DUF3347 - PFAM28P - GREMLIN Contacts

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DUF3347 - Protein of unknown function (DUF3347)

PFAM:	PF11827	Sequences: TIDAACQLQGKKSMMNPEGGKTMTGHEHHDMMGDSSEMAMKESEAFKAQLKAVLDAYLALKDALVADDAKKAAKAAKALLAALKKVDMSLLKGDAHKVWMKILEDLKEHAEHIAKSKDIEHQREHFEMLSEDLYDLVKAFGTDGKTLYYQFCPMANNNKGAYWLSEEKEIKNPYFGSKMLTCGEVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	186 (180)
Sequences:	4278 (3539)
Seq/√Len:	263.8
META:	0.829

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
151_F	162_Y	4.545	1.00
96_H	100_M	3.500	1.00
88_M	96_H	3.487	1.00
68_D	71_K	3.406	1.00
134_Y	149_Y	3.259	1.00
88_M	100_M	3.252	1.00
150_Q	185_V	3.016	1.00
127_E	156_N	2.709	1.00
64_L	72_A	2.675	1.00
69_A	122_Q	2.386	1.00
150_Q	170_I	2.378	1.00
56_A	82_A	2.250	1.00
65_V	180_L	2.207	1.00
67_D	119_I	2.201	1.00
58_L	147_L	2.178	1.00
171_K	181_T	2.166	1.00
61_K	126_F	2.156	1.00
67_D	177_S	2.048	1.00
79_L	110_A	2.040	1.00
84_K	107_K	2.018	1.00
112_H	121_H	1.974	1.00
127_E	161_A	1.941	1.00
46_F	49_Q	1.933	1.00
118_D	121_H	1.933	1.00
26_H	29_H	1.913	1.00
149_Y	162_Y	1.886	1.00
56_A	59_A	1.885	1.00
175_F	180_L	1.857	1.00
54_L	58_L	1.766	1.00
154_M	179_M	1.663	1.00
59_A	75_A	1.655	1.00
53_V	86_V	1.637	1.00
127_E	155_A	1.630	1.00
109_H	132_D	1.541	1.00
112_H	115_K	1.497	1.00
87_D	90_L	1.469	1.00
76_A	113_I	1.460	1.00
81_A	85_K	1.456	1.00
62_D	166_E	1.456	1.00
134_Y	138_K	1.443	1.00
83_L	106_L	1.433	1.00
171_K	180_L	1.406	1.00
150_Q	165_S	1.363	1.00
92_K	95_A	1.354	1.00
56_A	78_A	1.341	1.00
6_C	10_G	1.331	1.00
98_V	139_A	1.324	1.00
127_E	159_K	1.319	1.00
69_A	116_S	1.317	1.00
60_L	75_A	1.299	1.00
158_N	175_F	1.281	1.00
108_E	112_H	1.272	1.00
105_D	132_D	1.270	1.00
71_K	74_K	1.231	1.00
60_L	64_L	1.227	1.00
109_H	125_H	1.226	1.00
112_H	125_H	1.208	1.00
121_H	124_E	1.196	1.00
7_Q	15_M	1.188	1.00
156_N	159_K	1.176	1.00
80_L	111_E	1.175	1.00
58_L	166_E	1.164	1.00
127_E	131_E	1.155	1.00
106_L	129_L	1.152	1.00
7_Q	14_M	1.130	1.00
54_L	147_L	1.126	1.00
151_F	160_G	1.125	1.00
80_L	114_A	1.124	1.00
61_K	165_S	1.122	1.00
8_L	14_M	1.101	1.00
78_A	81_A	1.090	1.00
134_Y	162_Y	1.086	1.00
71_K	75_A	1.071	1.00
61_K	150_Q	1.069	1.00
8_L	13_S	1.060	1.00
152_C	182_C	1.059	1.00
73_A	122_Q	1.054	1.00
147_L	164_L	1.051	1.00
75_A	78_A	1.042	1.00
6_C	15_M	1.039	1.00
11_K	14_M	1.038	1.00
