DUF1990 - PFAM28P - GREMLIN Contacts

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DUF1990 - Domain of unknown function (DUF1990)

PFAM:	PF09348	Sequences: TYPEVGATRLPAGYRVDHNRVRLGRGEAVFERARAALRRWRMFRLGWVRVFPPDAPIEPGTTVAVLARHLGLWSLNPCRVVYVVDEPRRFGFAYGTLPGHPERGEERFLVEWDPDGSVWYDIRAFSRPAHWLARLGYPLARRLQRRFARRSLRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	154 (152)
Sequences:	4753 (3477)
Seq/√Len:	282.0
META:	0.842

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_R	44_R	3.228	1.00
82_Y	93_A	3.145	1.00
112_W	116_G	3.142	1.00
62_T	79_R	2.839	1.00
27_E	31_E	2.825	1.00
22_R	117_S	2.615	1.00
103_R	127_R	2.595	1.00
22_R	119_W	2.429	1.00
77_P	99_G	2.320	1.00
23_L	29_V	2.256	1.00
38_R	90_F	2.212	1.00
55_A	61_T	2.209	1.00
58_E	61_T	2.087	1.00
34_R	90_F	2.064	1.00
35_A	39_R	2.048	1.00
18_H	121_D	2.010	1.00
10_L	16_V	1.967	1.00
69_H	74_S	1.965	1.00
120_Y	151_S	1.953	1.00
88_R	112_W	1.948	1.00
69_H	72_L	1.919	1.00
27_E	112_W	1.889	1.00
37_L	110_V	1.880	1.00
88_R	114_P	1.845	1.00
133_A	140_A	1.791	1.00
20_R	121_D	1.775	1.00
18_H	123_R	1.734	1.00
34_R	38_R	1.727	1.00
111_E	121_D	1.725	1.00
22_R	25_R	1.723	1.00
20_R	119_W	1.607	1.00
81_V	93_A	1.599	1.00
89_R	111_E	1.594	1.00
84_V	91_G	1.552	1.00
4_E	14_Y	1.550	1.00
113_D	119_W	1.513	1.00
143_L	146_R	1.501	1.00
7_A	125_F	1.482	1.00
9_R	82_Y	1.474	1.00
76_N	101_P	1.441	1.00
113_D	117_S	1.437	1.00
4_E	7_A	1.431	1.00
102_E	140_A	1.415	1.00
129_A	133_A	1.386	1.00
95_G	105_E	1.381	1.00
147_F	151_S	1.339	1.00
49_R	66_L	1.335	1.00
130_H	133_A	1.334	1.00
132_L	136_G	1.330	1.00
36_A	41_R	1.307	1.00
145_R	148_A	1.276	1.00
47_W	150_R	1.257	1.00
25_R	116_G	1.247	1.00
10_L	123_R	1.212	1.00
84_V	109_L	1.206	1.00
103_R	129_A	1.202	1.00
137_Y	140_A	1.189	1.00
81_V	95_G	1.132	1.00
32_R	36_A	1.130	1.00
67_A	101_P	1.130	1.00
107_R	121_D	1.124	1.00
111_E	119_W	1.114	1.00
21_V	152_L	1.086	1.00
28_A	32_R	1.084	1.00
63_V	78_C	1.084	1.00
106_E	124_A	1.068	1.00
19_N	149_R	1.065	1.00
76_N	147_F	1.056	1.00
99_G	129_A	1.046	1.00
69_H	101_P	1.022	1.00
26_G	118_V	1.020	1.00
35_A	56_P	1.015	1.00
148_A	152_L	1.009	1.00
89_R	109_L	1.008	1.00
3_P	14_Y	1.006	1.00
45_L	48_V	1.003	1.00
95_G	125_F	1.001	1.00
87_P	114_P	0.998	1.00
93_A	107_R	0.998	1.00
91_G	109_L	0.986	1.00
48_V	76_N	0.982	1.00
66_L	75_L	0.979	1.00
138_P	142_R	0.963	1.00
19_N	148_A	0.960	1.00
7_A	10_L	0.957	1.00
67_A	76_N	0.957	1.00
57_I	80_V	0.923	1.00
57_I	83_V	0.913	1.00
42_M	120_Y	0.903	1.00
84_V	89_R	0.893	1.00
31_E	34_R	0.890	1.00
85_D	90_F	0.869	1.00
30_F	34_R	0.869	1.00
81_V	105_E	0.869	1.00
82_Y	105_E	0.865	1.00
4_E	125_F	0.860	1.00
109_L	121_D	0.856	1.00
17_D	124_A	0.850	1.00
15_R	102_E	0.831	1.00
139_L	142_R	0.829	1.00
38_R	85_D	0.828	1.00
34_R	85_D	0.828	1.00
70_L	139_L	0.822	1.00
51_F	66_L	0.813	0.99
59_P	83_V	0.809	0.99
28_A	31_E	0.807	0.99
82_Y	107_R	0.800	0.99
146_R	150_R	0.799	0.99
24_G	118_V	0.794	0.99
142_R	145_R	0.791	0.99
16_V	123_R	0.782	0.99
19_N	152_L	0.776	0.99
51_F	54_D	0.774	0.99
20_R	113_D	0.771	0.99
23_L	112_W	0.766	0.99
