DUF3047 - PFAM28P - GREMLIN Contacts

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DUF3047 - Protein of unknown function (DUF3047)

PFAM:	PF11249	Sequences: DGWEPLTFPGIKPKTRYSLVEDDGRRVLRAESDGSASGLVREVDIDLKETPILSWRWKVDNLPAGADERTKAGDDYAARVYVVFDGDPDRLPFFERTRALNYVWSSRLPVGTVIPNPYTDRVRMIVVRSGPAKLGQWVTERRNVAEDYRRAFGEEPPRIVGIAIMTDSDNTGSSAEAYYGDIR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	183 (180)
Sequences:	7555 (5335)
Seq/√Len:	397.7
META:	0.942

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_R	140_E	4.191	1.00
54_S	141_R	3.095	1.00
149_R	155_E	2.937	1.00
143_N	146_E	2.790	1.00
115_P	123_R	2.701	1.00
29_R	176_E	2.479	1.00
133_K	138_V	2.397	1.00
52_I	141_R	2.383	1.00
33_D	174_S	2.291	1.00
128_R	133_K	2.285	1.00
133_K	136_Q	2.270	1.00
78_A	177_A	2.247	1.00
102_Y	147_D	2.221	1.00
34_G	172_G	2.113	1.00
53_L	82_V	2.042	1.00
128_R	138_V	2.041	1.00
32_S	168_S	2.036	1.00
56_R	139_T	2.028	1.00
113_V	151_A	1.976	1.00
166_T	179_Y	1.971	1.00
56_R	180_G	1.866	1.00
25_R	56_R	1.858	1.00
82_V	144_V	1.796	1.00
44_D	158_R	1.795	1.00
82_V	159_I	1.788	1.00
146_E	150_R	1.753	1.00
31_E	176_E	1.745	1.00
69_R	108_L	1.705	1.00
21_E	26_R	1.691	1.00
60_D	178_Y	1.683	1.00
78_A	179_Y	1.670	1.00
5_P	14_K	1.667	1.00
70_T	73_G	1.644	1.00
145_A	149_R	1.643	1.00
63_P	77_A	1.621	1.00
19_L	26_R	1.618	1.00
18_S	29_R	1.596	1.00
46_D	49_E	1.593	1.00
125_I	151_A	1.587	1.00
100_L	151_A	1.575	1.00
62_L	134_L	1.553	1.00
22_D	58_K	1.549	1.00
68_E	114_I	1.525	1.00
127_V	142_R	1.524	1.00
54_S	139_T	1.509	1.00
31_E	174_S	1.493	1.00
113_V	150_R	1.450	1.00
63_P	168_S	1.393	1.00
56_R	181_D	1.370	1.00
51_P	143_N	1.357	1.00
85_D	160_V	1.352	1.00
48_K	145_A	1.338	1.00
28_L	164_I	1.335	1.00
127_V	140_E	1.315	1.00
142_R	147_D	1.305	1.00
25_R	180_G	1.305	1.00
27_V	178_Y	1.298	1.00
29_R	178_Y	1.294	1.00
20_V	29_R	1.274	1.00
17_Y	30_A	1.269	1.00
18_S	31_E	1.263	1.00
166_T	175_A	1.243	1.00
7_T	14_K	1.238	1.00
30_A	166_T	1.226	1.00
21_E	24_G	1.224	1.00
84_F	148_Y	1.219	1.00
109_P	112_T	1.196	1.00
167_D	170_N	1.191	1.00
16_R	31_E	1.184	1.00
22_D	27_V	1.172	1.00
113_V	125_I	1.166	1.00
4_E	42_E	1.156	1.00
67_D	70_T	1.150	1.00
92_P	95_E	1.143	1.00
60_D	176_E	1.133	1.00
166_T	177_A	1.129	1.00
59_V	62_L	1.097	1.00
105_S	108_L	1.068	1.00
61_N	174_S	1.065	1.00
66_A	106_S	1.064	1.00
30_A	179_Y	1.064	1.00
59_V	77_A	1.064	1.00