61_K	65_V	1.034	1.00
46_F	50_L	1.033	1.00
17_P	20_G	1.030	1.00
70_K	73_A	1.027	1.00
58_L	61_K	1.020	1.00
25_G	29_H	1.009	1.00
42_E	45_A	0.998	1.00
60_L	79_L	0.991	1.00
47_K	50_L	0.991	1.00
121_H	125_H	0.978	1.00
69_A	118_D	0.967	1.00
98_V	102_I	0.966	1.00
116_S	121_H	0.957	1.00
6_C	14_M	0.951	1.00
131_E	135_D	0.950	1.00
77_K	81_A	0.949	1.00
80_L	110_A	0.947	1.00
25_G	28_H	0.936	1.00
12_K	15_M	0.930	1.00
53_V	83_L	0.928	1.00
8_L	15_M	0.927	1.00
133_L	136_L	0.926	1.00
23_M	26_H	0.920	1.00
13_S	16_N	0.913	1.00
7_Q	13_S	0.911	1.00
35_S	38_M	0.909	1.00
103_L	107_K	0.905	1.00
21_K	24_T	0.904	1.00
46_F	91_L	0.902	1.00
86_V	99_W	0.900	1.00
10_G	14_M	0.893	1.00
19_G	25_G	0.889	1.00
28_H	31_M	0.885	1.00
59_A	78_A	0.884	1.00
111_E	115_K	0.882	1.00
80_L	84_K	0.881	1.00
20_G	23_M	0.875	1.00
169_E	181_T	0.875	1.00
12_K	17_P	0.872	1.00
170_I	185_V	0.868	1.00
132_D	135_D	0.867	1.00
9_Q	12_K	0.867	1.00
7_Q	10_G	0.865	1.00
20_G	25_G	0.850	1.00
155_A	161_A	0.849	1.00
63_A	71_K	0.842	0.99
165_S	170_I	0.837	0.99
55_D	59_A	0.830	0.99
77_K	114_A	0.826	0.99
10_G	13_S	0.819	0.99
27_E	31_M	0.817	0.99
69_A	119_I	0.817	0.99
50_L	136_L	0.813	0.99
6_C	9_Q	0.809	0.99
99_W	103_L	0.806	0.99
153_P	179_M	0.806	0.99
102_I	105_D	0.804	0.99
31_M	34_D	0.803	0.99
109_H	128_M	0.797	0.99
161_A	174_Y	0.790	0.99
113_I	122_Q	0.789	0.99
80_L	107_K	0.789	0.99
54_L	137_V	0.786	0.99
155_A	174_Y	0.784	0.99
29_H	32_M	0.766	0.99
34_D	37_E	0.761	0.99
160_G	175_F	0.757	0.99
33_G	38_M	0.749	0.99
7_Q	11_K	0.747	0.99
67_D	180_L	0.744	0.99
107_K	111_E	0.744	0.99
59_A	71_K	0.743	0.99
120_E	178_K	0.742	0.99
151_F	155_A	0.738	0.99
178_K	181_T	0.731	0.99
49_Q	52_A	0.730	0.99
65_V	165_S	0.720	0.98
14_M	17_P	0.715	0.98
53_V	79_L	0.715	0.98
62_D	65_V	0.710	0.98
56_A	75_A	0.708	0.98
22_T	25_G	0.701	0.98
170_I	183_G	0.700	0.98
53_V	133_L	0.699	0.98
88_M	103_L	0.695	0.98
79_L	129_L	0.693	0.98
64_L	67_D	0.692	0.98
27_E	30_D	0.691	0.98
12_K	16_N	0.691	0.98
8_L	11_K	0.687	0.98
69_A	73_A	0.685	0.98
19_G	22_T	0.684	0.98
30_D	33_G	0.680	0.98
16_N	21_K	0.678	0.98
13_S	17_P	0.676	0.98
12_K	18_E	0.673	0.97
8_L	12_K	0.672	0.97
63_A	72_A	0.661	0.97
6_C	16_N	0.658	0.97
8_L	16_N	0.656	0.97
32_M	36_S	0.651	0.97
113_I	129_L	0.651	0.97
20_G	24_T	0.651	0.97
29_H	33_G	0.650	0.97
151_F	184_E	0.648	0.97
24_T	27_E	0.648	0.97
112_H	116_S	0.644	0.97
