DUF1996 - PFAM28P - GREMLIN Contacts

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DUF1996 - Domain of unknown function (DUF1996)

PFAM:	PF09362	Sequences: DPIVFPGQPASHLHTFFGNTSTNAFSTYASLRAAGCTTCRGPGDRSAYWVPALYDKAGNGTVEPVGGATVYYKRRPKVTAFPPGLRMIAGDAKATTPQPANAAVSWSCGGGGTRDTATIPTTANCGSGLRAHVTFPSCWDGKNLDSPDHKSHMAYPSGGDGGGACPASHPVAIPQLFYEVRYPVPGFGSPFVLSSGDPTGYTAHADFFNGW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	211 (207)
Sequences:	3269 (2317)
Seq/√Len:	161.1
META:	0.628

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_D	143_N	7.924	1.00
148_D	151_S	5.832	1.00
145_D	149_H	4.433	1.00
89_A	155_Y	3.917	1.00
13_L	52_A	3.399	1.00
137_S	156_P	3.262	1.00
153_M	173_I	3.046	1.00
131_A	203_A	2.684	1.00
79_T	171_V	2.426	1.00
21_S	35_G	2.358	1.00
178_Y	205_A	2.354	1.00
5_F	8_Q	2.341	1.00
15_T	52_A	2.332	1.00
16_F	22_T	2.281	1.00
81_F	173_I	2.259	1.00
87_M	153_M	2.189	1.00
86_R	145_D	2.150	1.00
27_T	30_S	2.082	1.00
108_C	125_C	2.022	1.00
2_P	16_F	2.018	1.00
133_V	205_A	2.009	1.00
85_L	153_M	1.983	1.00
195_S	202_T	1.981	1.00
5_F	10_A	1.956	1.00
146_S	149_H	1.931	1.00
28_Y	32_R	1.898	1.00
28_Y	208_F	1.853	1.00
62_V	65_V	1.848	1.00
31_L	210_G	1.846	1.00
192_V	195_S	1.843	1.00
17_F	50_V	1.822	1.00
89_A	135_F	1.808	1.00
9_P	24_A	1.798	1.00
26_S	30_S	1.758	1.00
81_F	85_L	1.734	1.00
21_S	30_S	1.723	1.00
191_F	196_G	1.713	1.00
146_S	152_H	1.713	1.00
191_F	195_S	1.707	1.00
31_L	47_A	1.666	1.00
13_L	54_Y	1.645	1.00
22_T	47_A	1.625	1.00
134_T	175_Q	1.604	1.00
50_V	180_V	1.577	1.00
106_W	193_L	1.565	1.00
192_V	197_D	1.544	1.00
193_L	196_G	1.522	1.00
134_T	177_F	1.521	1.00
116_T	119_I	1.489	1.00
130_R	181_R	1.427	1.00
36_C	39_C	1.383	1.00
107_S	132_H	1.380	1.00
197_D	202_T	1.376	1.00
9_P	25_F	1.375	1.00
84_G	144_L	1.371	1.00
87_M	135_F	1.363	1.00
105_S	132_H	1.355	1.00
188_G	191_F	1.339	1.00
98_Q	101_N	1.335	1.00
50_V	182_Y	1.316	1.00
20_T	35_G	1.304	1.00
91_D	150_K	1.297	1.00
20_T	38_T	1.290	1.00
73_K	175_Q	1.289	1.00
55_D	59_N	1.280	1.00
22_T	26_S	1.264	1.00
17_F	70_V	1.263	1.00
86_R	149_H	1.248	1.00
5_F	11_S	1.243	1.00
26_S	31_L	1.218	1.00
138_C	165_C	1.177	1.00
89_A	133_V	1.152	1.00
50_V	205_A	1.142	1.00
44_D	207_F	1.141	1.00
191_F	194_S	1.116	1.00
145_D	150_K	1.112	1.00
55_D	61_T	1.107	1.00
192_V	196_G	1.105	1.00
139_W	142_K	1.096	1.00
98_Q	103_A	1.077	0.99
28_Y	83_P	1.077	0.99
86_R	208_F	1.071	0.99
32_R	83_P	1.060	0.99
11_S	24_A	1.058	0.99
145_D	148_D	1.048	0.99
136_P	155_Y	1.045	0.99
135_F	205_A	1.041	0.99
19_N	26_S	1.027	0.99
20_T	36_C	1.027	0.99
29_A	33_A	1.018	0.99
190_P	195_S	1.016	0.99
14_H	206_D	1.009	0.99
139_W	171_V	1.005	0.99
70_V	178_Y	0.993	0.99
26_S	47_A	0.985	0.99
