DUF3304 - PFAM28P - GREMLIN Contacts

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DUF3304 - Protein of unknown function (DUF3304)

PFAM:	PF11745	Sequences: LAGCSQAEPEYVGGSIEGYNHTDWAINRFSVNDAGGGGGGGDNIGPYGGGGGGVCCVSLPAKWRPGLTVTVEWETDPGPDADFPFADGDKYLAWEKKIKAQYRQHSAVVPVPPYTGQGGGGLTVHFLPCDQVKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	134 (126)
Sequences:	1254 (728)
Seq/√Len:	64.8
META:	0.53

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_E	106_S	2.602	1.00
18_G	29_F	2.580	1.00
63_W	114_Y	2.563	1.00
69_V	111_V	2.528	1.00
88_G	92_L	2.517	1.00
21_H	125_H	2.416	1.00
107_A	131_Q	2.402	1.00
29_F	124_V	2.385	1.00
91_Y	95_E	2.356	1.00
68_T	110_P	2.219	1.00
105_H	130_D	2.212	1.00
88_G	91_Y	2.208	1.00
19_Y	123_T	2.182	1.00
15_S	53_G	2.114	1.00
38_G	41_G	2.053	1.00
95_E	99_K	1.860	1.00
70_T	106_S	1.844	1.00
88_G	95_E	1.821	1.00
64_R	67_L	1.819	1.00
29_F	126_F	1.765	1.00
89_D	92_L	1.758	1.00
91_Y	94_W	1.756	1.00
90_K	93_A	1.749	1.00
70_T	108_V	1.703	0.99
75_T	105_H	1.651	0.99
92_L	95_E	1.625	0.99
89_D	93_A	1.585	0.99
90_K	95_E	1.575	0.99
88_G	94_W	1.553	0.99
69_V	134_V	1.522	0.99
73_W	126_F	1.486	0.98
83_F	88_G	1.442	0.98
63_W	66_G	1.435	0.98
18_G	124_V	1.374	0.97
2_A	10_E	1.367	0.97
67_L	111_V	1.324	0.97
90_K	94_W	1.305	0.96
44_I	51_G	1.276	0.96
79_P	82_D	1.262	0.96
90_K	96_K	1.252	0.95
37_G	41_G	1.252	0.95
89_D	95_E	1.206	0.94
83_F	90_K	1.194	0.94
2_A	8_E	1.172	0.94
72_E	104_Q	1.166	0.93
19_Y	125_H	1.161	0.93
57_V	122_L	1.159	0.93
93_A	97_K	1.156	0.93
113_P	116_G	1.137	0.93
39_G	42_D	1.135	0.92
12_V	59_L	1.125	0.92
93_A	96_K	1.121	0.92
13_G	54_V	1.119	0.92
66_G	110_P	1.106	0.91
71_V	109_V	1.075	0.90
49_G	52_G	1.060	0.90
92_L	96_K	1.059	0.90
88_G	93_A	1.059	0.90
114_Y	121_G	1.045	0.89
117_Q	120_G	1.044	0.89
89_D	96_K	1.036	0.89
32_N	57_V	1.014	0.87
21_H	123_T	0.998	0.87
60_P	63_W	0.995	0.86
16_I	31_V	0.995	0.86
16_I	39_G	0.977	0.85
75_T	78_G	0.971	0.85
48_G	52_G	0.961	0.84
83_F	89_D	0.961	0.84
12_V	61_A	0.961	0.84
89_D	94_W	0.956	0.84
98_I	102_Y	0.955	0.84
95_E	98_I	0.953	0.84
112_P	133_K	0.928	0.82
27_N	74_E	0.926	0.82
20_N	112_P	0.919	0.82
68_T	108_V	0.915	0.81
5_S	8_E	0.909	0.81
91_Y	97_K	0.909	0.81
94_W	98_I	0.907	0.81
103_R	106_S	0.906	0.81
92_L	98_I	0.904	0.81
84_P	88_G	0.904	0.81
83_F	91_Y	0.898	0.80
65_P	114_Y	0.886	0.79
92_L	97_K	0.885	0.79
63_W	67_L	0.884	0.79
97_K	101_Q	0.884	0.79
127_L	131_Q	0.882	0.79
66_G	114_Y	0.880	0.79
83_F	94_W	0.879	0.79
82_D	91_Y	0.875	0.78
41_G	46_P	0.862	0.77
94_W	97_K	0.850	0.76
17_E	123_T	0.848	0.76
