	1.00
26_A	35_V	1.009	1.00
55_E	59_R	1.008	1.00
5_P	28_Q	0.996	1.00
80_E	83_E	0.988	1.00
159_L	170_F	0.975	1.00
54_D	140_R	0.969	1.00
85_E	130_L	0.965	1.00
6_P	132_V	0.963	1.00
49_L	134_L	0.960	1.00
24_L	106_A	0.945	1.00
23_Y	82_V	0.943	1.00
7_D	27_R	0.943	1.00
25_Q	34_S	0.941	1.00
18_G	22_F	0.931	1.00
13_T	42_V	0.926	1.00
35_V	106_A	0.918	1.00
26_A	130_L	0.903	1.00
89_G	108_E	0.903	1.00
49_L	102_V	0.901	1.00
13_T	16_E	0.898	0.99
62_A	65_P	0.891	0.99
164_L	167_E	0.880	0.99
40_Q	107_Q	0.878	0.99
44_A	48_R	0.876	0.99
12_G	23_Y	0.871	0.99
40_Q	44_A	0.868	0.99
158_P	161_G	0.859	0.99
31_R	85_E	0.859	0.99
46_A	150_V	0.857	0.99
19_Q	167_E	0.856	0.99
119_D	127_P	0.849	0.99
119_D	126_G	0.846	0.99
55_E	58_R	0.840	0.99
147_A	151_A	0.837	0.99
11_A	142_F	0.835	0.99
63_E	66_A	0.831	0.99
53_L	136_R	0.830	0.99
12_G	25_Q	0.830	0.99
122_D	126_G	0.830	0.99
32_V	79_E	0.826	0.99
60_G	63_E	0.821	0.99
50_E	144_R	0.817	0.99
77_P	145_R	0.809	0.99
101_R	135_T	0.809	0.99
73_E	144_R	0.796	0.99
45_L	91_L	0.787	0.99
114_E	118_E	0.785	0.99
21_T	87_R	0.779	0.99
162_Q	170_F	0.777	0.99
15_G	18_G	0.777	0.99
57_A	60_G	0.777	0.99
86_F	130_L	0.774	0.99
23_Y	84_P	0.774	0.99
166_P	169_H	0.773	0.98
110_V	113_E	0.769	0.98
57_A	66_A	0.761	0.98
12_G	77_P	0.755	0.98
26_A	33_V	0.752	0.98
48_R	93_L	0.751	0.98
84_P	87_R	0.747	0.98
124_P	127_P	0.745	0.98
25_Q	81_P	0.742	0.98
105_E	131_R	0.740	0.98
15_G	20_R	0.739	0.98
56_L	95_Y	0.737	0.98
33_V	132_V	0.736	0.98
61_G	65_P	0.736	0.98
94_G	107_Q	0.730	0.98
143_A	150_V	0.730	0.98
48_R	51_E	0.729	0.98
42_V	150_V	0.725	0.98
4_D	133_R	0.723	0.98
74_D	145_R	0.721	0.98
39_K	153_G	0.719	0.98
78_L	132_V	0.718	0.98
6_P	138_Q	0.716	0.98
158_P	164_L	0.715	0.98
10_T	25_Q	0.711	0.97
115_D	119_D	0.709	0.97
148_E	151_A	0.707	0.97
69_P	72_L	0.702	0.97
32_V	82_V	0.701	0.97
34_S	82_V	0.698	0.97
139_A	142_F	0.697	0.97
23_Y	81_P	0.696	0.97
14_V	23_Y	0.691	0.97
58_R	61_G	0.689	0.97
10_T	145_R	0.683	0.97
40_Q	48_R	0.682	0.97
144_R	148_E	0.678	0.97
35_V	85_E	0.675	0.96
85_E	159_L	0.673	0.96
25_Q	32_V	0.673	0.96
97_E	100_D	0.672	0.96
17_P	20_R	0.671	0.96
103_V	133_R	0.667	0.96
44_A	47_E	0.665	0.96
159_L	164_L	0.662	0.96
164_L	168_G	0.660	0.96
34_S	84_P	0.657	0.96
44_A	51_E	0.655	0.96
37_L	142_F	0.653	0.96
