DUF512 - PFAM28P - GREMLIN Contacts

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DUF512 - Protein of unknown function (DUF512)

PFAM:	PF04459	Sequences: VPVGLTRYREGLPPLRPVTPEEARAVIDQVERWQKRFRKELGTRFVYAADEFYLLAGRPLPPAEHYEDFPQLENGVGMVRLFLDEFEEALRRLPRRVTIVTGTLAAPVLRPLLERLNNKIPGLDVRVVPVENDFFGETVTVAGLLTGQDIIAALKGKDLGDRLLLPDVMLRNGEGVFLDDMTLEDLERALGVPVRVVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	198 (197)
Sequences:	6954 (5255)
Seq/√Len:	374.4
META:	0.903

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_A	69_F	3.005	1.00
38_R	44_R	2.716	1.00
98_T	128_V	2.698	1.00
28_D	58_R	2.519	1.00
16_R	22_E	2.518	1.00
19_T	22_E	2.428	1.00
43_T	67_E	2.324	1.00
133_D	152_A	2.323	1.00
63_A	84_D	2.312	1.00
24_R	58_R	2.274	1.00
44_R	67_E	2.213	1.00
20_P	57_G	2.201	1.00
134_F	146_T	2.120	1.00
106_A	129_P	2.078	1.00
131_E	137_E	2.055	1.00
130_V	153_A	2.042	1.00
96_R	124_D	2.041	1.00
96_R	126_R	1.984	1.00
170_L	177_F	1.929	1.00
103_T	131_E	1.901	1.00
87_E	115_R	1.871	1.00
151_I	181_M	1.870	1.00
36_R	40_E	1.832	1.00
145_L	169_M	1.820	1.00
27_I	48_A	1.816	1.00
60_L	80_R	1.810	1.00
110_R	114_E	1.798	1.00
47_Y	67_E	1.782	1.00
30_V	48_A	1.746	1.00
53_Y	65_H	1.720	1.00
151_I	186_L	1.716	1.00
103_T	129_P	1.688	1.00
133_D	137_E	1.674	1.00
98_T	160_G	1.670	1.00
106_A	110_R	1.670	1.00
18_V	22_E	1.645	1.00
113_L	127_V	1.640	1.00
100_V	150_I	1.628	1.00
31_E	58_R	1.586	1.00
60_L	79_V	1.584	1.00
142_A	168_V	1.575	1.00
79_V	108_V	1.567	1.00
147_G	181_M	1.550	1.00
96_R	161_D	1.544	1.00
162_R	195_R	1.522	1.00
80_R	83_L	1.493	1.00
150_I	169_M	1.484	1.00
101_T	142_A	1.480	1.00
23_A	55_L	1.469	1.00
177_F	186_L	1.466	1.00
169_M	177_F	1.466	1.00
181_M	185_D	1.415	1.00
105_A	109_L	1.414	1.00
25_A	29_Q	1.391	1.00
9_R	12_L	1.375	1.00
71_Q	74_N	1.375	1.00
151_I	189_A	1.370	1.00
86_F	112_L	1.366	1.00
29_Q	33_W	1.337	1.00
24_R	28_D	1.334	1.00
126_R	157_K	1.334	1.00
148_Q	152_A	1.330	1.00
170_L	183_L	1.321	1.00
7_R	137_E	1.320	1.00
187_E	193_P	1.319	1.00
17_P	138_T	1.313	1.00
20_P	24_R	1.310	1.00
26_V	52_F	1.305	1.00
34_Q	65_H	1.298	1.00
80_R	84_D	1.287	1.00
78_M	168_V	1.280	1.00
63_A	80_R	1.277	1.00
142_A	166_P	1.264	1.00
41_L	45_F	1.260	1.00
171_R	174_E	1.236	1.00
185_D	188_R	1.231	1.00
83_L	111_P	1.228	1.00
155_K	189_A	1.185	1.00
164_L	197_V	1.183	1.00
72_L	81_L	1.181	1.00
171_R	176_V	1.174	1.00
79_V	105_A	1.168	1.00
175_G	184_E	1.168	1.00
105_A	142_A	1.166	1.00
165_L	196_V	1.161	1.00
146_T	178_L	1.160	1.00
101_T	105_A	1.158	1.00
69_F	80_R	1.153	1.00
95_R	162_R	1.141	1.00
33_W	37_F	1.137	1.00