19_N	34_A	0.968	0.99
189_S	192_V	0.966	0.99
19_N	35_G	0.961	0.99
19_N	22_T	0.954	0.99
139_W	173_I	0.953	0.99
183_P	186_G	0.937	0.98
83_P	210_G	0.932	0.98
61_T	64_P	0.932	0.98
107_S	130_R	0.919	0.98
3_I	208_F	0.919	0.98
190_P	193_L	0.918	0.98
191_F	197_D	0.898	0.98
154_A	169_H	0.896	0.98
81_F	176_L	0.895	0.98
75_R	175_Q	0.895	0.98
5_F	88_I	0.893	0.98
27_T	31_L	0.891	0.98
109_G	181_R	0.883	0.98
146_S	150_K	0.881	0.98
100_A	103_A	0.879	0.98
49_W	206_D	0.879	0.98
14_H	204_H	0.879	0.98
131_A	193_L	0.878	0.98
4_V	12_H	0.871	0.98
3_I	206_D	0.869	0.98
146_S	151_S	0.867	0.97
21_S	31_L	0.863	0.97
164_A	167_A	0.862	0.97
193_L	197_D	0.862	0.97
50_V	203_A	0.862	0.97
105_S	115_D	0.861	0.97
8_Q	11_S	0.857	0.97
17_F	68_A	0.856	0.97
46_S	210_G	0.851	0.97
94_A	98_Q	0.846	0.97
166_P	169_H	0.841	0.97
197_D	200_G	0.839	0.97
194_S	197_D	0.838	0.97
19_N	30_S	0.838	0.97
118_T	121_T	0.837	0.97
106_W	131_A	0.830	0.97
45_R	210_G	0.827	0.97
70_V	176_L	0.827	0.97
4_V	149_H	0.822	0.97
139_W	143_N	0.818	0.96
136_P	153_M	0.809	0.96
199_T	202_T	0.801	0.96
3_I	88_I	0.800	0.96
26_S	210_G	0.798	0.96
28_Y	31_L	0.793	0.96
149_H	152_H	0.786	0.96
132_H	177_F	0.785	0.96
49_W	71_Y	0.783	0.95
7_G	25_F	0.778	0.95
32_R	210_G	0.771	0.95
157_S	162_G	0.769	0.95
143_N	146_S	0.766	0.95
17_F	180_V	0.763	0.95
34_A	45_R	0.760	0.95
104_V	203_A	0.756	0.95
15_T	50_V	0.755	0.94
196_G	200_G	0.753	0.94
133_V	203_A	0.751	0.94
21_S	26_S	0.742	0.94
44_D	176_L	0.738	0.94
120_P	125_C	0.733	0.94
190_P	194_S	0.732	0.94
156_P	161_G	0.730	0.93
193_L	203_A	0.727	0.93
92_A	202_T	0.723	0.93
130_R	179_E	0.718	0.93
109_G	128_G	0.714	0.93
9_P	13_L	0.713	0.93
140_D	144_L	0.701	0.92
154_A	168_S	0.699	0.92
75_R	137_S	0.697	0.92
55_D	184_V	0.695	0.92
75_R	172_A	0.689	0.91
108_C	165_C	0.689	0.91
21_S	33_A	0.687	0.91
74_R	78_V	0.684	0.91
32_R	45_R	0.683	0.91
157_S	161_G	0.682	0.91
157_S	160_D	0.682	0.91
189_S	194_S	0.681	0.91
108_C	138_C	0.675	0.90
36_C	61_T	0.673	0.90
117_A	121_T	0.672	0.90
196_G	199_T	0.671	0.90
112_G	127_S	0.667	0.90
148_D	152_H	0.663	0.90
156_P	160_D	0.663	0.90
119_I	125_C	0.660	0.89
144_L	149_H	0.657	0.89
67_G	181_R	0.657	0.89
68_A	180_V	0.655	0.89
23_N	35_G	0.654	0.89
46_S	208_F	0.653	0.89
69_T	178_Y	0.645	0.88
29_A	32_R	0.642	0.88
36_C	45_R	0.641	0.88
27_T	32_R	0.639	0.88
96_T	99_P	0.639	0.88
14_H	18_G	0.638	0.88
31_L	208_F	0.635	0.88
83_P	209_N	0.633	0.87
74_R	172_A	0.632	0.87
105_S	134_T	0.632	0.87
116_T	121_T	0.629	0.87
29_A	83_P	0.629	0.87
140_D	171_V	0.628	0.87
14_H	49_W	0.627	0.87
96_T	101_N	0.625	0.87
12_H	206_D	0.624	0.87
16_F	26_S	0.623	0.87
35_G	45_R	0.622	0.87
19_N	47_A	0.622	0.87
184_V	191_F	0.619	0.86
69_T	181_R	0.618	0.86
