DUF1529 - PFAM28P - GREMLIN Contacts

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DUF1529 - Domain of Unknown Function (DUF1259)

PFAM:	PF07485	Sequences: QAIDQALGRKGKVNGGVYKVTIPRSDLKVTVDGVTIPPAMGLGTWAAFQPTGGGKAMVMGDFVLLEDEVNPVMKALRANGIEVTALHNHMLGEQPRVFFMHFWGHGDAVKLARGLRAALDK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (118)
Sequences:	16627 (6674)
Seq/√Len:	614.4
META:	0.967

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
93_E	96_R	3.657	1.00
79_N	114_G	2.816	1.00
4_D	18_Y	2.763	1.00
116_R	120_D	2.673	1.00
107_D	110_K	2.615	1.00
28_K	35_T	2.606	1.00
11_G	18_Y	2.478	1.00
2_A	5_Q	2.406	1.00
75_A	79_N	2.306	1.00
4_D	20_V	2.109	1.00
73_M	100_M	1.955	1.00
9_R	22_I	1.792	1.00
74_K	78_A	1.781	1.00
30_T	35_T	1.762	1.00
110_K	113_R	1.750	1.00
70_N	74_K	1.713	1.00
77_R	83_V	1.649	1.00
106_G	110_K	1.639	1.00
55_K	105_H	1.629	1.00
69_V	91_L	1.629	1.00
4_D	10_K	1.616	1.00
24_R	68_E	1.610	1.00
109_V	113_R	1.578	1.00
69_V	86_L	1.568	1.00
13_V	18_Y	1.493	1.00
70_N	73_M	1.477	1.00
75_A	78_A	1.447	1.00
104_G	111_L	1.446	1.00
79_N	117_A	1.406	1.00
88_N	98_F	1.398	1.00
13_V	16_G	1.389	1.00
64_L	72_V	1.363	1.00
113_R	117_A	1.360	1.00
27_L	65_L	1.340	1.00
110_K	114_G	1.336	1.00
73_M	86_L	1.327	1.00
66_E	94_Q	1.323	1.00
32_D	92_G	1.315	1.00
64_L	69_V	1.307	1.00
7_L	20_V	1.306	1.00
108_A	112_A	1.283	1.00
44_T	62_F	1.248	1.00
86_L	98_F	1.236	1.00
66_E	96_R	1.230	1.00
58_V	111_L	1.217	1.00
93_E	97_V	1.195	1.00
46_A	102_F	1.193	1.00
57_M	103_W	1.185	1.00
67_D	92_G	1.175	1.00
2_A	6_A	1.162	1.00
66_E	98_F	1.155	1.00
81_I	104_G	1.152	1.00
90_M	99_F	1.125	1.00
63_V	97_V	1.114	1.00
64_L	100_M	1.105	1.00
76_L	81_I	1.104	1.00
72_V	100_M	1.101	1.00
117_A	120_D	1.082	1.00
51_T	55_K	1.072	1.00
3_I	20_V	1.062	1.00
22_I	44_T	1.050	1.00
2_A	109_V	1.033	1.00
91_L	98_F	1.016	1.00
60_G	102_F	1.007	1.00
31_V	36_I	1.006	1.00
58_V	102_F	0.993	1.00
75_A	117_A	0.986	1.00
36_I	40_M	0.986	1.00
19_K	45_W	0.970	1.00
81_I	114_G	0.957	1.00
65_L	97_V	0.941	1.00
76_L	118_A	0.930	1.00
49_Q	57_M	0.924	1.00
51_T	105_H	0.924	1.00
61_D	87_H	0.919	1.00
114_G	117_A	0.914	1.00
38_P	42_L	0.911	1.00
48_F	58_V	0.886	1.00
46_A	115_L	0.880	1.00
70_N	91_L	0.864	1.00
4_D	13_V	0.862	1.00
46_A	58_V	0.861	1.00
89_H	101_H	0.860	1.00
86_L	100_M	0.859	1.00
4_D	11_G	0.849	1.00
13_V	17_V	0.844	1.00
90_M	93_E	0.825	1.00
56_A	111_L	0.818	1.00
50_P	55_K	0.815	1.00
14_N	19_K	0.810	1.00
