DUF4011 - PFAM28P - GREMLIN Contacts

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DUF4011 - Protein of unknown function (DUF4011)

PFAM:	PF13195	Sequences: KLLDLSLRNRLLNFRPTKKSTLRIVDPDPDELFDLLVDGEKSLRFLPPDERDEEESAEELEPDEELAAERLKDNRLQTLLTPEELEKRLRKLYRKARTALEEQGVNTLYLALGFLEWYESDDSEEPRRAPLLLVPVELERKSARSGFRLRLRDEEIEVNPTLLEKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	166 (160)
Sequences:	5930 (4713)
Seq/√Len:	372.6
META:	0.867

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_Y	126_P	3.930	1.00
116_E	128_R	3.354	1.00
116_E	126_P	3.126	1.00
137_E	150_R	2.753	1.00
99_A	107_T	2.746	1.00
139_E	150_R	2.734	1.00
97_R	101_E	2.526	1.00
7_L	127_R	2.433	1.00
111_A	114_F	2.264	1.00
33_F	37_V	2.196	1.00
91_K	95_K	2.189	1.00
28_D	31_E	2.109	1.00
34_D	39_G	2.031	1.00
120_S	123_S	2.015	1.00
42_S	150_R	2.007	1.00
134_V	156_I	1.932	1.00
117_W	129_A	1.922	1.00
7_L	13_N	1.843	1.00
158_V	163_L	1.836	1.00
20_S	95_K	1.824	1.00
90_R	94_R	1.786	1.00
27_P	73_D	1.772	1.00
14_F	114_F	1.744	1.00
35_L	43_L	1.740	1.00
31_E	34_D	1.730	1.00
45_F	89_L	1.662	1.00
118_Y	123_S	1.635	1.00
99_A	103_Q	1.629	1.00
100_L	106_N	1.615	1.00
32_L	76_L	1.606	1.00
119_E	123_S	1.597	1.00
81_T	84_E	1.565	1.00
46_L	75_R	1.559	1.00
90_R	93_Y	1.550	1.00
96_A	108_L	1.539	1.00
5_L	12_L	1.523	1.00
14_F	21_T	1.520	1.00
139_E	148_R	1.511	1.00
13_N	127_R	1.508	1.00
111_A	133_L	1.488	1.00
3_L	161_T	1.484	1.00
82_P	86_E	1.483	1.00
12_L	129_A	1.440	1.00
35_L	74_N	1.421	1.00
37_V	134_V	1.420	1.00
44_R	75_R	1.410	1.00
4_D	8_R	1.393	1.00
112_L	134_V	1.365	1.00
115_L	162_L	1.364	1.00
136_V	149_L	1.364	1.00
84_E	88_R	1.357	1.00
30_D	34_D	1.354	1.00
21_T	92_L	1.338	1.00
4_D	9_N	1.272	1.00
141_K	148_R	1.270	1.00
42_S	148_R	1.239	1.00
118_Y	124_E	1.233	1.00
51_R	54_E	1.223	1.00
93_Y	97_R	1.213	1.00
71_L	77_Q	1.186	1.00
55_E	60_L	1.179	1.00
80_L	88_R	1.168	1.00
34_D	38_D	1.159	1.00
43_L	76_L	1.159	1.00
71_L	74_N	1.155	1.00
33_F	112_L	1.155	1.00
22_L	89_L	1.150	1.00
23_R	79_L	1.133	1.00
45_F	78_T	1.132	1.00
74_N	77_Q	1.116	1.00
95_K	98_T	1.111	1.00
118_Y	127_R	1.110	1.00
90_R	140_R	1.096	1.00
119_E	165_K	1.094	1.00
115_L	131_L	1.087	1.00
68_A	71_L	1.079	1.00
90_R	147_F	1.075	1.00
84_E	87_K	1.066	1.00
70_R	75_R	1.051	1.00
151_L	156_I	1.040	1.00
47_P	82_P	1.029	1.00
137_E	152_R	1.028	1.00
28_D	71_L	1.010	1.00
44_R	74_N	1.002	1.00
7_L	129_A	0.999	1.00
42_S	139_E	0.996	1.00
19_K	91_K	0.985	1.00
11_L	133_L	0.979	1.00
44_R	148_R	0.977	1.00
110_L	149_L	0.969	1.00
71_L	75_R	0.946	1.00
131_L	158_V	0.938	1.00
129_A	165_K	0.931	1.00
157_E	160_P	0.926	1.00
100_L	137_E	0.924	1.00
16_P	23_R	0.921	1.00
6_S	10_R	0.918	1.00
142_S	146_G	0.910	1.00
67_A	71_L	0.910	1.00
98_T	102_E	0.887	1.00
98_T	101_E	0.887	1.00
134_V	151_L	0.884	1.00
10_R	15_R	0.870	1.00
161_T	164_E	0.860	1.00
45_F	85_L	0.854	1.00
6_S	12_L	0.850	1.00
35_L	41_K	0.849	1.00
24_I	45_F	0.844	1.00
118_Y	121_D	0.841	1.00
18_K	21_T	0.837	1.00
78_T	85_L	0.834	1.00
70_R	77_Q	0.833	1.00
5_L	9_N	0.831	1.00
93_Y	140_R	0.828	1.00
91_K	94_R	0.825	1.00
30_D	33_F	0.822	1.00
119_E	127_R	0.820	1.00
10_R	21_T	0.820	1.00
7_L	10_R	0.817	1.00
40_E	74_N	0.810	1.00