62_L	106_S	1.064	1.00
66_A	171_T	1.063	1.00
60_D	135_G	1.050	1.00
116_N	124_M	1.049	1.00
68_E	105_S	1.031	1.00
58_K	178_Y	1.031	1.00
146_E	149_R	1.027	1.00
55_W	140_E	1.022	1.00
123_R	151_A	1.009	1.00
108_L	112_T	1.002	1.00
69_R	112_T	0.999	1.00
59_V	78_A	0.999	1.00
62_L	131_P	0.983	1.00
118_Y	170_N	0.982	1.00
80_V	182_I	0.982	1.00
83_V	161_G	0.966	1.00
148_Y	154_E	0.956	1.00
5_P	37_S	0.955	1.00
47_L	159_I	0.945	1.00
52_I	143_N	0.945	1.00
45_I	159_I	0.937	1.00
65_G	173_S	0.936	1.00
58_K	137_W	0.934	1.00
10_G	13_P	0.931	1.00
94_F	97_T	0.927	1.00
145_A	155_E	0.926	1.00
47_L	50_T	0.919	1.00
46_D	51_P	0.908	1.00
168_S	175_A	0.904	1.00
130_G	133_K	0.903	1.00
63_P	173_S	0.897	1.00
113_V	123_R	0.893	1.00
6_L	40_V	0.888	1.00
22_D	25_R	0.878	1.00
76_Y	79_R	0.878	1.00
15_T	32_S	0.875	1.00
15_T	30_A	0.875	1.00
32_S	35_S	0.873	1.00
68_E	76_Y	0.863	1.00
59_V	177_A	0.863	1.00
68_E	103_V	0.862	1.00
81_Y	101_N	0.860	1.00
53_L	142_R	0.854	1.00
45_I	50_T	0.854	1.00
145_A	156_P	0.854	1.00
116_N	122_V	0.849	1.00
109_P	129_S	0.845	1.00
111_G	150_R	0.845	1.00
7_T	10_G	0.842	1.00
125_I	142_R	0.823	1.00
76_Y	103_V	0.823	1.00
46_D	158_R	0.822	1.00
91_L	96_R	0.817	1.00
105_S	126_V	0.816	1.00
102_Y	142_R	0.815	1.00
110_V	129_S	0.814	1.00
36_A	165_M	0.811	1.00
61_N	134_L	0.811	1.00
76_Y	117_P	0.810	1.00
20_V	27_V	0.794	1.00
131_P	134_L	0.791	1.00
64_A	173_S	0.790	1.00
63_P	106_S	0.789	1.00
21_E	25_R	0.787	1.00
123_R	152_F	0.785	1.00
69_R	114_I	0.782	1.00
103_V	124_M	0.779	1.00
101_N	122_V	0.777	1.00
48_K	157_P	0.775	1.00
71_K	117_P	0.774	1.00
73_G	118_Y	0.773	1.00
91_L	95_E	0.769	1.00
19_L	28_L	0.764	1.00
39_L	164_I	0.763	1.00
59_V	134_L	0.760	1.00
61_N	64_A	0.755	1.00
47_L	51_P	0.754	1.00
44_D	85_D	0.754	1.00
104_W	130_G	0.749	1.00
71_K	118_Y	0.736	1.00
53_L	80_V	0.734	1.00
93_F	96_R	0.733	1.00
61_N	176_E	0.732	1.00
92_P	96_R	0.732	1.00
15_T	35_S	0.726	1.00
168_S	173_S	0.723	1.00
13_P	33_D	0.718	1.00
40_V	83_V	0.714	1.00
32_S	166_T	0.714	1.00
148_Y	156_P	0.710	1.00
6_L	10_G	0.709	1.00
95_E	121_R	0.708	1.00
79_R	101_N	0.707	1.00
74_D	116_N	0.706	1.00
47_L	144_V	0.696	1.00
98_R	154_E	0.695	1.00
71_K	116_N	0.686	0.99
126_V	129_S	0.686	0.99
68_E	108_L	0.681	0.99
67_D	107_R	0.678	0.99
164_I	179_Y	0.675	0.99
145_A	148_Y	0.675	0.99
111_G	126_V	0.668	0.99
30_A	177_A	0.665	0.99
115_P	120_D	0.664	0.99
