DUF4893 - PFAM28P - GREMLIN Contacts

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DUF4893 - Domain of unknown function (DUF4893)

PFAM:	PF16233	Sequences: WRAVATAADRDRLRRWRAAWVAALAEARAAGHAADIAAEGALLDPDAALPGPAPPPGSYRCRTIKLGAKGGLDYVAYPPFFCRVEAEGGLLRFVKLTGSQRPVGRLFPDDDRRLVFLGTLALGDETRALAYGQDPERDMAGVVERIGPNRWRLVLPWPHFESKLDVIEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	169 (169)
Sequences:	1407 (862)
Seq/√Len:	66.3
META:	0.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_F	99_S	2.867	1.00
19_A	157_W	2.816	1.00
80_F	95_K	2.803	1.00
141_G	153_L	2.781	1.00
95_K	99_S	2.626	1.00
32_H	35_D	2.513	1.00
154_V	164_L	2.403	1.00
102_P	116_F	2.383	1.00
20_W	154_V	2.348	1.00
157_W	163_K	2.325	1.00
116_F	139_M	2.320	1.00
155_L	167_I	2.264	1.00
141_G	155_L	2.231	1.00
143_V	153_L	2.229	1.00
23_A	164_L	2.183	1.00
106_L	143_V	2.174	1.00
5_A	117_L	2.080	1.00
162_S	165_D	2.059	1.00
77_Y	99_S	2.057	1.00
77_Y	80_F	1.984	1.00
1_W	5_A	1.984	1.00
65_K	161_E	1.983	1.00
19_A	23_A	1.930	1.00
72_L	77_Y	1.923	1.00
39_E	43_L	1.882	1.00
77_Y	95_K	1.768	1.00
56_P	91_L	1.748	1.00
113_R	142_V	1.738	1.00
58_S	83_R	1.738	1.00
26_E	163_K	1.736	1.00
83_R	96_L	1.732	1.00
81_F	96_L	1.713	1.00
5_A	140_A	1.690	0.99
102_P	167_I	1.564	0.99
72_L	99_S	1.561	0.99
26_E	73_D	1.561	0.99
33_A	37_A	1.560	0.99
87_E	105_R	1.537	0.99
102_P	139_M	1.515	0.99
72_L	75_V	1.461	0.98
93_F	102_P	1.457	0.98
93_F	167_I	1.429	0.98
65_K	162_S	1.394	0.98
92_R	105_R	1.372	0.98
133_Q	136_E	1.367	0.98
39_E	166_V	1.352	0.97
58_S	81_F	1.351	0.97
68_A	71_G	1.348	0.97
11_D	15_R	1.341	0.97
117_L	140_A	1.329	0.97
43_L	166_V	1.320	0.97
25_A	29_A	1.314	0.97
42_L	45_P	1.314	0.97
65_K	100_Q	1.309	0.97
50_P	53_A	1.303	0.97
161_E	165_D	1.299	0.97
146_I	150_R	1.254	0.96
80_F	97_T	1.251	0.96
86_A	90_L	1.244	0.96
134_D	137_R	1.242	0.96
9_D	12_R	1.224	0.95
43_L	47_A	1.222	0.95
17_R	21_V	1.197	0.95
94_V	103_V	1.197	0.95
120_L	160_F	1.194	0.95
121_A	128_A	1.178	0.94
7_A	10_R	1.172	0.94
7_A	11_D	1.149	0.93
158_P	162_S	1.145	0.93
86_A	89_G	1.140	0.93
132_G	138_D	1.127	0.93
54_P	84_V	1.117	0.92
8_A	11_D	1.114	0.92
106_L	114_L	1.112	0.92
139_M	155_L	1.106	0.92
85_E	94_V	1.100	0.92
69_K	72_L	1.099	0.92
59_Y	151_W	1.099	0.92
136_E	159_H	1.095	0.92
81_F	97_T	1.093	0.91
87_E	92_R	1.087	0.91
72_L	80_F	1.082	0.91
77_Y	161_E	1.076	0.91
144_E	154_V	1.076	0.91
19_A	22_A	1.036	0.89
109_D	115_V	1.028	0.89
52_P	56_P	1.023	0.88
63_T	165_D	1.021	0.88
84_V	151_W	1.017	0.88
15_R	18_A	1.009	0.88
107_F	117_L	0.999	0.87
30_A	73_D	0.992	0.87
165_D	168_E	0.975	0.86
56_P	86_A	0.974	0.86
58_S	96_L	0.965	0.85
54_P	114_L	0.963	0.85
24_L	28_R	0.956	0.85
63_T	167_I	0.951	0.85
38_A	76_A	0.951	0.85
65_K	77_Y	0.943	0.84
65_K	74_Y	0.941	0.84
87_E	90_L	0.940	0.84
85_E	127_R	0.935	0.84
60_R	79_P	0.927	0.83
85_E	92_R	0.919	0.82
17_R	46_D	0.917	0.82
15_R	157_W	0.909	0.82
92_R	103_V	0.902	0.81
18_A	22_A	0.898	0.81
145_R	150_R	0.895	0.81
55_P	59_Y	0.885	0.80
61_C	82_C	0.881	0.80
20_W	54_P	0.877	0.79
54_P	91_L	0.872	0.79
5_A	11_D	0.867	0.79
43_L	64_I	0.865	0.78
53_A	56_P	0.863	0.78
22_A	25_A	0.850	0.77
158_P	161_E	0.848	0.77
31_G	36_I	0.835	0.76
13_L	115_V	0.835	0.76
150_R	153_L	0.830	0.76
2_R	85_E	0.820	0.75
109_D	113_R	0.818	0.74
32_H	73_D	0.809	0.74
54_P	59_Y	0.804	0.73
14_R	17_R	0.800	0.73
39_E	64_I	0.799	0.73