97_K	101_K	0.643	0.97
137_V	164_L	0.643	0.97
176_G	179_M	0.635	0.96
74_K	78_A	0.634	0.96
26_H	30_D	0.632	0.96
110_A	114_A	0.631	0.96
17_P	22_T	0.629	0.96
142_T	147_L	0.628	0.96
104_E	108_E	0.625	0.96
119_I	123_R	0.624	0.96
155_A	160_G	0.622	0.96
149_Y	185_V	0.621	0.96
17_P	21_K	0.614	0.96
37_E	40_M	0.611	0.96
137_V	142_T	0.608	0.95
91_L	99_W	0.607	0.95
93_G	97_K	0.606	0.95
67_D	72_A	0.604	0.95
79_L	106_L	0.603	0.95
148_Y	165_S	0.598	0.95
36_S	40_M	0.595	0.95
167_E	171_K	0.594	0.95
165_S	185_V	0.593	0.95
63_A	75_A	0.593	0.95
130_S	134_Y	0.591	0.95
72_A	122_Q	0.590	0.95
22_T	26_H	0.588	0.95
19_G	24_T	0.586	0.94
67_D	123_R	0.582	0.94
18_E	21_K	0.578	0.94
19_G	29_H	0.577	0.94
154_M	180_L	0.577	0.94
19_G	26_H	0.576	0.94
111_E	114_A	0.571	0.94
91_L	95_A	0.571	0.94
86_V	91_L	0.565	0.93
11_K	15_M	0.561	0.93
77_K	80_L	0.560	0.93
34_D	38_M	0.560	0.93
126_F	130_S	0.557	0.93
60_L	113_I	0.557	0.93
78_A	82_A	0.556	0.93
150_Q	167_E	0.555	0.93
32_M	40_M	0.555	0.93
19_G	28_H	0.554	0.93
120_E	124_E	0.551	0.92
134_Y	137_V	0.550	0.92
16_N	19_G	0.550	0.92
9_Q	15_M	0.549	0.92
12_K	19_G	0.549	0.92
7_Q	12_K	0.546	0.92
96_H	99_W	0.542	0.92
47_K	51_K	0.541	0.92
19_G	23_M	0.541	0.92
14_M	20_G	0.535	0.91
18_E	22_T	0.534	0.91
17_P	25_G	0.533	0.91
109_H	112_H	0.532	0.91
60_L	76_A	0.531	0.91
33_G	36_S	0.528	0.91
38_M	41_K	0.522	0.90
176_G	180_L	0.522	0.90
99_W	140_F	0.522	0.90
156_N	160_G	0.521	0.90
108_E	125_H	0.520	0.90
102_I	135_D	0.517	0.90
28_H	32_M	0.517	0.90
93_G	96_H	0.515	0.90
74_K	77_K	0.514	0.90
57_Y	61_K	0.513	0.90
175_F	178_K	0.510	0.89
23_M	27_E	0.510	0.89
106_L	109_H	0.510	0.89
27_E	33_G	0.509	0.89
132_D	136_L	0.508	0.89
9_Q	13_S	0.508	0.89
105_D	109_H	0.507	0.89
51_K	55_D	0.506	0.89
125_H	128_M	0.502	0.89
67_D	176_G	0.501	0.88
76_A	122_Q	0.500	0.88
22_T	30_D	0.500	0.88

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
1j7nA	2	0.9462	31.4	0.936	Contact Map
1xfxA	1	0.9086	18.1	0.943	Contact Map
1y6dA	1	0.5591	15.8	0.944	Contact Map
4h8sA	2	0.5323	15.8	0.944	Contact Map
1sr2A	1	0.6237	12.6	0.947	Contact Map
3iqtA	1	0.6129	11.1	0.948	Contact Map
4l8tA	1	0.4247	11	0.948	Contact Map
1s05A	1	0.5699	6.9	0.952	Contact Map
3l6aA	1	0.7043	6.4	0.953	Contact Map
4jeaA	4	0.5054	6	0.954	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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