DUF1705 - PFAM28P - GREMLIN Contacts

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DUF1705 - Domain of unknown function (DUF1705)

PFAM:	PF08019	Sequences: LFALLVLLLSLLSWRYLLKPLLILLLLVSAAASYFMDTYGVVIDPSMIRNVLETDPAEARDLLSLKLLLYLLLLGVLPALLLWRVRIRYRPWKRELLRRLLLILLALLVIVLLLLLFYKDYASFFRNHKELRYLINPTNYIYSLGKYAKKQY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	152 (148)
Sequences:	5234 (4033)
Seq/√Len:	331.5
META:	0.786

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_I	83_W	4.118	1.00
75_G	79_A	3.182	1.00
47_M	50_N	3.135	1.00
23_I	79_A	2.941	1.00
26_L	82_L	2.676	1.00
95_E	99_R	2.661	1.00
6_V	106_A	2.642	1.00
31_A	71_L	2.250	1.00
56_P	60_R	2.220	1.00
81_L	85_V	2.200	1.00
80_L	84_R	2.140	1.00
37_D	70_Y	2.123	1.00
6_V	102_L	2.062	1.00
14_W	17_L	1.929	1.00
32_A	140_Y	1.878	1.00
7_L	103_I	1.854	1.00
70_Y	74_L	1.853	1.00
117_F	121_Y	1.851	1.00
33_S	37_D	1.838	1.00
46_S	49_R	1.783	1.00
32_A	43_I	1.771	1.00
13_S	18_L	1.762	1.00
118_Y	122_A	1.751	1.00
139_N	143_S	1.729	1.00
97_L	101_L	1.716	1.00
29_S	140_Y	1.698	1.00
56_P	59_A	1.662	1.00
34_Y	70_Y	1.581	1.00
36_M	136_N	1.572	1.00
6_V	10_S	1.550	1.00
90_R	95_E	1.533	1.00
72_L	76_V	1.514	1.00
24_L	28_V	1.513	1.00
63_L	68_L	1.494	1.00
23_I	82_L	1.445	1.00
48_I	147_Y	1.442	1.00
33_S	70_Y	1.425	1.00
20_P	23_I	1.409	1.00
49_R	53_E	1.409	1.00
76_V	80_L	1.405	1.00
36_M	43_I	1.398	1.00
101_L	105_L	1.388	1.00
89_Y	95_E	1.386	1.00
30_A	75_G	1.382	1.00
90_R	98_R	1.353	1.00
136_N	139_N	1.350	1.00
54_T	58_E	1.345	1.00
94_R	97_L	1.337	1.00
25_L	141_I	1.335	1.00
45_P	146_K	1.314	1.00
132_R	142_Y	1.291	1.00
67_L	71_L	1.288	1.00
23_I	27_L	1.270	1.00
94_R	98_R	1.266	1.00
27_L	75_G	1.264	1.00
93_K	97_L	1.256	1.00
142_Y	146_K	1.255	1.00
35_F	62_L	1.240	1.00
98_R	101_L	1.231	1.00
145_G	149_K	1.224	1.00
91_P	94_R	1.219	1.00
145_G	148_A	1.208	1.00
42_V	134_L	1.178	1.00
52_L	147_Y	1.145	1.00
69_L	73_L	1.123	1.00
68_L	72_L	1.117	1.00
97_L	100_L	1.113	1.00
112_L	116_L	1.108	1.00
2_F	6_V	1.080	1.00
65_L	69_L	1.069	1.00
71_L	76_V	1.065	1.00
144_L	148_A	1.057	1.00
142_Y	145_G	1.050	1.00
66_K	70_Y	1.044	1.00
123_S	127_N	1.044	1.00
49_R	147_Y	1.026	1.00
135_I	138_T	1.002	1.00
117_F	120_D	0.988	1.00
27_L	79_A	0.971	1.00
100_L	104_L	0.952	1.00
140_Y	144_L	0.945	1.00
38_T	66_K	0.945	1.00
136_N	142_Y	0.941	1.00
44_D	47_M	0.908	1.00
118_Y	125_F	0.904	1.00
18_L	22_L	0.898	1.00
29_S	33_S	0.897	1.00
146_K	149_K	0.893	1.00
98_R	102_L	0.892	1.00
26_L	79_A	0.886	1.00
29_S	136_N	0.881	1.00
35_F	67_L	0.871	1.00
105_L	109_V	0.866	1.00
138_T	142_Y	0.863	1.00
17_L	20_P	0.852	1.00
102_L	106_A	0.852	1.00
11_L	14_W	0.846	1.00
7_L	110_I	0.838	1.00
84_R	88_R	0.836	1.00
90_R	94_R	0.833	1.00
3_A	109_V	0.829	1.00
106_A	110_I	0.827	1.00
113_L	116_L	0.827	1.00
30_A	78_P	0.819	1.00
130_E	134_L	0.819	1.00
28_V	140_Y	0.811	1.00
12_L	21_L	0.810	1.00
136_N	140_Y	0.807	1.00
133_Y	138_T	0.801	1.00
85_V	89_Y	0.790	1.00
109_V	113_L	0.788	1.00
