DUF3015 - PFAM28P - GREMLIN Contacts

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DUF3015 - Protein of unknown function (DUF3015)

PFAM:	PF11220	Sequences: AAAYGGAGCGLGSMLFKGQSGLVPQVLAATTNGTFGNQTFGITSGTSGCTQDGVVKSNEKAAVFVAANMDNLARDMARGQGETLDTLAELLGVPDADRAAFAALLQENFATIFPSEDVTAAEVLDNLKAVMAADPVLAKYC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	141 (136)
Sequences:	2576 (1822)
Seq/√Len:	156.2
META:	0.915

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_G	39_T	3.504	1.00
76_M	105_L	2.642	1.00
11_L	47_S	2.613	1.00
40_F	44_S	2.590	1.00
64_F	86_T	2.512	1.00
108_N	111_T	2.427	1.00
27_L	31_T	2.281	1.00
105_L	127_L	2.268	1.00
26_V	29_A	2.234	1.00
65_V	123_V	2.096	1.00
75_D	78_R	2.027	1.00
7_A	28_A	2.001	1.00
37_N	47_S	1.953	1.00
37_N	41_G	1.944	1.00
27_L	30_T	1.855	1.00
98_R	102_A	1.821	1.00
114_P	118_V	1.816	1.00
100_A	134_D	1.744	1.00
119_T	122_E	1.733	1.00
88_A	101_F	1.729	1.00
87_L	127_L	1.726	1.00
16_F	31_T	1.673	1.00
9_C	49_C	1.663	1.00
74_R	78_R	1.656	1.00
34_T	37_N	1.605	1.00
22_L	26_V	1.599	1.00
13_S	48_G	1.596	1.00
94_P	97_D	1.583	1.00
18_G	21_G	1.572	1.00
64_F	68_N	1.565	1.00
84_L	102_A	1.553	1.00
38_Q	42_I	1.532	1.00
76_M	113_F	1.526	1.00
19_Q	24_P	1.482	1.00
33_G	37_N	1.464	1.00
118_V	126_N	1.462	1.00
114_P	126_N	1.451	1.00
69_M	113_F	1.413	1.00
36_G	40_F	1.399	1.00
41_G	46_T	1.389	1.00
37_N	40_F	1.379	1.00
112_I	123_V	1.379	1.00
72_L	76_M	1.353	1.00
87_L	91_L	1.350	1.00
4_Y	7_A	1.316	1.00
72_L	87_L	1.316	1.00
11_L	15_L	1.312	1.00
23_V	26_V	1.310	1.00
85_D	98_R	1.244	1.00
108_N	130_V	1.242	1.00
103_A	107_E	1.224	1.00
25_Q	42_I	1.218	1.00
41_G	49_C	1.218	1.00
29_A	39_T	1.216	1.00
65_V	124_L	1.198	1.00
91_L	128_K	1.186	1.00
85_D	102_A	1.180	1.00
122_E	125_D	1.142	1.00
93_V	97_D	1.132	1.00
89_E	98_R	1.126	1.00
21_G	24_P	1.121	1.00
23_V	27_L	1.110	1.00
40_F	46_T	1.101	0.99
64_F	90_L	1.100	0.99
115_S	118_V	1.092	0.99
16_F	28_A	1.091	0.99
69_M	120_A	1.080	0.99
124_L	128_K	1.073	0.99
118_V	123_V	1.060	0.99
50_T	53_G	1.033	0.99
33_G	36_G	1.029	0.99
6_G	25_Q	1.028	0.99
125_D	128_K	1.024	0.99
59_E	62_A	1.018	0.99
65_V	72_L	1.008	0.99
38_Q	41_G	1.005	0.99
73_A	113_F	0.993	0.99
28_A	32_N	0.975	0.99
73_A	109_F	0.958	0.99
100_A	104_L	0.955	0.99
13_S	28_A	0.942	0.98
99_A	102_A	0.932	0.98
84_L	105_L	0.931	0.98
63_V	66_A	0.923	0.98
61_A	128_K	0.902	0.98
126_N	130_V	0.901	0.98
62_A	121_A	0.893	0.98
104_L	130_V	0.887	0.98
4_Y	13_S	0.885	0.98
61_A	91_L	0.885	0.98
135_P	138_A	0.883	0.98
101_F	105_L	0.878	0.97
21_G	28_A	0.865	0.97
85_D	88_A	0.853	0.97
6_G	13_S	0.850	0.97
8_G	11_L	0.848	0.97
76_M	127_L	0.841	0.97
83_T	87_L	0.833	0.97
22_L	25_Q	0.826	0.96
11_L	35_F	0.819	0.96
115_S	122_E	0.813	0.96
86_T	90_L	0.810	0.96
11_L	41_G	0.809	0.96
