DUF3109 - PFAM28P - GREMLIN Contacts

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DUF3109 - Protein of unknown function (DUF3109)

PFAM:	PF11307	Sequences: MIQIGDTLVSDDILEKKFVCDLSKCKGACCVEGDAGAPLEEEELEILEEIYPKVKPYLSPEGIAAIEKQGVYVIDEDGDLVTPLVNGKECAFVIFDENGIAKCAIEKAYNEGKIDFKKPISCHLYPIRIKKYKEFEAVNYHRWDICKPACELGKKLKVPVYKFLKEPLIRKFGEEWYEELE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	181 (180)
Sequences:	6126 (3975)
Seq/√Len:	296.3
META:	0.934

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_E	172_F	2.715	1.00
55_K	63_I	2.614	1.00
174_E	178_E	2.607	1.00
19_V	158_V	2.506	1.00
5_G	179_E	2.442	1.00
57_Y	111_E	2.418	1.00
123_H	170_R	2.247	1.00
58_L	66_I	2.217	1.00
165_K	169_I	2.137	1.00
65_A	69_Q	2.133	1.00
46_I	49_E	2.127	1.00
110_N	117_K	2.109	1.00
129_I	136_E	2.108	1.00
152_L	156_L	2.090	1.00
159_P	162_K	2.083	1.00
55_K	67_E	2.067	1.00
95_F	101_A	1.989	1.00
169_I	174_E	1.963	1.00
60_P	64_A	1.923	1.00
50_I	54_V	1.922	1.00
19_V	156_L	1.866	1.00
17_K	157_K	1.851	1.00
164_L	167_P	1.839	1.00
117_K	166_E	1.822	1.00
58_L	104_A	1.780	1.00
50_I	114_I	1.752	1.00
132_Y	135_F	1.751	1.00
7_T	176_W	1.722	1.00
46_I	50_I	1.717	1.00
93_V	101_A	1.642	1.00
28_A	32_E	1.634	1.00
17_K	154_K	1.626	1.00
53_K	113_K	1.620	1.00
13_I	127_I	1.617	1.00
131_K	136_E	1.601	1.00
47_L	105_I	1.599	1.00
45_E	49_E	1.569	1.00
51_Y	63_I	1.561	1.00
83_P	92_F	1.553	1.00
48_E	71_V	1.520	1.00
168_L	176_W	1.499	1.00
75_D	81_V	1.483	1.00
24_K	148_P	1.471	1.00
50_I	115_D	1.464	1.00
51_Y	71_V	1.451	1.00
109_Y	117_K	1.442	1.00
125_Y	141_H	1.426	1.00
44_L	72_Y	1.425	1.00
40_E	171_K	1.406	1.00
50_I	53_K	1.397	1.00
44_L	80_L	1.369	1.00
62_G	91_A	1.332	1.00
64_A	68_K	1.318	1.00
3_Q	6_D	1.313	1.00
35_A	81_V	1.302	1.00
72_Y	80_L	1.294	1.00
107_K	111_E	1.289	1.00
21_D	152_L	1.282	1.00
31_V	101_A	1.276	1.00
56_P	113_K	1.247	1.00
73_V	83_P	1.245	1.00
16_K	150_C	1.243	1.00
125_Y	143_W	1.241	1.00
54_V	105_I	1.237	1.00
60_P	63_I	1.233	1.00
74_I	80_L	1.212	1.00
94_I	102_K	1.205	1.00
129_I	138_V	1.201	1.00
94_I	107_K	1.192	1.00
45_E	48_E	1.180	1.00
51_Y	55_K	1.178	1.00
46_I	115_D	1.166	1.00
147_K	150_C	1.163	1.00
65_A	68_K	1.159	1.00
2_I	14_L	1.152	1.00
19_V	152_L	1.145	1.00
105_I	114_I	1.143	1.00
120_I	171_K	1.135	1.00
69_Q	83_P	1.132	1.00
63_I	67_E	1.129	1.00
32_E	88_K	1.111	1.00
58_L	62_G	1.105	1.00
