DUF1109 - PFAM28P - GREMLIN Contacts

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DUF1109 - Protein of unknown function (DUF1109)

PFAM:	PF06532	Sequences: LAADLRPVRPLAPPRRRALLLAGALAALALVLAALGLRPDLAAALATPRFWLKLALTLALAVAAAAAALRLARPGRSLRRRWLLLALPALLLWLAALGELLAAPPAGWAALLLGHSWRVCLLLILLLSLPPLAALLWALRRGAPTRPALAGAAAGLAAGALGATAYALHCPEDSPLFVLVWHGLAIALVAALGALLGRRLLRW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	203 (201)
Sequences:	7298 (5784)
Seq/√Len:	408.0
META:	0.899

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_S	189_V	3.453	1.00
177_F	182_H	3.418	1.00
151_G	193_G	3.073	1.00
135_L	154_A	2.622	1.00
152_A	190_A	2.428	1.00
148_A	198_R	2.400	1.00
139_L	154_A	2.390	1.00
156_L	190_A	2.340	1.00
148_A	194_A	2.300	1.00
196_L	200_L	2.240	1.00
11_L	14_P	2.238	1.00
22_A	26_A	2.225	1.00
72_A	142_G	2.221	1.00
146_R	149_L	2.108	1.00
197_G	201_L	2.108	1.00
65_A	157_A	2.106	1.00
90_L	93_W	2.103	1.00
2_A	5_L	1.966	1.00
57_T	164_T	1.939	1.00
112_L	180_V	1.863	1.00
22_A	29_A	1.835	1.00
170_C	177_F	1.835	1.00
65_A	69_L	1.798	1.00
71_L	150_A	1.780	1.00
135_L	157_A	1.768	1.00
61_A	161_L	1.764	1.00
125_L	189_V	1.722	1.00
155_G	159_G	1.703	1.00
159_G	186_I	1.696	1.00
119_V	169_H	1.628	1.00
73_R	76_R	1.617	1.00
86_A	90_L	1.600	1.00
55_A	59_A	1.598	1.00
44_A	47_T	1.560	1.00
8_V	11_L	1.560	1.00
54_L	57_T	1.555	1.00
12_A	16_R	1.552	1.00
112_L	116_S	1.543	1.00
88_P	92_L	1.530	1.00
37_L	41_L	1.502	1.00
104_P	107_G	1.476	1.00
166_Y	182_H	1.451	1.00
14_P	17_R	1.419	1.00
53_K	57_T	1.418	1.00
53_K	182_H	1.404	1.00
71_L	74_P	1.382	1.00
42_A	45_L	1.365	1.00
130_P	134_A	1.358	1.00
74_P	77_S	1.342	1.00
54_L	167_A	1.340	1.00
131_P	162_G	1.339	1.00
40_D	44_A	1.335	1.00
191_A	194_A	1.334	1.00
124_I	166_Y	1.330	1.00
80_R	83_L	1.324	1.00
104_P	108_W	1.318	1.00
72_A	139_L	1.316	1.00
191_A	195_L	1.313	1.00
20_L	24_A	1.308	1.00
24_A	27_A	1.297	1.00
71_L	153_A	1.289	1.00
26_A	29_A	1.281	1.00
62_V	65_A	1.280	1.00
11_L	17_R	1.278	1.00
108_W	111_L	1.270	1.00
38_R	41_L	1.267	1.00
13_P	16_R	1.263	1.00
131_P	165_A	1.258	1.00
132_L	136_L	1.258	1.00
13_P	17_R	1.243	1.00
28_L	31_V	1.234	1.00
69_L	73_R	1.232	1.00
106_A	109_A	1.200	1.00
86_A	93_W	1.181	1.00
109_A	113_L	1.180	1.00
187_A	191_A	1.174	1.00
152_A	194_A	1.172	1.00
45_L	48_P	1.171	1.00
166_Y	169_H	1.168	1.00
12_A	18_A	1.157	1.00
151_G	155_G	1.150	1.00
93_W	97_L	1.144	1.00
62_V	66_A	1.135	1.00
129_L	133_A	1.134	1.00
22_A	25_L	1.132	1.00
21_L	25_L	1.130	1.00
120_C	170_C	1.130	1.00
75_G	145_T	1.127	1.00
95_A	99_E	1.122	1.00
108_W	112_L	1.116	1.00
98_G	102_A	1.115	1.00
158_A	162_G	1.113	1.00