118_E	123_D	0.652	0.96
93_L	140_R	0.649	0.96
46_A	147_A	0.646	0.95
9_F	146_A	0.646	0.95
65_P	68_A	0.644	0.95
156_P	159_L	0.644	0.95
101_R	133_R	0.640	0.95
8_R	27_R	0.637	0.95
147_A	152_A	0.636	0.95
63_E	144_R	0.634	0.95
134_L	138_Q	0.634	0.95
17_P	169_H	0.633	0.95
39_K	154_R	0.627	0.95
110_V	114_E	0.626	0.95
43_A	47_E	0.620	0.94
139_A	143_A	0.619	0.94
62_A	66_A	0.614	0.94
94_G	133_R	0.609	0.94
161_G	170_F	0.609	0.94
15_G	22_F	0.608	0.94
91_L	107_Q	0.604	0.94
13_T	21_T	0.599	0.93
71_P	137_A	0.597	0.93
119_D	123_D	0.595	0.93
9_F	132_V	0.593	0.93
81_P	84_P	0.590	0.93
47_E	51_E	0.589	0.93
121_D	126_G	0.587	0.93
3_F	6_P	0.586	0.93
111_E	125_E	0.586	0.93
25_Q	78_L	0.585	0.92
79_E	82_V	0.582	0.92
112_E	118_E	0.582	0.92
48_R	90_T	0.580	0.92
80_E	85_E	0.579	0.92
156_P	161_G	0.579	0.92
158_P	170_F	0.577	0.92
4_D	28_Q	0.575	0.92
138_Q	141_A	0.572	0.92
3_F	26_A	0.567	0.91
3_F	28_Q	0.567	0.91
17_P	22_F	0.567	0.91
108_E	127_P	0.563	0.91
7_D	30_G	0.559	0.91
41_Q	92_G	0.556	0.90
92_G	105_E	0.554	0.90
24_L	37_L	0.551	0.90
115_D	121_D	0.550	0.90
65_P	69_P	0.544	0.90
113_E	123_D	0.544	0.90
18_G	153_G	0.543	0.89
112_E	126_G	0.542	0.89
38_E	154_R	0.540	0.89
33_V	85_E	0.540	0.89
35_V	132_V	0.538	0.89
52_L	93_L	0.534	0.89
38_E	153_G	0.533	0.89
160_C	171_C	0.533	0.89
133_R	148_E	0.529	0.88
73_E	76_M	0.526	0.88
41_Q	91_L	0.524	0.88
50_E	140_R	0.524	0.88
123_D	126_G	0.520	0.87
150_V	153_G	0.519	0.87
70_D	144_R	0.519	0.87
11_A	149_V	0.518	0.87
93_L	159_L	0.518	0.87
75_D	78_L	0.512	0.87
86_F	128_D	0.511	0.86
53_L	140_R	0.508	0.86
46_A	50_E	0.508	0.86
21_T	84_P	0.507	0.86
120_P	123_D	0.507	0.86
156_P	162_Q	0.506	0.86
14_V	21_T	0.506	0.86
88_V	105_E	0.502	0.85
6_P	134_L	0.501	0.85
14_V	82_V	0.500	0.85

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
2r6fA	2	0.6667	45.7	0.933	Contact Map
1l8dA	2	0.3743	40.3	0.935	Contact Map
3zqjA	1	0.6784	38.2	0.936	Contact Map
3m86A	4	0.3216	19.8	0.944	Contact Map
4h9dA	3	0.3041	17.8	0.945	Contact Map
3pihA	2	0.6257	16.6	0.946	Contact Map
2h7wA	1	0.3216	16	0.946	Contact Map
2e1vA	1	0.2982	15.4	0.947	Contact Map
4gxbA	1	0.345	15.4	0.947	Contact Map
2c34A	1	0.3333	15.2	0.947	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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