89_H	99_F	0.803	1.00
79_N	113_R	0.802	1.00
48_F	56_A	0.793	1.00
87_H	101_H	0.780	1.00
66_E	92_G	0.780	1.00
62_F	119_L	0.779	1.00
69_V	98_F	0.777	1.00
7_L	22_I	0.774	1.00
50_P	56_A	0.760	1.00
36_I	42_L	0.757	1.00
88_N	93_E	0.750	1.00
9_R	20_V	0.745	1.00
113_R	120_D	0.743	1.00
72_V	118_A	0.741	1.00
66_E	91_L	0.739	1.00
21_T	38_P	0.738	1.00
80_G	110_K	0.736	1.00
27_L	35_T	0.733	1.00
50_P	53_G	0.730	1.00
31_V	34_V	0.714	1.00
27_L	30_T	0.707	1.00
19_K	47_A	0.698	1.00
29_V	36_I	0.685	1.00
76_L	102_F	0.678	1.00
58_V	115_L	0.678	1.00
21_T	43_G	0.672	1.00
114_G	118_A	0.668	1.00
22_I	46_A	0.657	1.00
30_T	33_G	0.655	1.00
50_P	54_G	0.652	1.00
51_T	54_G	0.650	1.00
31_V	92_G	0.647	1.00
37_P	40_M	0.646	1.00
77_R	82_E	0.644	1.00
30_T	94_Q	0.639	1.00
105_H	108_A	0.637	1.00
106_G	111_L	0.630	1.00
11_G	20_V	0.630	1.00
61_D	101_H	0.623	1.00
59_M	84_T	0.623	1.00
78_A	117_A	0.623	1.00
62_F	72_V	0.618	1.00
102_F	115_L	0.614	1.00
58_V	104_G	0.613	1.00
110_K	117_A	0.613	1.00
4_D	12_K	0.613	1.00
85_A	89_H	0.600	1.00
3_I	108_A	0.598	1.00
6_A	112_A	0.591	1.00
82_E	103_W	0.582	1.00
56_A	108_A	0.580	1.00
73_M	77_R	0.578	1.00
12_K	21_T	0.578	1.00
29_V	97_V	0.573	1.00
50_P	108_A	0.568	1.00
82_E	105_H	0.566	1.00
63_V	99_F	0.564	1.00
58_V	81_I	0.563	1.00
74_K	77_R	0.562	1.00
21_T	45_W	0.558	1.00
71_P	75_A	0.555	1.00
75_A	114_G	0.552	1.00
48_F	112_A	0.549	0.99
51_T	57_M	0.549	0.99
25_S	35_T	0.546	0.99
107_D	113_R	0.536	0.99
77_R	81_I	0.536	0.99
64_L	71_P	0.531	0.99
17_V	47_A	0.531	0.99
62_F	76_L	0.529	0.99
3_I	6_A	0.529	0.99
30_T	34_V	0.523	0.99
5_Q	10_K	0.521	0.99
62_F	118_A	0.521	0.99
64_L	86_L	0.518	0.99
29_V	42_L	0.518	0.99
57_M	105_H	0.514	0.99
65_L	68_E	0.514	0.99
26_D	97_V	0.513	0.99
67_D	71_P	0.510	0.99
61_D	89_H	0.508	0.99
4_D	9_R	0.508	0.99
22_I	119_L	0.506	0.99
54_G	107_D	0.505	0.99
23_P	43_G	0.503	0.99
41_G	61_D	0.501	0.99
3_I	112_A	0.500	0.99

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
2zwsA	2	0.8678	18.1	0.919	Contact Map
4x9tA	1	0.9752	15.9	0.921	Contact Map
2mdaA	2	0.6446	15.4	0.922	Contact Map
1sznA	1	0.6198	15.3	0.922	Contact Map
2jwkA	2	0.5537	14.8	0.922	Contact Map
4qq0A	1	0.8595	12.8	0.924	Contact Map
1ycgA	5	0.9339	11.8	0.926	Contact Map
1we3A	5	0.9339	10.2	0.927	Contact Map
4wgkA	2	0.9008	9.9	0.928	Contact Map
3qe2A	1	0.3223	8.7	0.93	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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