132_L	189_V	1.112	1.00
177_F	185_A	1.105	1.00
20_L	27_A	1.102	1.00
43_A	46_A	1.096	1.00
54_L	164_T	1.094	1.00
121_L	125_L	1.092	1.00
164_T	168_L	1.090	1.00
26_A	30_L	1.074	1.00
114_G	117_W	1.073	1.00
137_W	141_R	1.069	1.00
147_P	198_R	1.067	1.00
15_R	18_A	1.062	1.00
144_P	150_A	1.049	1.00
58_L	164_T	1.042	1.00
178_V	181_W	1.028	1.00
16_R	19_L	1.027	1.00
113_L	116_S	1.023	1.00
166_Y	177_F	1.020	1.00
172_E	177_F	1.018	1.00
70_R	76_R	1.017	1.00
91_L	95_A	1.015	1.00
110_A	114_G	1.011	1.00
130_P	133_A	1.007	1.00
107_G	111_L	0.989	1.00
19_L	22_A	0.982	1.00
66_A	70_R	0.981	1.00
111_L	115_H	0.979	1.00
82_W	86_A	0.977	1.00
68_A	139_L	0.974	1.00
131_P	161_L	0.967	1.00
137_W	140_R	0.961	1.00
105_P	108_W	0.956	1.00
194_A	198_R	0.954	1.00
132_L	193_G	0.953	1.00
198_R	202_R	0.932	1.00
92_L	96_A	0.930	1.00
5_L	8_V	0.929	1.00
105_P	109_A	0.918	1.00
113_L	117_W	0.916	1.00
160_A	164_T	0.915	1.00
57_T	163_A	0.911	1.00
60_L	63_A	0.910	1.00
56_L	183_G	0.910	1.00
67_A	153_A	0.905	1.00
107_G	112_L	0.891	1.00
103_A	107_G	0.887	1.00
22_A	34_A	0.887	1.00
100_L	108_W	0.884	1.00
9_R	12_A	0.873	1.00
64_A	160_A	0.872	1.00
10_P	13_P	0.868	1.00
163_A	167_A	0.861	1.00
132_L	158_A	0.858	1.00
186_I	189_V	0.857	1.00
124_I	162_G	0.854	1.00
121_L	188_L	0.850	1.00
53_K	56_L	0.838	1.00
123_L	169_H	0.838	1.00
12_A	17_R	0.837	1.00
70_R	75_G	0.834	1.00
38_R	44_A	0.833	1.00
91_L	94_L	0.828	1.00
192_L	196_L	0.827	1.00
23_G	26_A	0.826	1.00
52_L	56_L	0.825	1.00
120_C	182_H	0.820	1.00
57_T	64_A	0.812	1.00
100_L	103_A	0.811	1.00
154_A	158_A	0.810	1.00
111_L	116_S	0.809	1.00
136_L	200_L	0.809	1.00
172_E	185_A	0.803	1.00
103_A	111_L	0.802	1.00
123_L	126_L	0.796	1.00
68_A	157_A	0.794	1.00
40_D	43_A	0.794	1.00
14_P	18_A	0.794	1.00
119_V	123_L	0.793	1.00
24_A	28_L	0.792	1.00
43_A	47_T	0.789	1.00
167_A	173_D	0.786	1.00
111_L	114_G	0.785	1.00
60_L	160_A	0.783	1.00
77_S	80_R	0.782	1.00
41_L	45_L	0.776	1.00
78_L	82_W	0.774	1.00
127_L	162_G	0.767	1.00
85_L	95_A	0.751	1.00
29_A	33_A	0.749	1.00
68_A	72_A	0.749	1.00
48_P	51_W	0.748	1.00
21_L	24_A	0.746	1.00
124_I	163_A	0.743	1.00
121_L	124_I	0.741	1.00
88_P	95_A	0.741	1.00
12_A	15_R	0.738	1.00
177_F	181_W	0.736	1.00
107_G	110_A	0.735	1.00
84_L	88_P	0.735	1.00
45_L	49_R	0.731	1.00
32_L	37_L	0.728	1.00
182_H	185_A	0.728	1.00
190_A	193_G	0.726	1.00
77_S	81_R	0.725	1.00
184_L	187_A	0.723	1.00
42_A	46_A	0.722	1.00
155_G	193_G	0.721	1.00
167_A	178_V	0.721	1.00
72_A	77_S	0.720	1.00
64_A	68_A	0.717	1.00
167_A	182_H	0.713	1.00
57_T	60_L	0.712	1.00
31_V	165_A	0.710	1.00
139_L	150_A	0.698	1.00
180_V	183_G	0.698	1.00
33_A	37_L	0.697	1.00
