DUF2480 - PFAM28P - GREMLIN Contacts

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DUF2480 - Protein of unknown function (DUF2480)

PFAM:	PF10652	Sequences: EEIVNKVANSGLITIDLEDYYPKGERVVFDIKDWLFMGLILKEKDFREALKNHDWSQYQDKYVAITCSADAIIPTWAYMLVASYLQPFAKKVVFGDLEELETALFLEAISKIDLSEYKDKRVVIKGCSDKPVPESAYVELTKKLQPVAKSIMYGEPCSTVPLYKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	165 (164)
Sequences:	4078 (2864)
Seq/√Len:	223.6
META:	0.904

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_E	52_N	3.255	1.00
115_S	118_K	2.930	1.00
91_K	107_E	2.890	1.00
62_Y	91_K	2.796	1.00
27_V	61_K	2.786	1.00
53_H	58_Y	2.766	1.00
28_V	66_T	2.644	1.00
50_L	84_Y	2.583	1.00
99_E	102_T	2.487	1.00
56_S	59_Q	2.454	1.00
96_D	99_E	2.444	1.00
63_V	85_L	2.433	1.00
25_E	61_K	2.390	1.00
148_A	151_I	2.297	1.00
113_D	116_E	2.213	1.00
139_E	142_K	2.141	1.00
121_R	149_K	2.113	1.00
34_W	49_A	2.021	1.00
156_P	159_T	2.011	1.00
29_F	34_W	1.993	1.00
86_Q	145_Q	1.927	1.00
32_K	38_G	1.897	1.00
46_F	81_V	1.896	1.00
83_S	162_L	1.860	1.00
4_V	9_N	1.836	1.00
114_L	147_V	1.705	1.00
11_G	121_R	1.675	1.00
53_H	57_Q	1.655	1.00
64_A	100_L	1.647	1.00
33_D	38_G	1.607	1.00
62_Y	90_K	1.574	1.00
54_D	57_Q	1.546	1.00
114_L	143_K	1.511	1.00
75_T	153_Y	1.490	1.00
106_L	139_E	1.486	1.00
124_I	140_L	1.449	1.00
28_V	64_A	1.433	1.00
36_F	40_I	1.433	1.00
82_A	92_V	1.431	1.00
26_R	101_E	1.427	1.00
102_T	135_S	1.416	1.00
51_K	84_Y	1.407	1.00
28_V	97_L	1.397	1.00
62_Y	100_L	1.381	1.00
107_E	110_S	1.360	1.00
141_T	145_Q	1.356	1.00
123_V	156_P	1.347	1.00
65_I	138_V	1.339	1.00
103_A	106_L	1.338	1.00
94_F	138_V	1.327	1.00
89_A	92_V	1.294	1.00
36_F	42_K	1.282	1.00
16_D	19_D	1.281	1.00
93_V	100_L	1.278	1.00
64_A	97_L	1.273	1.00
110_S	143_K	1.254	1.00
100_L	104_L	1.244	1.00
108_A	111_K	1.216	1.00
83_S	141_T	1.215	1.00
31_I	81_V	1.192	1.00
48_E	51_K	1.191	1.00
123_V	159_T	1.176	1.00
59_Q	88_F	1.171	1.00
119_D	149_K	1.162	1.00
119_D	165_K	1.159	1.00
15_I	20_Y	1.153	1.00
29_F	49_A	1.125	1.00
37_M	42_K	1.124	1.00
26_R	100_L	1.122	1.00
97_L	101_E	1.121	1.00
83_S	145_Q	1.117	1.00
79_M	141_T	1.106	1.00
60_D	90_K	1.103	1.00
36_F	45_D	1.100	1.00
22_P	108_A	1.093	1.00
13_I	120_K	1.080	1.00
103_A	107_E	1.076	1.00
34_W	53_H	1.075	1.00
75_T	134_E	1.075	1.00
101_E	105_F	1.068	1.00
73_I	78_Y	1.068	1.00
104_L	108_A	1.054	1.00
29_F	33_D	1.043	1.00
23_K	130_K	1.041	1.00
105_F	132_V	1.039	1.00
62_Y	104_L	1.031	1.00
87_P	145_Q	1.012	1.00
38_G	69_A	0.998	1.00
17_L	136_A	0.981	1.00
12_L	123_V	0.979	1.00
109_I	114_L	0.976	1.00
21_Y	105_F	0.968	1.00
49_A	53_H	0.964	1.00
20_Y	112_I	0.954	1.00
45_D	48_E	0.953	1.00
55_W	84_Y	0.953	1.00
17_L	140_L	0.946	1.00
32_K	68_S	0.943	1.00
107_E	111_K	0.941	1.00
110_S	139_E	0.933	1.00
82_A	138_V	0.932	1.00
32_K	69_A	0.929	1.00
31_I	34_W	0.929	1.00
85_L	88_F	0.913	0.99
109_I	143_K	0.911	0.99
24_G	90_K	0.906	0.99
15_I	112_I	0.899	0.99
18_E	129_D	0.889	0.99
122_V	148_A	0.865	0.99
15_I	140_L	0.859	0.99
40_I	69_A	0.857	0.99
20_Y	117_Y	0.849	0.99
101_E	104_L	0.848	0.99
22_P	62_Y	0.840	0.99
21_Y	130_K	0.831	0.99
91_K	142_K	0.826	0.99
39_L	69_A	0.824	0.99
73_I	77_A	0.817	0.99
56_S	88_F	0.813	0.99
94_F	134_E	0.811	0.99
139_E	143_K	0.800	0.99
65_I	81_V	0.793	0.99
99_E	103_A	0.787	0.98
91_K	103_A	0.783	0.98