131_E	153_A	1.128	1.00
135_F	146_T	1.127	1.00
114_E	117_N	1.123	1.00
103_T	137_E	1.123	1.00
62_P	65_H	1.119	1.00
183_L	187_E	1.119	1.00
96_R	158_D	1.104	1.00
97_V	162_R	1.101	1.00
48_A	52_F	1.100	1.00
27_I	58_R	1.100	1.00
128_V	157_K	1.089	1.00
54_L	108_V	1.079	1.00
18_V	52_F	1.069	1.00
86_F	116_L	1.060	1.00
104_L	140_T	1.054	1.00
83_L	108_V	1.044	1.00
26_V	29_Q	1.044	1.00
34_Q	44_R	1.044	1.00
163_L	192_V	1.042	1.00
133_D	153_A	1.042	1.00
113_L	117_N	1.031	1.00
31_E	65_H	1.029	1.00
81_L	85_E	1.029	1.00
97_V	125_V	1.023	1.00
132_N	135_F	1.022	1.00
44_R	65_H	1.017	1.00
137_E	140_T	1.016	1.00
182_T	185_D	1.015	1.00
100_V	163_L	1.014	1.00
22_E	26_V	1.011	1.00
72_L	78_M	1.006	1.00
33_W	36_R	0.999	1.00
183_L	196_V	0.981	1.00
98_T	159_L	0.972	1.00
82_F	112_L	0.969	1.00
162_R	193_P	0.965	1.00
186_L	194_V	0.958	1.00
31_E	34_Q	0.957	1.00
185_D	189_A	0.955	1.00
171_R	175_G	0.946	1.00
37_F	46_V	0.942	1.00
108_V	111_P	0.932	1.00
27_I	31_E	0.923	1.00
82_F	105_A	0.909	1.00
184_E	188_R	0.905	1.00
21_E	24_R	0.901	1.00
31_E	53_Y	0.896	1.00
151_I	155_K	0.880	1.00
83_L	87_E	0.873	1.00
22_E	25_A	0.871	1.00
176_V	180_D	0.868	1.00
105_A	108_V	0.867	1.00
83_L	112_L	0.864	1.00
38_R	67_E	0.855	1.00
54_L	79_V	0.849	1.00
33_W	46_V	0.847	1.00
3_V	15_L	0.840	1.00
98_T	126_R	0.834	1.00
90_L	115_R	0.831	1.00
170_L	196_V	0.824	1.00
95_R	161_D	0.819	1.00
176_V	182_T	0.813	1.00
86_F	90_L	0.805	1.00
31_E	35_K	0.800	1.00
100_V	130_V	0.791	1.00
184_E	187_E	0.789	1.00
18_V	26_V	0.786	1.00
163_L	190_L	0.785	1.00
48_A	53_Y	0.783	1.00
29_Q	32_R	0.779	1.00
172_N	175_G	0.778	1.00
165_L	170_L	0.761	1.00
99_I	164_L	0.759	1.00
57_G	107_P	0.759	1.00
55_L	58_R	0.756	1.00
21_E	25_A	0.745	1.00
69_F	84_D	0.744	1.00
100_V	154_L	0.742	1.00
109_L	127_V	0.730	1.00
128_V	163_L	0.727	1.00
79_V	83_L	0.725	1.00
188_R	191_G	0.721	1.00
24_R	56_A	0.720	1.00
86_F	115_R	0.714	1.00
175_G	183_L	0.713	1.00
150_I	186_L	0.707	0.99
47_Y	70_P	0.707	0.99
88_E	92_R	0.705	0.99
173_G	176_V	0.701	0.99
37_F	45_F	0.698	0.99
113_L	125_V	0.698	0.99
9_R	14_P	0.696	0.99
120_I	123_L	0.693	0.99
102_G	129_P	0.690	0.99
98_T	163_L	0.688	0.99
98_T	161_D	0.688	0.99
49_A	52_F	0.686	0.99
128_V	153_A	0.681	0.99
129_P	145_L	0.681	0.99
165_L	169_M	0.680	0.99
130_V	145_L	0.679	0.99
103_T	140_T	0.676	0.99
27_I	56_A	0.673	0.99
112_L	115_R	0.671	0.99
37_F	41_L	0.666	0.99
25_A	28_D	0.664	0.99
35_K	39_K	0.664	0.99
117_N	124_D	0.661	0.99
43_T	47_Y	0.660	0.99
32_R	36_R	0.660	0.99
7_R	133_D	0.659	0.99
44_R	47_Y	0.656	0.99
54_L	104_L	0.651	0.99
107_P	111_P	0.649	0.99
69_F	72_L	0.649	0.99