96_D	102_K	1.102	1.00
132_Y	137_A	1.100	1.00
14_L	180_L	1.094	1.00
129_I	171_K	1.073	1.00
83_P	91_A	1.055	1.00
117_K	123_H	1.049	1.00
57_Y	113_K	1.048	1.00
140_Y	150_C	1.046	1.00
17_K	21_D	1.039	1.00
44_L	71_V	1.039	1.00
1_M	11_D	1.036	1.00
73_V	81_V	1.033	1.00
57_Y	108_A	1.029	1.00
59_S	62_G	1.027	1.00
107_K	110_N	1.025	1.00
71_V	92_F	1.025	1.00
102_K	110_N	1.014	1.00
21_D	24_K	0.996	1.00
10_S	139_N	0.993	1.00
3_Q	11_D	0.988	1.00
16_K	142_R	0.987	1.00
17_K	159_P	0.983	1.00
64_A	67_E	0.982	1.00
41_E	80_L	0.982	1.00
1_M	8_L	0.980	1.00
96_D	100_I	0.971	1.00
61_E	86_N	0.969	1.00
69_Q	73_V	0.948	1.00
59_S	95_F	0.948	1.00
59_S	89_E	0.940	1.00
4_I	7_T	0.933	1.00
94_I	104_A	0.928	1.00
65_A	85_V	0.922	1.00
127_I	138_V	0.918	1.00
2_I	11_D	0.916	1.00
48_E	72_Y	0.915	1.00
65_A	83_P	0.911	1.00
3_Q	8_L	0.909	1.00
39_L	72_Y	0.908	1.00
65_A	91_A	0.906	1.00
165_K	174_E	0.904	1.00
44_L	48_E	0.897	1.00
13_I	160_V	0.892	1.00
47_L	54_V	0.888	1.00
35_A	75_D	0.879	1.00
39_L	82_T	0.872	1.00
156_L	159_P	0.869	1.00
9_V	180_L	0.865	1.00
59_S	93_V	0.860	1.00
152_L	155_K	0.858	1.00
5_G	175_E	0.849	1.00
12_D	16_K	0.834	1.00
49_E	115_D	0.831	1.00
16_K	154_K	0.831	1.00
53_K	114_I	0.830	1.00
129_I	172_F	0.826	1.00
151_E	154_K	0.824	1.00
40_E	131_K	0.818	1.00
148_P	152_L	0.818	1.00
144_D	147_K	0.811	1.00
176_W	180_L	0.810	1.00
6_D	136_E	0.810	1.00
84_L	91_A	0.809	1.00
94_I	111_E	0.807	1.00
136_E	171_K	0.800	1.00
39_L	44_L	0.795	0.99
11_D	14_L	0.795	0.99
21_D	155_K	0.785	0.99
84_L	93_V	0.784	0.99
151_E	155_K	0.781	0.99
148_P	151_E	0.778	0.99
50_I	105_I	0.776	0.99
59_S	94_I	0.774	0.99
106_E	117_K	0.773	0.99
51_Y	66_I	0.766	0.99
89_E	95_F	0.766	0.99
47_L	71_V	0.762	0.99
62_G	85_V	0.761	0.99
61_E	89_E	0.755	0.99
52_P	56_P	0.752	0.99
26_K	99_G	0.751	0.99
51_Y	92_F	0.745	0.99
169_I	178_E	0.744	0.99
49_E	52_P	0.744	0.99
142_R	150_C	0.744	0.99
162_K	167_P	0.741	0.99
168_L	172_F	0.739	0.99
51_Y	54_V	0.733	0.99
14_L	17_K	0.731	0.99
53_K	56_P	0.730	0.99
105_I	116_F	0.727	0.99
66_I	91_A	0.724	0.99
41_E	45_E	0.716	0.99
41_E	44_L	0.705	0.99
28_A	145_I	0.704	0.99
66_I	70_G	0.700	0.99
22_L	100_I	0.697	0.99
31_V	93_V	0.696	0.99
52_P	55_K	0.693	0.99
12_D	142_R	0.691	0.99
75_D	78_G	0.689	0.99
85_V	88_K	0.688	0.99
77_D	81_V	0.686	0.98
31_V	95_F	0.685	0.98
54_V	114_I	0.681	0.98
57_Y	107_K	0.678	0.98
