UPF0167 - PFAM28P - GREMLIN Contacts

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UPF0167 - Uncharacterised protein family (UPF0167)

PFAM:	PF03691	Sequences: LPTFKYHPDPLATGSFEESDATCECCGQARGYIYTGPVYAEEDLEALCPWCIADGSAAEKFDAEFTDDAGLEGVDGVPEEVVEELAERTPGYSSWQQERWLTHCGDACAFLGYVGWKELEALGIALEALALYAIRDDLGLSGEWEELLESLDKDGSPTAYLFRCLHCGKYRLYVDC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (176)
Sequences:	1100 (908)
Seq/√Len:	68.4
META:	0.818

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
109_A	165_L	5.479	1.00
83_E	87_E	4.245	1.00
38_V	63_A	3.452	1.00
7_H	13_T	3.053	1.00
85_L	107_A	3.043	1.00
5_K	84_E	2.749	1.00
164_C	167_C	2.649	1.00
78_P	81_V	2.521	1.00
147_L	174_V	2.451	1.00
115_G	118_E	2.388	1.00
101_L	171_R	2.355	1.00
9_D	12_A	2.350	1.00
114_V	161_L	2.259	1.00
6_Y	106_D	2.246	1.00
92_Y	173_Y	2.146	1.00
94_S	97_Q	2.141	1.00
5_K	165_L	2.066	1.00
19_S	31_G	2.028	1.00
77_V	81_V	1.924	1.00
10_P	13_T	1.889	1.00
81_V	107_A	1.866	1.00
84_E	88_R	1.865	1.00
40_A	63_A	1.796	1.00
94_S	98_E	1.793	1.00
110_F	113_Y	1.766	1.00
44_L	61_F	1.747	1.00
64_E	68_D	1.745	1.00
103_H	171_R	1.731	1.00
104_C	167_C	1.725	1.00
25_C	47_L	1.723	1.00
106_D	166_H	1.720	1.00
7_H	10_P	1.686	1.00
50_W	54_D	1.679	0.99
104_C	164_C	1.643	0.99
113_Y	158_T	1.574	0.99
13_T	112_G	1.552	0.99
151_L	154_D	1.512	0.99
108_C	171_R	1.484	0.99
24_E	46_A	1.461	0.99
16_F	32_Y	1.446	0.98
8_P	109_A	1.437	0.98
113_Y	153_K	1.434	0.98
108_C	172_L	1.405	0.98
115_G	151_L	1.375	0.98
67_D	70_G	1.358	0.98
23_C	26_C	1.332	0.97
161_L	170_Y	1.306	0.97
131_L	135_R	1.305	0.97
37_P	94_S	1.304	0.97
34_Y	52_I	1.303	0.97
103_H	167_C	1.301	0.97
66_T	85_L	1.296	0.97
110_F	160_Y	1.291	0.97
82_V	107_A	1.290	0.97
57_A	65_F	1.267	0.96
79_E	83_E	1.267	0.96
101_L	172_L	1.242	0.96
67_D	97_Q	1.226	0.96
22_T	29_A	1.225	0.96
58_A	87_E	1.223	0.96
111_L	163_R	1.223	0.96
81_V	106_D	1.222	0.96
35_T	38_V	1.201	0.95
74_V	102_T	1.198	0.95
114_V	159_A	1.184	0.95
116_W	120_E	1.180	0.95
103_H	169_K	1.176	0.95
95_W	160_Y	1.156	0.94
30_R	50_W	1.152	0.94
159_A	172_L	1.147	0.94
64_E	87_E	1.146	0.94
34_Y	37_P	1.114	0.93
118_E	121_A	1.111	0.93
25_C	56_S	1.110	0.93
103_H	164_C	1.107	0.93
108_C	159_A	1.105	0.92
163_R	170_Y	1.104	0.92
17_E	35_T	1.079	0.92
99_R	173_Y	1.062	0.91
40_A	62_D	1.060	0.91