48_A	65_H	0.648	0.99
34_Q	38_R	0.648	0.99
89_A	93_L	0.648	0.99
84_D	87_E	0.643	0.99
114_E	118_N	0.639	0.99
134_F	148_Q	0.637	0.99
97_V	123_L	0.633	0.99
170_L	175_G	0.630	0.99
47_Y	74_N	0.628	0.99
100_V	166_P	0.624	0.99
93_L	120_I	0.623	0.99
5_L	15_L	0.623	0.99
26_V	30_V	0.622	0.99
54_L	60_L	0.620	0.99
107_P	110_R	0.619	0.99
145_L	153_A	0.613	0.99
49_A	76_V	0.611	0.99
154_L	159_L	0.610	0.99
165_L	177_F	0.609	0.98
145_L	150_I	0.608	0.98
97_V	164_L	0.607	0.98
99_I	113_L	0.605	0.98
116_L	123_L	0.600	0.98
152_A	155_K	0.599	0.98
106_A	127_V	0.591	0.98
16_R	19_T	0.588	0.98
175_G	182_T	0.588	0.98
102_G	105_A	0.588	0.98
55_L	104_L	0.585	0.98
64_E	88_E	0.584	0.98
103_T	106_A	0.583	0.98
172_N	176_V	0.582	0.98
84_D	88_E	0.579	0.98
117_N	123_L	0.575	0.98
111_P	115_R	0.571	0.98
117_N	120_I	0.571	0.98
186_L	190_L	0.571	0.98
88_E	91_R	0.571	0.98
94_P	124_D	0.569	0.98
94_P	120_I	0.568	0.98
30_V	34_Q	0.568	0.98
94_P	122_G	0.566	0.98
5_L	138_T	0.566	0.98
85_E	89_A	0.565	0.98
63_A	68_D	0.564	0.98
142_A	169_M	0.563	0.98
86_F	89_A	0.560	0.97
7_R	138_T	0.556	0.97
34_Q	48_A	0.550	0.97
17_P	22_E	0.550	0.97
10_E	13_P	0.549	0.97
145_L	166_P	0.545	0.97
23_A	26_V	0.541	0.97
38_R	41_L	0.541	0.97
95_R	123_L	0.540	0.97
126_R	161_D	0.539	0.97
35_K	65_H	0.539	0.97
153_A	156_G	0.539	0.97
115_R	118_N	0.533	0.97
49_A	104_L	0.533	0.97
175_G	187_E	0.527	0.96
89_A	92_R	0.527	0.96
163_L	194_V	0.526	0.96
60_L	65_H	0.526	0.96
26_V	33_W	0.525	0.96
111_P	114_E	0.524	0.96
157_K	163_L	0.524	0.96
73_E	78_M	0.524	0.96
85_E	88_E	0.523	0.96
9_R	15_L	0.522	0.96
23_A	56_A	0.522	0.96
151_I	190_L	0.520	0.96
154_L	163_L	0.518	0.96
34_Q	46_V	0.517	0.96
110_R	129_P	0.517	0.96
148_Q	189_A	0.516	0.96
94_P	121_P	0.516	0.96
181_M	186_L	0.516	0.96
5_L	17_P	0.515	0.96
115_R	119_K	0.514	0.96
90_L	93_L	0.513	0.96
38_R	43_T	0.510	0.96
59_P	62_P	0.508	0.95
3_V	18_V	0.508	0.95
72_L	139_V	0.507	0.95
15_L	18_V	0.506	0.95
147_G	177_F	0.505	0.95
35_K	62_P	0.501	0.95
90_L	120_I	0.501	0.95
100_V	142_A	0.501	0.95
159_L	192_V	0.500	0.95

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
2qu7A	2	0.4293	38.1	0.951	Contact Map
3cs3A	2	0.4242	34.2	0.952	Contact Map
3c3kA	2	0.4394	31.8	0.953	Contact Map
1dbqA	2	0.4394	28.6	0.954	Contact Map
3cijA	1	0.4394	25.4	0.955	Contact Map
3cfxA	1	0.4444	25	0.955	Contact Map
3egcA	2	0.4444	24.6	0.955	Contact Map
3o8oB	1	0.4899	23.7	0.956	Contact Map
1atgA	1	0.4242	23.1	0.956	Contact Map
3clkA	2	0.4141	20.4	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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