16_F	19_N	0.617	0.86
96_T	100_A	0.616	0.86
66_G	69_T	0.616	0.86
25_F	29_A	0.608	0.85
21_S	34_A	0.606	0.85
58_G	61_T	0.603	0.85
161_G	164_A	0.602	0.85
114_R	117_A	0.601	0.85
98_Q	102_A	0.600	0.85
46_S	209_N	0.598	0.84
118_T	201_Y	0.597	0.84
28_Y	210_G	0.597	0.84
128_G	181_R	0.597	0.84
49_W	84_G	0.595	0.84
137_S	155_Y	0.592	0.84
53_L	182_Y	0.587	0.83
19_N	210_G	0.587	0.83
143_N	171_V	0.586	0.83
159_G	162_G	0.585	0.83
44_D	48_Y	0.584	0.83
23_N	26_S	0.583	0.83
94_A	201_Y	0.582	0.83
89_A	205_A	0.581	0.83
166_P	170_P	0.580	0.82
36_C	42_P	0.579	0.82
107_S	111_G	0.578	0.82
95_T	199_T	0.577	0.82
137_S	175_Q	0.576	0.82
134_T	137_S	0.571	0.82
111_G	127_S	0.571	0.82
152_H	169_H	0.570	0.81
92_A	150_K	0.569	0.81
16_F	47_A	0.562	0.80
78_V	172_A	0.562	0.80
107_S	180_V	0.561	0.80
190_P	196_G	0.558	0.80
55_D	190_P	0.557	0.80
8_Q	147_P	0.556	0.80
187_F	190_P	0.554	0.80
172_A	175_Q	0.554	0.80
135_F	176_L	0.553	0.79
132_H	181_R	0.552	0.79
37_T	44_D	0.550	0.79
60_G	63_E	0.550	0.79
30_S	33_A	0.550	0.79
97_P	100_A	0.549	0.79
75_R	109_G	0.548	0.79
94_A	101_N	0.547	0.79
119_I	122_T	0.546	0.79
156_P	175_Q	0.542	0.78
7_G	29_A	0.541	0.78
138_C	166_P	0.538	0.78
96_T	201_Y	0.536	0.77
107_S	179_E	0.535	0.77
176_L	179_E	0.534	0.77
141_G	152_H	0.533	0.77
118_T	122_T	0.533	0.77
141_G	144_L	0.533	0.77
145_D	152_H	0.531	0.77
91_D	94_A	0.530	0.77
198_P	201_Y	0.528	0.76
72_Y	211_W	0.528	0.76
47_A	208_F	0.527	0.76
79_T	172_A	0.526	0.76
88_I	206_D	0.523	0.76
113_T	116_T	0.521	0.75
54_Y	61_T	0.519	0.75
52_A	194_S	0.516	0.75
195_S	198_P	0.516	0.75
68_A	178_Y	0.515	0.74
140_D	170_P	0.515	0.74
52_A	176_L	0.515	0.74
26_S	45_R	0.514	0.74
153_M	169_H	0.514	0.74
154_A	166_P	0.511	0.74
188_G	194_S	0.510	0.74
70_V	74_R	0.510	0.74
206_D	211_W	0.507	0.73
119_I	200_G	0.507	0.73
184_V	187_F	0.507	0.73
207_F	210_G	0.506	0.73
87_M	136_P	0.505	0.73
12_H	18_G	0.504	0.73
20_T	40_R	0.503	0.73
61_T	65_V	0.502	0.73
53_L	106_W	0.502	0.73
30_S	47_A	0.502	0.73
66_G	183_P	0.502	0.73
192_V	198_P	0.502	0.73
160_D	163_G	0.501	0.72
95_T	197_D	0.501	0.72
144_L	171_V	0.501	0.72
22_T	25_F	0.500	0.72
149_H	154_A	0.500	0.72
40_R	43_G	0.500	0.72
128_G	132_H	0.500	0.72

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
2x3mA	1	0.0474	2.5	0.971	Contact Map
2mioA	1	0.2322	2	0.972	Contact Map
4zf5A	1	0.2227	1.7	0.973	Contact Map
3lazA	2	0.1517	1.3	0.975	Contact Map
1negA	1	0.1706	1.2	0.975	Contact Map
3wmqA	4	0.3507	1.2	0.976	Contact Map
3n75A	4	0.2512	1.1	0.976	Contact Map
1jo8A	1	0.1659	1	0.977	Contact Map
2qp2A	1	0.4502	1	0.977	Contact Map
1q1lA	4	0.2654	1	0.977	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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