133_A	136_D	1.037	0.90
92_Y	172_L	1.035	0.90
153_K	158_T	1.027	0.89
6_Y	107_A	1.013	0.89
19_S	33_I	1.010	0.89
119_L	126_L	0.989	0.88
135_R	139_G	0.959	0.86
115_G	158_T	0.955	0.86
66_T	91_G	0.950	0.85
116_W	149_E	0.949	0.85
7_H	15_S	0.948	0.85
151_L	159_A	0.946	0.85
115_G	159_A	0.939	0.85
124_I	127_E	0.937	0.85
20_D	29_A	0.925	0.84
101_L	173_Y	0.919	0.83
108_C	161_L	0.915	0.83
127_E	130_A	0.913	0.83
123_G	126_L	0.913	0.83
58_A	63_A	0.903	0.82
20_D	31_G	0.902	0.82
70_G	97_Q	0.896	0.82
9_D	13_T	0.891	0.82
31_G	50_W	0.888	0.81
81_V	85_L	0.887	0.81
47_L	57_A	0.887	0.81
134_I	139_G	0.887	0.81
56_S	59_E	0.883	0.81
132_Y	135_R	0.874	0.80
119_L	130_A	0.872	0.80
157_P	176_C	0.870	0.80
134_I	137_D	0.870	0.80
113_Y	154_D	0.867	0.80
24_E	61_F	0.862	0.79
131_L	137_D	0.855	0.79
30_R	49_P	0.855	0.79
34_Y	49_P	0.853	0.79
115_G	153_K	0.849	0.78
161_L	172_L	0.846	0.78
24_E	44_L	0.846	0.78
58_A	101_L	0.841	0.78
105_G	166_H	0.831	0.77
7_H	91_G	0.817	0.76
109_A	163_R	0.815	0.75
26_C	51_C	0.808	0.75
152_D	158_T	0.807	0.75
95_W	115_G	0.803	0.74
78_P	105_G	0.797	0.74
11_L	15_S	0.797	0.74
59_E	79_E	0.789	0.73
16_F	49_P	0.787	0.73
101_L	108_C	0.782	0.72
16_F	19_S	0.781	0.72
8_P	13_T	0.779	0.72
98_E	166_H	0.767	0.71
11_L	32_Y	0.767	0.71
10_P	15_S	0.765	0.71
10_P	14_G	0.764	0.71
156_S	176_C	0.754	0.70
95_W	155_G	0.753	0.69
98_E	160_Y	0.752	0.69
18_E	32_Y	0.752	0.69
17_E	20_D	0.750	0.69
97_Q	160_Y	0.748	0.69
25_C	28_Q	0.747	0.69
152_D	156_S	0.740	0.68
22_T	168_G	0.737	0.68
118_E	153_K	0.736	0.68
129_L	132_Y	0.735	0.68
19_S	29_A	0.732	0.67
15_S	93_S	0.727	0.67
70_G	94_S	0.723	0.66
11_L	14_G	0.722	0.66
163_R	168_G	0.721	0.66
126_L	130_A	0.721	0.66
15_S	36_G	0.716	0.66
62_D	87_E	0.713	0.65
12_A	24_E	0.709	0.65
114_V	118_E	0.707	0.65
12_A	20_D	0.704	0.64
49_P	57_A	0.702	0.64
135_R	147_L	0.699	0.64
48_C	51_C	0.698	0.64
131_L	134_I	0.691	0.63
33_I	46_A	0.688	0.63
16_F	52_I	0.682	0.62
15_S	113_Y	0.682	0.62
117_K	152_D	0.682	0.62
24_E	45_E	0.680	0.62
125_A	130_A	0.678	0.61
111_L	165_L	0.675	0.61
133_A	138_L	0.673	0.61
83_E	86_A	0.672	0.61
3_T	56_S	0.672	0.61
24_E	38_V	0.668	0.60
106_D	165_L	0.668	0.60
154_D	158_T	0.665	0.60
21_A	29_A	0.664	0.60
11_L	16_F	0.653	0.58
3_T	117_K	0.652	0.58
131_L	136_D	0.652	0.58
21_A	33_I	0.649	0.58
50_W	57_A	0.646	0.58
41_E	149_E	0.644	0.57