11_L	15_R	0.694	1.00
93_W	99_E	0.693	1.00
85_L	89_A	0.689	1.00
14_P	19_L	0.688	1.00
53_K	167_A	0.687	1.00
94_L	98_G	0.683	1.00
23_G	27_A	0.679	1.00
72_A	76_R	0.677	0.99
109_A	112_L	0.674	0.99
31_V	34_A	0.670	0.99
114_G	118_R	0.668	0.99
16_R	141_R	0.667	0.99
164_T	167_A	0.665	0.99
85_L	92_L	0.663	0.99
186_I	190_A	0.656	0.99
124_I	185_A	0.656	0.99
124_I	189_V	0.648	0.99
22_A	27_A	0.645	0.99
70_R	77_S	0.644	0.99
75_G	78_L	0.641	0.99
94_L	97_L	0.641	0.99
116_S	172_E	0.639	0.99
99_E	108_W	0.639	0.99
60_L	186_I	0.639	0.99
53_K	166_Y	0.638	0.99
31_V	35_L	0.638	0.99
39_P	44_A	0.636	0.99
151_G	197_G	0.635	0.99
55_A	58_L	0.624	0.99
169_H	172_E	0.623	0.99
63_A	66_A	0.620	0.99
159_G	193_G	0.618	0.99
49_R	52_L	0.618	0.99
88_P	96_A	0.614	0.99
118_R	122_L	0.606	0.99
41_L	50_F	0.606	0.99
64_A	156_L	0.605	0.99
108_W	116_S	0.605	0.99
88_P	91_L	0.602	0.99
35_L	123_L	0.598	0.99
184_L	188_L	0.596	0.99
71_L	75_G	0.592	0.99
25_L	28_L	0.592	0.99
122_L	126_L	0.591	0.99
126_L	130_P	0.590	0.99
184_L	191_A	0.590	0.99
150_A	154_A	0.590	0.99
174_S	177_F	0.590	0.99
72_A	75_G	0.589	0.99
59_A	63_A	0.585	0.99
95_A	98_G	0.585	0.99
110_A	113_L	0.580	0.98
166_Y	170_C	0.573	0.98
185_A	189_V	0.572	0.98
143_A	181_W	0.571	0.98
121_L	181_W	0.570	0.98
52_L	55_A	0.566	0.98
13_P	18_A	0.562	0.98
48_P	52_L	0.560	0.98
81_R	88_P	0.559	0.98
104_P	112_L	0.557	0.98
5_L	10_P	0.557	0.98
21_L	27_A	0.557	0.98
45_L	50_F	0.555	0.98
2_A	6_R	0.554	0.98
37_L	42_A	0.554	0.98
99_E	102_A	0.552	0.98
170_C	182_H	0.547	0.98
21_L	32_L	0.547	0.98
147_P	150_A	0.546	0.98
170_C	175_P	0.543	0.98
139_L	142_G	0.539	0.98
91_L	97_L	0.537	0.97
78_L	81_R	0.536	0.97
133_A	155_G	0.530	0.97
90_L	94_L	0.528	0.97
37_L	44_A	0.527	0.97
149_L	152_A	0.526	0.97
90_L	103_A	0.524	0.97
153_A	157_A	0.524	0.97
71_L	76_R	0.520	0.97
83_L	87_L	0.519	0.97
50_F	53_K	0.517	0.97
181_W	184_L	0.514	0.97
98_G	101_L	0.510	0.97
124_I	128_S	0.510	0.97
129_L	162_G	0.509	0.97
11_L	19_L	0.506	0.96
10_P	14_P	0.504	0.96
104_P	116_S	0.502	0.96
50_F	58_L	0.502	0.96
15_R	19_L	0.501	0.96
112_L	115_H	0.500	0.96
123_L	127_L	0.500	0.96

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
1u7gA	3	0.9655	6	0.934	Contact Map
2b2hA	3	0.9606	3.9	0.94	Contact Map
4djkA	2	0.9606	2	0.948	Contact Map
4zw9A	1	0.8966	2	0.949	Contact Map
3orgA	2	0.3153	1.7	0.95	Contact Map
2wswA	3	0.3448	1.5	0.952	Contact Map
2ls4A	1	0.1084	1.5	0.952	Contact Map
1iijA	1	0.1724	1.4	0.953	Contact Map
4pypA	1	0.8818	1.4	0.953	Contact Map
3l1lA	2	0.931	1.3	0.953	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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