169_I	177_Y	0.673	0.98
59_S	63_I	0.672	0.98
46_I	53_K	0.670	0.98
62_G	89_E	0.663	0.98
85_V	89_E	0.662	0.98
172_F	176_W	0.660	0.98
147_K	151_E	0.658	0.98
35_A	77_D	0.654	0.98
102_K	107_K	0.650	0.98
28_A	148_P	0.643	0.98
120_I	170_R	0.642	0.98
166_E	169_I	0.636	0.98
103_C	106_E	0.636	0.98
160_V	164_L	0.629	0.97
7_T	138_V	0.629	0.97
109_Y	112_G	0.627	0.97
74_I	78_G	0.627	0.97
162_K	177_Y	0.621	0.97
138_V	168_L	0.621	0.97
149_A	160_V	0.618	0.97
42_E	46_I	0.614	0.97
146_C	153_G	0.614	0.97
158_V	162_K	0.614	0.97
22_L	102_K	0.613	0.97
23_S	98_N	0.611	0.97
52_P	71_V	0.610	0.97
144_D	148_P	0.605	0.97
57_Y	104_A	0.603	0.97
59_S	85_V	0.601	0.97
28_A	31_V	0.600	0.97
158_V	163_F	0.598	0.96
165_K	177_Y	0.598	0.96
125_Y	145_I	0.597	0.96
14_L	161_Y	0.597	0.96
97_E	107_K	0.593	0.96
110_N	113_K	0.591	0.96
175_E	179_E	0.589	0.96
127_I	168_L	0.584	0.96
130_K	137_A	0.584	0.96
4_I	179_E	0.583	0.96
8_L	11_D	0.583	0.96
140_Y	160_V	0.582	0.96
161_Y	180_L	0.576	0.96
74_I	79_D	0.576	0.96
48_E	52_P	0.573	0.95
42_E	45_E	0.573	0.95
164_L	169_I	0.571	0.95
150_C	154_K	0.566	0.95
7_T	11_D	0.561	0.95
11_D	15_E	0.560	0.95
60_P	67_E	0.557	0.95
62_G	65_A	0.556	0.95
23_S	100_I	0.556	0.95
44_L	92_F	0.553	0.95
85_V	93_V	0.553	0.95
44_L	50_I	0.552	0.94
84_L	87_G	0.551	0.94
14_L	160_V	0.550	0.94
149_A	153_G	0.550	0.94
138_V	172_F	0.545	0.94
75_D	79_D	0.544	0.94
175_E	178_E	0.543	0.94
16_K	157_K	0.538	0.94
127_I	164_L	0.536	0.94
35_A	76_E	0.534	0.93
53_K	57_Y	0.533	0.93
4_I	9_V	0.532	0.93
95_F	99_G	0.532	0.93
3_Q	135_F	0.525	0.93
46_I	116_F	0.521	0.93
65_A	84_L	0.520	0.93
121_S	128_R	0.519	0.92
3_Q	14_L	0.518	0.92
82_T	86_N	0.518	0.92
41_E	72_Y	0.517	0.92
22_L	148_P	0.513	0.92
19_V	23_S	0.511	0.92
7_T	129_I	0.511	0.92
132_Y	138_V	0.510	0.92
35_A	79_D	0.507	0.92
94_I	99_G	0.505	0.91
81_V	93_V	0.500	0.91

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
1lwuA	2	0.3149	8.2	0.951	Contact Map
1fzcA	1	0.2652	8.1	0.951	Contact Map
4qtqA	1	0.3591	6	0.953	Contact Map
1pm4A	3	0.2928	5.7	0.954	Contact Map
4jf3A	3	0.3149	4.6	0.956	Contact Map
1jg5A	3	0.2652	4.5	0.956	Contact Map
4ylfA	1	0.3757	3.3	0.959	Contact Map
2eboA	3	0.2707	3.3	0.959	Contact Map
2qpxA	3	0.3923	3	0.96	Contact Map
2gp4A	2	0.3646	2.8	0.96	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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