14_Y	103_R	0.762	0.99
86_E	89_R	0.758	0.99
38_R	56_P	0.758	0.99
44_R	47_W	0.757	0.99
63_V	94_Y	0.751	0.99
33_A	110_V	0.749	0.99
48_V	67_A	0.746	0.99
4_E	10_L	0.743	0.99
143_L	147_F	0.743	0.99
24_G	29_V	0.742	0.99
46_G	150_R	0.742	0.99
4_E	103_R	0.742	0.99
110_V	118_V	0.734	0.99
122_I	148_A	0.733	0.99
139_L	143_L	0.732	0.99
144_Q	148_A	0.732	0.99
82_Y	95_G	0.731	0.99
65_V	78_C	0.730	0.99
35_A	38_R	0.725	0.99
17_D	141_R	0.719	0.99
23_L	33_A	0.710	0.99
57_I	90_F	0.708	0.99
109_L	113_D	0.700	0.98
37_L	42_M	0.698	0.98
59_P	82_Y	0.694	0.98
54_D	58_E	0.687	0.98
94_Y	100_H	0.684	0.98
31_E	35_A	0.683	0.98
43_F	65_V	0.683	0.98
94_Y	126_S	0.680	0.98
149_R	153_R	0.678	0.98
93_A	105_E	0.678	0.98
25_R	117_S	0.678	0.98
79_R	97_L	0.675	0.98
65_V	76_N	0.674	0.98
102_E	133_A	0.673	0.98
107_R	123_R	0.670	0.98
2_Y	6_G	0.668	0.98
15_R	137_Y	0.667	0.98
19_N	145_R	0.663	0.98
40_W	52_P	0.660	0.98
30_F	112_W	0.659	0.98
102_E	124_A	0.657	0.98
146_R	149_R	0.651	0.98
148_A	151_S	0.648	0.97
66_L	73_W	0.646	0.97
42_M	92_F	0.642	0.97
2_Y	8_T	0.642	0.97
149_R	152_L	0.637	0.97
136_G	139_L	0.636	0.97
54_D	61_T	0.635	0.97
13_G	127_R	0.631	0.97
42_M	57_I	0.630	0.97
27_E	116_G	0.629	0.97
40_W	94_Y	0.628	0.97
136_G	140_A	0.628	0.97
129_A	140_A	0.627	0.97
33_A	42_M	0.625	0.97
44_R	48_V	0.624	0.97
43_F	151_S	0.617	0.97
20_R	111_E	0.613	0.96
150_R	153_R	0.609	0.96
21_V	120_Y	0.604	0.96
17_D	148_A	0.602	0.96
87_P	113_D	0.602	0.96
66_L	69_H	0.600	0.96
7_A	16_V	0.594	0.96
133_A	136_G	0.593	0.96
15_R	145_R	0.587	0.95
64_A	77_P	0.586	0.95
37_L	91_G	0.582	0.95
101_P	130_H	0.582	0.95
85_D	88_R	0.580	0.95
26_G	112_W	0.577	0.95
57_I	61_T	0.576	0.95
4_E	8_T	0.576	0.95
2_Y	5_V	0.571	0.95
43_F	78_C	0.567	0.95
14_Y	127_R	0.567	0.95
140_A	148_A	0.566	0.94
132_L	137_Y	0.561	0.94
105_E	125_F	0.560	0.94
17_D	126_S	0.559	0.94
69_H	75_L	0.556	0.94
51_F	64_A	0.555	0.94
61_T	80_V	0.555	0.94
64_A	75_L	0.553	0.94
15_R	19_N	0.553	0.94
50_V	53_P	0.550	0.94
144_Q	147_F	0.546	0.93
65_V	94_Y	0.541	0.93
110_V	120_Y	0.538	0.93
4_E	16_V	0.536	0.93
140_A	143_L	0.531	0.92
27_E	88_R	0.529	0.92
52_P	55_A	0.524	0.92
32_R	35_A	0.521	0.92
40_W	92_F	0.520	0.92
62_T	98_P	0.518	0.91
83_V	90_F	0.517	0.91
85_D	91_G	0.514	0.91
42_M	52_P	0.513	0.91
30_F	37_L	0.511	0.91
124_A	141_R	0.511	0.91
43_F	47_W	0.508	0.91
133_A	137_Y	0.507	0.91
14_Y	125_F	0.506	0.91
141_R	145_R	0.506	0.91
2_Y	95_G	0.505	0.90
88_R	113_D	0.504	0.90
26_G	29_V	0.504	0.90
109_L	123_R	0.500	0.90
145_R	149_R	0.500	0.90

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
4r7kA	4	0.9026	33.5	0.925	Contact Map
2m47A	1	0.8766	29.4	0.927	Contact Map
2d4rA	4	0.8636	13.4	0.937	Contact Map
1xuvA	2	0.8896	13.1	0.938	Contact Map
3ggnA	2	0.7597	11.8	0.939	Contact Map
3p9vA	2	0.8766	11.3	0.939	Contact Map
2pcsA	1	0.8636	10.4	0.94	Contact Map
3k3kA	4	0.9351	9.8	0.941	Contact Map
2ns9A	2	0.9091	8.2	0.943	Contact Map
1t17A	1	0.8571	7.6	0.944	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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