113_Y	159_A	0.643	0.57
24_E	33_I	0.641	0.57
42_E	99_R	0.640	0.57
132_Y	136_D	0.635	0.56
128_A	131_L	0.633	0.56
123_G	129_L	0.632	0.56
127_E	161_L	0.625	0.55
133_A	137_D	0.625	0.55
135_R	140_L	0.622	0.55
23_C	90_P	0.622	0.55
25_C	60_K	0.615	0.54
125_A	129_L	0.613	0.54
23_C	48_C	0.610	0.53
82_V	85_L	0.607	0.53
49_P	52_I	0.601	0.52
112_G	123_G	0.597	0.52
8_P	88_R	0.594	0.52
130_A	134_I	0.593	0.51
134_I	140_L	0.593	0.51
74_V	77_V	0.592	0.51
20_D	32_Y	0.592	0.51
130_A	144_W	0.588	0.51
79_E	139_G	0.584	0.50
121_A	170_Y	0.583	0.50
151_L	161_L	0.581	0.50
78_P	110_F	0.580	0.50
151_L	158_T	0.579	0.50
126_L	129_L	0.577	0.49
40_A	61_F	0.577	0.49
30_R	34_Y	0.576	0.49
59_E	169_K	0.574	0.49
70_G	86_A	0.573	0.49
114_V	122_L	0.570	0.49
72_E	77_V	0.569	0.49
111_L	159_A	0.568	0.48
139_G	149_E	0.568	0.48
49_P	65_F	0.567	0.48
48_C	90_P	0.566	0.48
16_F	31_G	0.566	0.48
59_E	161_L	0.566	0.48
25_C	30_R	0.564	0.48
123_G	128_A	0.559	0.47
122_L	163_R	0.557	0.47
141_S	144_W	0.556	0.47
153_K	157_P	0.556	0.47
155_G	160_Y	0.556	0.47
132_Y	137_D	0.551	0.46
32_Y	50_W	0.547	0.46
125_A	147_L	0.547	0.46
115_G	161_L	0.541	0.45
110_F	158_T	0.541	0.45
6_Y	81_V	0.537	0.45
47_L	168_G	0.535	0.44
22_T	27_G	0.534	0.44
67_D	71_L	0.534	0.44
59_E	87_E	0.531	0.44
18_E	21_A	0.530	0.44
4_F	55_G	0.530	0.44
21_A	46_A	0.529	0.44
95_W	158_T	0.527	0.44
38_V	44_L	0.520	0.43
3_T	28_Q	0.519	0.43
82_V	110_F	0.518	0.42
111_L	170_Y	0.518	0.42
94_S	147_L	0.517	0.42
71_L	101_L	0.516	0.42
172_L	176_C	0.514	0.42
109_A	113_Y	0.511	0.42
135_R	145_E	0.511	0.42
7_H	14_G	0.507	0.41
52_I	91_G	0.507	0.41
70_G	101_L	0.505	0.41
127_E	131_L	0.504	0.41
133_A	139_G	0.504	0.41
42_E	87_E	0.502	0.41
160_Y	174_V	0.502	0.41
116_W	148_L	0.501	0.40
44_L	63_A	0.501	0.40
170_Y	173_Y	0.500	0.40
20_D	117_K	0.500	0.40

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
4aybP	1	0.0795	22.8	0.942	Contact Map
2ds5A	2	0.25	19.9	0.943	Contact Map
1yk4A	1	0.2273	12.6	0.948	Contact Map
4d02A	2	0	11.1	0.949	Contact Map
2v3bB	1	0.233	10.8	0.95	Contact Map
1e8jA	1	0.2273	10.6	0.95	Contact Map
4qf3A	2	0.233	9.9	0.95	Contact Map
1tfiA	1	0.2841	9.6	0.951	Contact Map
2l43A	1	0.3295	8.8	0.952	Contact Map
6rxnA	1	0.2273	8.7	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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