121_Y	125_F	0.788	1.00
3_A	110_I	0.787	1.00
3_A	113_L	0.786	1.00
48_I	144_L	0.784	1.00
3_A	6_V	0.781	1.00
124_F	131_L	0.779	1.00
110_I	114_L	0.767	1.00
19_K	87_I	0.766	1.00
133_Y	142_Y	0.765	1.00
10_S	102_L	0.762	1.00
43_I	51_V	0.743	0.99
79_A	82_L	0.730	0.99
133_Y	139_N	0.729	0.99
36_M	39_Y	0.728	0.99
75_G	78_P	0.725	0.99
109_V	112_L	0.725	0.99
55_D	132_R	0.723	0.99
7_L	106_A	0.720	0.99
47_M	62_L	0.717	0.99
15_R	18_L	0.717	0.99
19_K	23_I	0.716	0.99
5_L	138_T	0.715	0.99
31_A	67_L	0.712	0.99
5_L	9_L	0.712	0.99
141_I	145_G	0.702	0.99
136_N	143_S	0.701	0.99
123_S	126_R	0.690	0.99
55_D	61_D	0.685	0.99
88_R	91_P	0.684	0.99
20_P	24_L	0.683	0.99
122_A	125_F	0.667	0.99
68_L	71_L	0.663	0.99
125_F	128_H	0.657	0.99
34_Y	66_K	0.653	0.99
114_L	121_Y	0.653	0.99
3_A	106_A	0.649	0.99
45_P	49_R	0.647	0.98
81_L	84_R	0.645	0.98
35_F	43_I	0.643	0.98
135_I	139_N	0.642	0.98
22_L	26_L	0.640	0.98
10_S	14_W	0.635	0.98
27_L	71_L	0.633	0.98
28_V	32_A	0.632	0.98
107_L	111_V	0.631	0.98
41_V	51_V	0.630	0.98
50_N	62_L	0.629	0.98
128_H	131_L	0.627	0.98
129_K	133_Y	0.627	0.98
30_A	74_L	0.623	0.98
122_A	126_R	0.613	0.98
120_D	124_F	0.613	0.98
43_I	139_N	0.613	0.98
44_D	50_N	0.612	0.98
43_I	48_I	0.611	0.98
57_A	61_D	0.610	0.98
105_L	112_L	0.607	0.98
55_D	58_E	0.606	0.98
9_L	25_L	0.604	0.98
102_L	105_L	0.603	0.98
10_S	13_S	0.602	0.98
114_L	122_A	0.601	0.98
57_A	60_R	0.601	0.98
51_V	59_A	0.588	0.97
104_L	108_L	0.587	0.97
35_F	41_V	0.584	0.97
134_L	139_N	0.582	0.97
4_L	8_L	0.581	0.97
22_L	82_L	0.580	0.97
4_L	7_L	0.578	0.97
65_L	68_L	0.577	0.97
47_M	58_E	0.576	0.97
15_R	89_Y	0.574	0.97
39_Y	62_L	0.570	0.97
50_N	58_E	0.567	0.97
27_L	30_A	0.567	0.97
125_F	135_I	0.565	0.96
113_L	117_F	0.564	0.96
46_S	50_N	0.563	0.96
45_P	143_S	0.562	0.96
47_M	54_T	0.562	0.96
16_Y	20_P	0.562	0.96
33_S	74_L	0.560	0.96
110_I	113_L	0.558	0.96
52_L	144_L	0.558	0.96
45_P	133_Y	0.553	0.96
64_S	67_L	0.553	0.96
48_I	143_S	0.552	0.96
72_L	77_L	0.551	0.96
59_A	63_L	0.547	0.96
9_L	12_L	0.544	0.96
96_L	100_L	0.543	0.96
66_K	69_L	0.536	0.95
71_L	75_G	0.536	0.95
28_V	48_I	0.531	0.95
8_L	12_L	0.529	0.95
10_S	99_R	0.526	0.95
34_Y	38_T	0.526	0.95
54_T	59_A	0.521	0.94
23_I	26_L	0.518	0.94
119_K	122_A	0.517	0.94
45_P	142_Y	0.517	0.94
120_D	123_S	0.515	0.94
25_L	29_S	0.514	0.94
76_V	79_A	0.513	0.94
27_L	31_A	0.512	0.94
43_I	62_L	0.510	0.94
48_I	52_L	0.505	0.94
32_A	36_M	0.503	0.93
18_L	89_Y	0.501	0.93
7_L	99_R	0.500	0.93

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
4av3A	2	0.3487	3.7	0.925	Contact Map
3k6vA	1	0.1579	3.4	0.926	Contact Map
1rz2A	1	0.2171	3.2	0.927	Contact Map
4httA	1	0.875	2.7	0.93	Contact Map
2hi7B	1	0.4737	2.2	0.933	Contact Map
4i0uA	4	0.4737	2	0.935	Contact Map
2w3zA	1	0.1184	1.7	0.937	Contact Map
2zy9A	2	0.4934	1.6	0.938	Contact Map
4ev6A	3	0.5066	1.5	0.939	Contact Map
3owqA	1	0.0658	1.5	0.939	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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