29_F	81_V	0.778	0.98
109_I	139_E	0.772	0.98
150_S	164_K	0.767	0.98
32_K	36_F	0.758	0.98
21_Y	101_E	0.757	0.98
135_S	139_E	0.756	0.98
12_L	159_T	0.743	0.98
65_I	85_L	0.742	0.98
132_V	137_Y	0.736	0.98
13_I	122_V	0.731	0.97
86_Q	142_K	0.729	0.97
106_L	135_S	0.728	0.97
102_T	106_L	0.728	0.97
137_Y	140_L	0.723	0.97
134_E	138_V	0.720	0.97
50_L	80_L	0.717	0.97
14_T	125_K	0.713	0.97
75_T	94_F	0.707	0.97
64_A	96_D	0.702	0.97
93_V	103_A	0.700	0.97
149_K	165_K	0.691	0.96
20_Y	108_A	0.691	0.96
18_E	21_Y	0.689	0.96
140_L	144_L	0.689	0.96
146_P	151_I	0.688	0.96
121_R	150_S	0.686	0.96
131_P	134_E	0.681	0.96
118_K	147_V	0.679	0.96
26_R	62_Y	0.674	0.96
94_F	135_S	0.673	0.96
36_F	39_L	0.670	0.96
49_A	84_Y	0.660	0.95
133_P	136_A	0.657	0.95
34_W	81_V	0.657	0.95
157_C	160_V	0.656	0.95
106_L	110_S	0.656	0.95
21_Y	26_R	0.654	0.95
101_E	130_K	0.650	0.95
26_R	104_L	0.646	0.95
128_S	132_V	0.643	0.95
19_D	23_K	0.643	0.95
144_L	151_I	0.643	0.95
157_C	161_P	0.642	0.95
98_E	102_T	0.641	0.95
138_V	141_T	0.640	0.95
24_G	62_Y	0.640	0.95
11_G	120_K	0.639	0.95
117_Y	144_L	0.639	0.95
14_T	156_P	0.636	0.94
18_E	130_K	0.636	0.94
158_S	161_P	0.634	0.94
8_A	11_G	0.631	0.94
65_I	92_V	0.629	0.94
75_T	78_Y	0.624	0.94
31_I	46_F	0.621	0.94
26_R	97_L	0.621	0.94
79_M	124_I	0.620	0.94
22_P	90_K	0.618	0.94
84_Y	88_F	0.616	0.93
34_W	50_L	0.612	0.93
34_W	84_Y	0.612	0.93
109_I	112_I	0.612	0.93
105_F	133_P	0.605	0.93
15_I	109_I	0.602	0.93
145_Q	151_I	0.601	0.93
114_L	140_L	0.600	0.92
45_D	72_I	0.598	0.92
53_H	88_F	0.596	0.92
135_S	138_V	0.594	0.92
34_W	38_G	0.591	0.92
116_E	120_K	0.588	0.92
112_I	116_E	0.588	0.92
47_R	80_L	0.587	0.92
109_I	136_A	0.585	0.92
150_S	159_T	0.583	0.91
84_Y	87_P	0.582	0.91
50_L	81_V	0.582	0.91
62_Y	101_E	0.580	0.91
66_T	97_L	0.576	0.91
130_K	133_P	0.575	0.91
67_C	71_A	0.573	0.91
24_G	60_D	0.573	0.91
37_M	69_A	0.572	0.91
3_I	16_D	0.570	0.90
14_T	140_L	0.565	0.90
42_K	45_D	0.554	0.89
42_K	46_F	0.553	0.89
79_M	162_L	0.552	0.89
41_L	77_A	0.552	0.89
98_E	131_P	0.549	0.89
68_S	71_A	0.547	0.89
95_G	103_A	0.547	0.89
143_K	146_P	0.546	0.89
58_Y	85_L	0.545	0.88
120_K	123_V	0.542	0.88
12_L	121_R	0.542	0.88
146_P	163_Y	0.541	0.88
55_W	58_Y	0.540	0.88
41_L	45_D	0.538	0.88
30_D	68_S	0.537	0.88
12_L	120_K	0.535	0.88
118_K	165_K	0.534	0.87
33_D	49_A	0.528	0.87
24_G	101_E	0.528	0.87
65_I	82_A	0.526	0.87
91_K	100_L	0.524	0.86
14_T	123_V	0.522	0.86
3_I	6_K	0.522	0.86
25_E	60_D	0.519	0.86
66_T	96_D	0.519	0.86
26_R	64_A	0.518	0.86
140_L	143_K	0.517	0.86
112_I	117_Y	0.516	0.86
125_K	156_P	0.515	0.85
73_I	79_M	0.514	0.85
129_D	132_V	0.514	0.85
75_T	138_V	0.512	0.85
93_V	99_E	0.511	0.85
6_K	11_G	0.511	0.85
150_S	163_Y	0.502	0.84
114_L	118_K	0.501	0.84
141_T	162_L	0.500	0.84

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
3h5jA	1	0.5818	27.6	0.957	Contact Map
3q3wA	1	0.6364	11.4	0.964	Contact Map
4i9fA	2	0.9697	11.3	0.964	Contact Map
2cunA	2	0.3333	9.9	0.965	Contact Map
5bt8A	1	0.3576	8.9	0.966	Contact Map
1v6sA	1	0.3333	8	0.966	Contact Map
1zkrA	2	0.4788	8	0.966	Contact Map
4jgtA	1	0.6303	7.1	0.967	Contact Map
1vpeA	1	0.3333	6.9	0.967	Contact Map
1t3kA	1	0.6364	6.3	0.968	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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