DUF3703 - PFAM28P - GREMLIN Contacts

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DUF3703 - Protein of unknown function (DUF3703)

PFAM:	PF12487	Sequences: KRLRPAYEAELAAARAARAAGDLAAAWRHLERAHILGQPYTGPHVRVHWLMLRFGLRRRDRREVLGQLLRLVVAALGSLVGRVPVGNTGGANVSAFKPMPIPEDLQALL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	109 (107)
Sequences:	2386 (1687)
Seq/√Len:	163.1
META:	0.864

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_D	25_A	3.065	1.00
93_V	99_M	2.868	1.00
10_E	29_H	2.599	1.00
55_G	64_V	2.565	1.00
88_T	99_M	2.419	1.00
14_A	30_L	2.250	1.00
18_R	26_A	2.243	1.00
54_F	58_R	2.131	1.00
32_R	104_D	2.120	1.00
10_E	32_R	1.989	1.00
94_S	97_K	1.957	1.00
41_T	78_S	1.841	1.00
32_R	102_P	1.805	1.00
40_Y	43_P	1.765	1.00
45_V	75_A	1.720	1.00
103_E	106_Q	1.719	1.00
74_A	78_S	1.627	1.00
11_L	47_V	1.597	1.00
41_T	74_A	1.597	1.00
49_W	71_L	1.580	1.00
49_W	53_R	1.569	1.00
46_R	50_L	1.528	1.00
66_G	91_A	1.494	1.00
18_R	57_R	1.482	1.00
9_A	13_A	1.482	1.00
52_L	64_V	1.481	1.00
73_V	77_G	1.464	1.00
65_L	69_L	1.443	1.00
56_L	64_V	1.437	1.00
39_P	83_V	1.395	1.00
31_E	90_G	1.376	1.00
50_L	53_R	1.373	1.00
23_L	58_R	1.361	1.00
41_T	79_L	1.346	1.00
36_L	105_L	1.330	1.00
73_V	96_F	1.284	1.00
69_L	96_F	1.230	1.00
6_A	108_L	1.228	1.00
77_G	81_G	1.180	1.00
69_L	95_A	1.157	1.00
7_Y	46_R	1.148	1.00
54_F	90_G	1.128	1.00
23_L	54_F	1.126	1.00
53_R	57_R	1.109	1.00
8_E	12_A	1.101	1.00
52_L	71_L	1.093	1.00
11_L	50_L	1.087	1.00
14_A	26_A	1.084	1.00
17_A	22_D	1.070	0.99
17_A	25_A	1.065	0.99
35_I	102_P	1.054	0.99
12_A	16_A	1.038	0.99
14_A	54_F	1.017	0.99
68_L	72_V	1.003	0.99
37_G	83_V	0.996	0.99
31_E	92_N	0.986	0.99
61_R	65_L	0.983	0.99
75_A	78_S	0.971	0.99
12_A	15_R	0.966	0.99
26_A	54_F	0.957	0.99
4_R	43_P	0.950	0.99
16_A	20_A	0.941	0.99
33_A	47_V	0.940	0.99
25_A	29_H	0.936	0.99
70_R	84_P	0.931	0.98
18_R	53_R	0.920	0.98
85_V	98_P	0.920	0.98
18_R	50_L	0.902	0.98
8_E	46_R	0.899	0.98
68_L	101_I	0.893	0.98
78_S	83_V	0.884	0.98
73_V	82_R	0.879	0.98
30_L	51_M	0.877	0.98
5_P	9_A	0.864	0.98
41_T	75_A	0.861	0.97
27_W	90_G	0.858	0.97
7_Y	11_L	0.855	0.97
102_P	105_L	0.853	0.97
10_E	13_A	0.844	0.97
27_W	51_M	0.835	0.97
25_A	28_R	0.827	0.97
101_I	106_Q	0.824	0.97
84_P	87_N	0.823	0.97
24_A	31_E	0.822	0.97
55_G	60_D	0.822	0.97
45_V	77_G	0.810	0.96
27_W	54_F	0.808	0.96
7_Y	37_G	0.807	0.96
45_V	74_A	0.802	0.96
3_L	40_Y	0.801	0.96
32_R	105_L	0.795	0.96
15_R	19_A	0.782	0.96
39_P	109_L	0.778	0.95
7_Y	47_V	0.777	0.95
58_R	90_G	0.773	0.95
106_Q	109_L	0.773	0.95
76_L	81_G	0.764	0.95
103_E	107_A	0.762	0.95
73_V	95_A	0.757	0.95
88_T	92_N	0.751	0.95
35_I	105_L	0.744	0.94
29_H	32_R	0.739	0.94
41_T	83_V	0.734	0.94
13_A	16_A	0.733	0.94
20_A	25_A	0.724	0.93
16_A	19_A	0.723	0.93
9_A	16_A	0.723	0.93
75_A	79_L	0.707	0.93
37_G	40_Y	0.702	0.92
7_Y	43_P	0.695	0.92
41_T	45_V	0.686	0.91
18_R	54_F	0.686	0.91
17_A	20_A	0.684	0.91
35_I	39_P	0.681	0.91
13_A	17_A	0.679	0.91
73_V	76_L	0.668	0.90
70_R	87_N	0.668	0.90
55_G	63_E	0.658	0.90
45_V	71_L	0.645	0.89
83_V	94_S	0.638	0.88
100_P	106_Q	0.622	0.87
6_A	36_L	0.612	0.86
27_W	80_V	0.610	0.86
37_G	47_V	0.607	0.86
73_V	78_S	0.606	0.85
42_G	45_V	0.598	0.85
12_A	21_G	0.595	0.84
91_A	94_S	0.595	0.84
56_L	61_R	0.592	0.84
78_S	82_R	0.589	0.84
27_W	41_T	0.583	0.83
69_L	72_V	0.579	0.83
76_L	83_V	0.575	0.82
74_A	83_V	0.574	0.82
37_G	74_A	0.574	0.82
35_I	99_M	0.572	0.82
18_R	21_G	0.572	0.82
41_T	77_G	0.570	0.82
19_A	24_A	0.565	0.81
4_R	8_E	0.563	0.81
63_E	91_A	0.562	0.81
101_I	105_L	0.556	0.80
45_V	73_V	0.551	0.80
93_V	98_P	0.549	0.79
3_L	7_Y	0.542	0.79
6_A	9_A	0.539	0.78
39_P	46_R	0.539	0.78
16_A	24_A	0.536	0.78
90_G	99_M	0.533	0.77
34_H	67_Q	0.529	0.77
8_E	20_A	0.528	0.77
41_T	73_V	0.521	0.76
43_P	50_L	0.517	0.75
5_P	12_A	0.516	0.75
56_L	62_R	0.514	0.75
24_A	58_R	0.512	0.75
76_L	80_V	0.505	0.74
23_L	85_V	0.505	0.74
9_A	12_A	0.501	0.73
91_A	99_M	0.500	0.73

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
4js0B	1	0.2294	10.8	0.937	Contact Map
4bluA	2	0.8624	8.8	0.939	Contact Map
2di0A	1	0.2202	8.7	0.94	Contact Map
4ui9C	2	0.4862	8.6	0.94	Contact Map
4lctA	2	0.7798	8.2	0.94	Contact Map
3b1fA	2	0.3761	8.1	0.94	Contact Map
2nygA	2	0.8532	7.9	0.941	Contact Map
2kygA	2	0.1743	7	0.942	Contact Map
3ijwA	2	0.8624	6.7	0.943	Contact Map
3ax2A	1	0.5688	6.2	0.943	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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