68_A	73_D	0.799	0.73
32_H	36_I	0.797	0.73
26_E	68_A	0.794	0.72
119_T	129_L	0.786	0.72
28_R	31_G	0.784	0.71
129_L	134_D	0.784	0.71
138_D	151_W	0.784	0.71
101_R	124_D	0.778	0.71
110_D	148_P	0.772	0.70
35_D	38_A	0.769	0.70
81_F	126_T	0.769	0.70
11_D	14_R	0.752	0.68
122_L	137_R	0.750	0.68
22_A	163_K	0.750	0.68
16_W	142_V	0.746	0.68
140_A	163_K	0.738	0.67
120_L	137_R	0.735	0.66
78_P	93_F	0.735	0.66
163_K	167_I	0.733	0.66
100_Q	162_S	0.725	0.65
90_L	105_R	0.723	0.65
39_E	47_A	0.723	0.65
4_V	10_R	0.715	0.64
45_P	146_I	0.704	0.63
92_R	129_L	0.702	0.63
121_A	127_R	0.701	0.63
8_A	159_H	0.696	0.62
152_R	168_E	0.695	0.62
101_R	123_G	0.693	0.62
91_L	107_F	0.692	0.62
5_A	13_L	0.687	0.61
146_I	151_W	0.687	0.61
27_A	67_G	0.686	0.61
114_L	119_T	0.685	0.61
126_T	143_V	0.681	0.60
10_R	140_A	0.680	0.60
100_Q	161_E	0.680	0.60
58_S	97_T	0.677	0.60
3_A	126_T	0.673	0.60
20_W	164_L	0.670	0.59
75_V	161_E	0.668	0.59
84_V	145_R	0.663	0.58
21_V	25_A	0.659	0.58
86_A	91_L	0.658	0.58
45_P	141_G	0.657	0.58
70_G	73_D	0.656	0.58
105_R	130_A	0.655	0.57
30_A	33_A	0.655	0.57
83_R	149_N	0.650	0.57
5_A	10_R	0.646	0.56
56_P	105_R	0.636	0.55
156_P	162_S	0.633	0.55
78_P	138_D	0.633	0.55
138_D	159_H	0.632	0.55
3_A	84_V	0.631	0.55
40_G	47_A	0.629	0.54
53_A	114_L	0.626	0.54
146_I	149_N	0.621	0.54
23_A	124_D	0.617	0.53
22_A	26_E	0.616	0.53
75_V	99_S	0.615	0.53
40_G	43_L	0.611	0.52
92_R	102_P	0.611	0.52
80_F	135_P	0.609	0.52
20_W	144_E	0.609	0.52
2_R	14_R	0.605	0.52
50_P	91_L	0.604	0.52
77_Y	97_T	0.601	0.51
44_D	47_A	0.594	0.50
42_L	144_E	0.593	0.50
89_G	92_R	0.591	0.50
52_P	58_S	0.591	0.50
87_E	108_P	0.590	0.50
19_A	24_L	0.586	0.49
94_V	148_P	0.586	0.49
15_R	20_W	0.585	0.49
49_L	52_P	0.579	0.49
60_R	108_P	0.579	0.49
18_A	34_A	0.577	0.48
18_A	25_A	0.576	0.48
77_Y	100_Q	0.573	0.48
8_A	135_P	0.573	0.48
53_A	84_V	0.568	0.47
65_K	75_V	0.566	0.47
120_L	139_M	0.564	0.47
16_W	113_R	0.559	0.46
54_P	145_R	0.558	0.46
36_I	137_R	0.556	0.46
114_L	136_E	0.554	0.46
138_D	146_I	0.553	0.46
100_Q	122_L	0.547	0.45
42_L	59_Y	0.546	0.45
18_A	21_V	0.545	0.45
91_L	111_D	0.544	0.44
108_P	114_L	0.544	0.44
36_I	43_L	0.544	0.44
41_A	126_T	0.541	0.44
89_G	93_F	0.539	0.44
166_V	169_L	0.538	0.44
35_D	64_I	0.538	0.44
114_L	142_V	0.530	0.43
155_L	163_K	0.530	0.43
71_G	80_F	0.529	0.43
6_T	9_D	0.529	0.43
59_Y	102_P	0.526	0.42
53_A	91_L	0.525	0.42
42_L	146_I	0.524	0.42
65_K	165_D	0.521	0.42
42_L	46_D	0.520	0.42
7_A	15_R	0.519	0.42
57_G	61_C	0.515	0.41
32_H	76_A	0.515	0.41
100_Q	125_E	0.513	0.41
35_D	76_A	0.513	0.41
21_V	96_L	0.512	0.41
86_A	106_L	0.512	0.41
31_G	74_Y	0.510	0.41
144_E	150_R	0.509	0.40
13_L	17_R	0.508	0.40
24_L	42_L	0.508	0.40
102_P	141_G	0.505	0.40
27_A	31_G	0.503	0.40
95_K	98_G	0.502	0.40
99_S	122_L	0.501	0.40
41_A	62_R	0.500	0.39
56_P	112_R	0.500	0.39

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
5bypA	1	0.574	23.1	0.946	Contact Map
1hjiB	1	0.1538	7.8	0.957	Contact Map
4qrlA	1	0.6095	6.7	0.958	Contact Map
4l9nA	2	0.3077	5.7	0.959	Contact Map
1n0zA	1	0.2663	4.2	0.962	Contact Map
2nnnA	2	0.2781	4	0.962	Contact Map
3swrA	1	0.3373	4	0.962	Contact Map
2c0hA	1	0.426	3.7	0.963	Contact Map
1iicA	1	0.426	3.6	0.963	Contact Map
4s39A	2	0.3669	3.1	0.964	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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