83_F	95_E	0.847	0.76
17_E	53_G	0.843	0.76
38_G	43_N	0.832	0.75
115_T	119_G	0.827	0.74
74_E	104_Q	0.812	0.73
99_K	102_Y	0.806	0.73
84_P	91_Y	0.799	0.72
83_F	92_L	0.775	0.70
80_D	83_F	0.773	0.69
84_P	90_K	0.765	0.69
32_N	38_G	0.759	0.68
60_P	67_L	0.756	0.68
78_G	81_A	0.752	0.67
11_Y	16_I	0.749	0.67
111_V	114_Y	0.746	0.67
91_Y	96_K	0.745	0.66
96_K	100_A	0.741	0.66
3_G	7_A	0.737	0.66
31_V	50_G	0.733	0.65
92_L	99_K	0.732	0.65
119_G	123_T	0.730	0.65
26_I	126_F	0.726	0.64
81_A	92_L	0.725	0.64
80_D	84_P	0.720	0.64
28_R	71_V	0.708	0.63
91_Y	99_K	0.703	0.62
75_T	103_R	0.698	0.61
19_Y	23_D	0.691	0.61
63_W	112_P	0.691	0.61
112_P	127_L	0.684	0.60
97_K	100_A	0.679	0.59
6_Q	10_E	0.677	0.59
21_H	69_V	0.675	0.59
76_D	98_I	0.671	0.58
9_P	61_A	0.669	0.58
32_N	69_V	0.665	0.58
98_I	101_Q	0.662	0.57
45_G	48_G	0.660	0.57
13_G	18_G	0.654	0.56
71_V	122_L	0.654	0.56
41_G	47_Y	0.649	0.56
79_P	83_F	0.646	0.56
81_A	98_I	0.646	0.56
30_S	112_P	0.642	0.55
22_T	130_D	0.636	0.54
89_D	99_K	0.627	0.53
15_S	57_V	0.626	0.53
94_W	99_K	0.622	0.53
18_G	44_I	0.618	0.52
20_N	52_G	0.617	0.52
71_V	133_K	0.611	0.51
9_P	65_P	0.605	0.51
51_G	56_C	0.604	0.51
93_A	99_K	0.597	0.50
29_F	55_C	0.590	0.49
83_F	93_A	0.587	0.49
58_S	61_A	0.583	0.48
77_P	80_D	0.582	0.48
80_D	88_G	0.579	0.48
3_G	110_P	0.578	0.48
21_H	128_P	0.575	0.47
31_V	43_N	0.574	0.47
27_N	71_V	0.570	0.47
26_I	48_G	0.569	0.47
105_H	108_V	0.566	0.46
115_T	118_G	0.566	0.46
38_G	57_V	0.557	0.45
24_W	76_D	0.550	0.44
42_D	45_G	0.550	0.44
51_G	55_C	0.542	0.43
31_V	109_V	0.539	0.43
60_P	114_Y	0.536	0.43
40_G	132_V	0.536	0.43
76_D	79_P	0.536	0.43
93_A	101_Q	0.536	0.43
81_A	84_P	0.534	0.43
3_G	6_Q	0.534	0.43
113_P	118_G	0.533	0.42
81_A	89_D	0.531	0.42
7_A	10_E	0.528	0.42
63_W	113_P	0.525	0.42
88_G	99_K	0.525	0.42
6_Q	18_G	0.516	0.41
2_A	7_A	0.514	0.40
40_G	54_V	0.514	0.40
120_G	123_T	0.513	0.40
42_D	46_P	0.513	0.40
26_I	54_V	0.511	0.40
17_E	50_G	0.510	0.40
22_T	25_A	0.508	0.40
22_T	26_I	0.504	0.39
29_F	56_C	0.503	0.39
26_I	73_W	0.501	0.39
112_P	122_L	0.500	0.39

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
2ldmA	1	0.3284	6.8	0.934	Contact Map
4g2kA	3	0.5597	5.6	0.936	Contact Map
3p8dA	2	0.3209	5.1	0.937	Contact Map
2hqlA	2	0.3731	4.9	0.938	Contact Map
2do3A	1	0.194	4.5	0.939	Contact Map
3zbiC	1	0.1866	3.9	0.941	Contact Map
3h8zA	1	0.4776	3.6	0.942	Contact Map
4hczA	1	0.3358	3.4	0.943	Contact Map
3s6wA	1	0.3209	3.1	0.944	Contact Map
4qq6A	1	0.3433	2.5	0.946	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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