26_D	71_L	0.800	1.00
29_P	112_L	0.792	1.00
117_W	165_K	0.789	1.00
160_P	164_E	0.786	1.00
15_R	21_T	0.773	1.00
14_F	17_T	0.772	1.00
143_A	146_G	0.767	1.00
31_E	35_L	0.763	1.00
44_R	146_G	0.759	1.00
103_Q	107_T	0.756	1.00
67_A	70_R	0.752	1.00
63_D	66_L	0.751	1.00
25_V	79_L	0.744	1.00
31_E	72_K	0.742	1.00
65_E	68_A	0.741	1.00
142_S	145_S	0.735	1.00
115_L	166_L	0.727	1.00
93_Y	147_F	0.726	1.00
43_L	46_L	0.725	1.00
15_R	18_K	0.722	1.00
110_L	136_V	0.721	1.00
94_R	98_T	0.714	1.00
27_P	31_E	0.712	1.00
10_R	13_N	0.711	1.00
3_L	164_E	0.711	1.00
33_F	38_D	0.709	0.99
141_K	144_R	0.707	0.99
28_D	73_D	0.705	0.99
7_L	125_E	0.705	0.99
26_D	77_Q	0.704	0.99
19_K	84_E	0.694	0.99
65_E	69_E	0.694	0.99
138_L	149_L	0.693	0.99
96_A	106_N	0.689	0.99
99_A	105_V	0.686	0.99
32_L	36_L	0.684	0.99
140_R	147_F	0.680	0.99
61_E	64_E	0.679	0.99
46_L	77_Q	0.679	0.99
162_L	166_L	0.677	0.99
89_L	138_L	0.676	0.99
108_L	136_V	0.671	0.99
38_D	41_K	0.669	0.99
12_L	161_T	0.656	0.99
83_E	87_K	0.654	0.99
113_G	117_W	0.652	0.99
24_I	27_P	0.652	0.99
106_N	154_E	0.651	0.99
106_N	152_R	0.643	0.99
132_L	156_I	0.633	0.99
100_L	103_Q	0.631	0.99
10_R	95_K	0.629	0.99
88_R	95_K	0.625	0.99
152_R	155_E	0.623	0.99
33_F	156_I	0.621	0.99
3_L	13_N	0.620	0.99
23_R	78_T	0.619	0.99
10_R	20_S	0.616	0.99
80_L	85_L	0.612	0.99
68_A	72_K	0.612	0.99
69_E	73_D	0.612	0.99
7_L	15_R	0.611	0.99
63_D	73_D	0.607	0.98
15_R	24_I	0.604	0.98
89_L	147_F	0.602	0.98
95_K	99_A	0.599	0.98
70_R	73_D	0.598	0.98
62_P	67_A	0.590	0.98
73_D	77_Q	0.590	0.98
10_R	17_T	0.590	0.98
54_E	61_E	0.588	0.98
14_F	18_K	0.585	0.98
17_T	20_S	0.584	0.98
54_E	60_L	0.584	0.98
115_L	125_E	0.583	0.98
26_D	32_L	0.581	0.98
64_E	68_A	0.570	0.98
82_P	87_K	0.567	0.98
88_R	91_K	0.567	0.98
143_A	148_R	0.563	0.97
62_P	65_E	0.561	0.97
17_T	21_T	0.560	0.97
156_I	160_P	0.558	0.97
19_K	88_R	0.557	0.97
16_P	114_F	0.555	0.97
121_D	124_E	0.555	0.97
94_R	97_R	0.554	0.97
149_L	152_R	0.552	0.97
7_L	14_F	0.548	0.97
66_L	77_Q	0.548	0.97
102_E	106_N	0.543	0.97
159_N	162_L	0.542	0.97
95_K	107_T	0.540	0.97
22_L	88_R	0.540	0.97
108_L	138_L	0.539	0.97
21_T	25_V	0.538	0.97
62_P	66_L	0.535	0.97
27_P	71_L	0.532	0.96
12_L	162_L	0.528	0.96
43_L	71_L	0.528	0.96
32_L	43_L	0.527	0.96
147_F	150_R	0.527	0.96
12_L	85_L	0.525	0.96
20_S	91_K	0.525	0.96
12_L	127_R	0.523	0.96
80_L	84_E	0.522	0.96
117_W	133_L	0.522	0.96
112_L	132_L	0.519	0.96
41_K	74_N	0.517	0.96
63_D	72_K	0.516	0.96
60_L	66_L	0.513	0.96
11_L	104_G	0.512	0.96
7_L	119_E	0.509	0.95
24_I	78_T	0.508	0.95
16_P	21_T	0.508	0.95
50_E	60_L	0.508	0.95
5_L	109_Y	0.502	0.95
66_L	69_E	0.501	0.95
25_V	29_P	0.500	0.95
85_L	96_A	0.500	0.95

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
1x9yA	1	0.5542	3.1	0.938	Contact Map
2l0cA	1	0.2349	1.4	0.949	Contact Map
3rd4A	3	0.2108	1.4	0.949	Contact Map
3tweA	2	0.1566	1.4	0.949	Contact Map
1qc6A	2	0.3675	1.4	0.949	Contact Map
2c1lA	2	0.5301	1.3	0.95	Contact Map
1lngA	1	0.2048	1.3	0.95	Contact Map
4lnsA	2	0.3976	1.2	0.951	Contact Map
4f0hA	4	0.9217	1.2	0.951	Contact Map
1n0wB	1	0.1988	1.1	0.952	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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