130_V	133_A	0.809	0.96
62_A	66_A	0.790	0.95
80_Q	102_A	0.788	0.95
15_L	37_N	0.785	0.95
33_G	41_G	0.784	0.95
24_P	27_L	0.779	0.95
31_T	34_T	0.779	0.95
16_F	24_P	0.775	0.95
38_Q	47_S	0.773	0.95
45_G	49_C	0.760	0.94
4_Y	25_Q	0.750	0.94
11_L	34_T	0.748	0.94
11_L	14_M	0.742	0.93
14_M	48_G	0.739	0.93
6_G	50_T	0.738	0.93
125_D	129_A	0.736	0.93
39_T	43_T	0.734	0.93
20_S	24_P	0.733	0.93
16_F	21_G	0.732	0.93
11_L	31_T	0.731	0.93
35_F	41_G	0.719	0.92
55_V	58_N	0.712	0.92
97_D	100_A	0.712	0.92
29_A	34_T	0.712	0.92
7_A	25_Q	0.706	0.92
63_V	67_A	0.706	0.92
29_A	38_Q	0.704	0.92
20_S	23_V	0.698	0.91
3_A	6_G	0.695	0.91
83_T	86_T	0.693	0.91
75_D	109_F	0.678	0.90
36_G	44_S	0.672	0.90
102_A	105_L	0.670	0.89
9_C	41_G	0.661	0.89
31_T	35_F	0.660	0.89
26_V	30_T	0.659	0.89
69_M	123_V	0.657	0.89
95_D	98_R	0.657	0.89
100_A	103_A	0.653	0.88
127_L	132_A	0.641	0.87
112_I	130_V	0.640	0.87
121_A	125_D	0.636	0.87
122_E	126_N	0.634	0.87
19_Q	22_L	0.634	0.87
126_N	129_A	0.626	0.86
15_L	35_F	0.620	0.85
40_F	43_T	0.620	0.85
93_V	101_F	0.619	0.85
31_T	37_N	0.619	0.85
71_N	83_T	0.618	0.85
5_G	13_S	0.615	0.85
25_Q	28_A	0.611	0.85
93_V	102_A	0.607	0.84
115_S	119_T	0.607	0.84
6_G	20_S	0.604	0.84
103_A	129_A	0.604	0.84
65_V	87_L	0.599	0.83
113_F	123_V	0.598	0.83
39_T	44_S	0.598	0.83
45_G	48_G	0.592	0.83
129_A	133_A	0.591	0.83
85_D	90_L	0.586	0.82
22_L	51_Q	0.585	0.82
41_G	45_G	0.584	0.82
82_E	91_L	0.579	0.81
32_N	38_Q	0.578	0.81
85_D	89_E	0.575	0.81
7_A	42_I	0.573	0.81
4_Y	48_G	0.568	0.80
14_M	17_K	0.567	0.80
37_N	44_S	0.564	0.80
86_T	89_E	0.562	0.79
39_T	42_I	0.560	0.79
72_L	84_L	0.556	0.79
22_L	27_L	0.555	0.79
30_T	41_G	0.555	0.79
95_D	100_A	0.554	0.78
85_D	96_A	0.548	0.78
132_A	136_V	0.546	0.77
47_S	50_T	0.542	0.77
73_A	77_A	0.538	0.76
61_A	86_T	0.535	0.76
15_L	31_T	0.533	0.76
94_P	99_A	0.531	0.76
41_G	47_S	0.528	0.75
11_L	37_N	0.523	0.74
7_A	13_S	0.523	0.74
75_D	83_T	0.523	0.74
42_I	45_G	0.522	0.74
130_V	135_P	0.521	0.74
68_N	72_L	0.520	0.74
42_I	53_G	0.518	0.74
114_P	122_E	0.517	0.74
100_A	136_V	0.515	0.73
130_V	134_D	0.513	0.73
111_T	126_N	0.511	0.73
111_T	114_P	0.509	0.72
80_Q	85_D	0.509	0.72
61_A	124_L	0.505	0.72
36_G	46_T	0.501	0.71
120_A	127_L	0.500	0.71

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
4aj5K	4	0.4255	10.3	0.936	Contact Map
2k85A	1	0.305	10	0.936	Contact Map
2ccyA	2	0.6525	8.3	0.938	Contact Map
4i98B	2	0.5248	7.7	0.939	Contact Map
1mqvA	1	0.617	7.3	0.94	Contact Map
1s05A	1	0.617	6.4	0.942	Contact Map
3licA	2	0.5319	6	0.942	Contact Map
2jn6A	1	0.5603	5.9	0.943	Contact Map
1r5qA	2	0.3191	5.8	0.943	Contact Map
1t6sA	4	0.5461	5	0.945	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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