8_F	12_K	0.663	0.99
48_K	155_E	0.655	0.99
99_A	122_V	0.653	0.99
90_R	94_F	0.651	0.99
90_R	154_E	0.651	0.99
13_P	34_G	0.648	0.99
110_V	132_A	0.645	0.99
68_E	74_D	0.644	0.99
68_E	106_S	0.632	0.99
104_W	128_R	0.632	0.99
76_Y	106_S	0.627	0.99
63_P	175_A	0.627	0.99
108_L	114_I	0.624	0.99
38_G	83_V	0.614	0.99
87_D	90_R	0.608	0.99
103_V	126_V	0.608	0.99
66_A	76_Y	0.608	0.99
84_F	156_P	0.606	0.99
104_W	140_E	0.605	0.99
44_D	160_V	0.601	0.99
2_G	41_R	0.598	0.99
76_Y	114_I	0.594	0.99
30_A	37_S	0.589	0.98
86_G	154_E	0.589	0.98
125_I	150_R	0.585	0.98
75_D	169_D	0.584	0.98
171_T	175_A	0.579	0.98
26_R	136_Q	0.578	0.98
45_I	144_V	0.574	0.98
95_E	98_R	0.572	0.98
84_F	159_I	0.570	0.98
85_D	158_R	0.568	0.98
93_F	97_T	0.566	0.98
8_F	38_G	0.560	0.98
164_I	182_I	0.559	0.98
43_V	159_I	0.558	0.98
22_D	178_Y	0.557	0.98
40_V	161_G	0.556	0.98
81_Y	165_M	0.554	0.98
83_V	163_A	0.551	0.98
148_Y	152_F	0.549	0.98
17_Y	179_Y	0.547	0.98
53_L	144_V	0.546	0.98
83_V	160_V	0.545	0.97
66_A	73_G	0.545	0.97
12_K	36_A	0.544	0.97
45_I	51_P	0.544	0.97
165_M	179_Y	0.542	0.97
32_S	63_P	0.541	0.97
9_P	13_P	0.539	0.97
103_V	114_I	0.538	0.97
76_Y	124_M	0.538	0.97
79_R	165_M	0.538	0.97
25_R	181_D	0.538	0.97
50_T	143_N	0.538	0.97
58_K	135_G	0.538	0.97
91_L	94_F	0.538	0.97
110_V	128_R	0.537	0.97
139_T	181_D	0.537	0.97
80_V	140_E	0.533	0.97
15_T	37_S	0.530	0.97
110_V	126_V	0.524	0.97
38_G	41_R	0.524	0.97
46_D	50_T	0.524	0.97
76_Y	101_N	0.524	0.97
2_G	42_E	0.523	0.97
6_L	9_P	0.520	0.97
64_A	131_P	0.519	0.97
92_P	97_T	0.518	0.97
148_Y	157_P	0.517	0.97
85_D	159_I	0.517	0.97
111_G	129_S	0.516	0.97
32_S	175_A	0.516	0.97
48_K	51_P	0.516	0.97
37_S	165_M	0.516	0.97
42_E	161_G	0.515	0.96
86_G	90_R	0.514	0.96
165_M	170_N	0.514	0.96
6_L	38_G	0.507	0.96
61_N	175_A	0.503	0.96
5_P	9_P	0.503	0.96
95_E	120_D	0.502	0.96
82_V	102_Y	0.500	0.96

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
2vtfA	1	0.694	21.8	0.934	Contact Map
3hbkA	1	0.8142	21	0.934	Contact Map
4qhzA	3	0.7705	15.9	0.938	Contact Map
3u1xA	2	0.7869	12.5	0.941	Contact Map
1l8wA	2	0.2732	12	0.941	Contact Map
3h3lA	2	0.8087	10.8	0.942	Contact Map
3osdA	1	0.8087	9.7	0.943	Contact Map
4jqtA	2	0.7814	8.2	0.945	Contact Map
3immA	1	0.765	7.1	0.947	Contact Map
3s5qA	1	0.765	7	0.947	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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