DUF4080 - PFAM28P - GREMLIN Contacts

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DUF4080 - Protein of unknown function (DUF4080)

PFAM:	PF13311	Sequences: EEYGYVYMDYPPYEVLSTKWLSYEEILRLKRVEEMLEKYYNSGRFDHTLEYLIKKFESPFDFFEELGDYWEEKGYFRIGHSLEDLYEILLEFLEERLPEDLELLRELLKFDYLLREKYKPRPDFLEREDDKEEKEEIREFLKNEEEIPKYLPEYEGLDEKQLYKHTHIEVFSFDVTGEIEKKETYILF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	188 (173)
Sequences:	2112 (1832)
Seq/√Len:	139.3
META:	0.724

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_V	17_S	3.784	1.00
3_Y	20_W	3.471	1.00
5_Y	18_T	3.375	1.00
22_S	25_E	3.255	1.00
14_E	30_K	3.181	1.00
73_K	91_E	2.685	1.00
28_R	64_E	2.671	1.00
4_G	19_K	2.498	1.00
58_S	61_D	2.450	1.00
48_T	104_L	2.432	1.00
90_L	105_R	2.429	1.00
31_R	71_E	2.360	1.00
51_Y	107_L	2.251	1.00
93_L	104_L	2.233	1.00
44_R	82_L	2.164	1.00
65_E	96_R	2.161	1.00
43_G	46_D	2.143	1.00
47_H	114_L	2.095	1.00
35_M	66_L	2.061	1.00
31_R	67_G	1.921	1.00
21_L	26_I	1.916	1.00
16_L	23_Y	1.902	1.00
53_I	62_F	1.876	1.00
47_H	110_F	1.803	1.00
21_L	25_E	1.737	1.00
65_E	92_F	1.723	1.00
84_D	87_E	1.683	1.00
34_E	38_K	1.667	1.00
106_E	172_S	1.662	1.00
5_Y	15_V	1.632	1.00
32_V	67_G	1.613	1.00
87_E	91_E	1.557	1.00
28_R	68_D	1.521	1.00
2_E	19_K	1.511	1.00
113_L	121_R	1.498	1.00
138_R	142_K	1.493	1.00
62_F	66_L	1.479	1.00
94_E	101_L	1.408	1.00
141_L	166_T	1.404	1.00
15_V	18_T	1.367	1.00
4_G	17_S	1.366	1.00
32_V	35_M	1.351	1.00
38_K	85_L	1.344	1.00
80_H	84_D	1.333	1.00
122_P	125_L	1.322	1.00
143_N	147_I	1.305	1.00
70_W	85_L	1.302	1.00
148_P	151_L	1.292	1.00
69_Y	92_F	1.285	1.00
83_E	112_Y	1.277	1.00
87_E	124_F	1.253	1.00
75_Y	88_I	1.251	1.00
52_L	62_F	1.245	1.00
39_Y	89_L	1.198	1.00
121_R	125_L	1.198	1.00
61_D	64_E	1.195	1.00
133_E	137_I	1.193	1.00
52_L	93_L	1.192	1.00
55_K	100_D	1.192	1.00
28_R	60_F	1.178	1.00
130_D	133_E	1.178	1.00
44_R	115_R	1.174	1.00
32_V	36_L	1.164	0.99
151_L	154_Y	1.154	0.99
148_P	152_P	1.143	0.99
34_E	37_E	1.134	0.99
53_I	63_F	1.131	0.99
161_Q	164_K	1.124	0.99
161_Q	165_H	1.123	0.99
73_K	95_E	1.106	0.99
143_N	146_E	1.102	0.99
158_D	161_Q	1.084	0.99
64_E	68_D	1.079	0.99
129_D	133_E	1.076	0.99
87_E	123_D	1.075	0.99
141_L	144_E	1.075	0.99
159_E	166_T	1.074	0.99
110_F	171_F	1.068	0.99
140_F	150_Y	1.066	0.99
23_Y	30_K	1.063	0.99
112_Y	118_Y	1.059	0.99
147_I	152_P	1.058	0.99
53_I	59_P	1.057	0.99
72_E	95_E	1.052	0.99
78_I	84_D	1.051	0.99
42_S	45_F	1.049	0.99
93_L	108_L	1.038	0.99
31_R	68_D	1.027	0.99
144_E	148_P	1.018	0.99
80_H	88_I	1.008	0.98
157_L	161_Q	1.006	0.98
86_Y	124_F	1.003	0.98
109_K	169_E	1.000	0.98
160_K	163_Y	0.992	0.98
35_M	67_G	0.992	0.98
35_M	70_W	0.989	0.98
29_L	36_L	0.987	0.98
171_F	175_V	0.985	0.98
29_L	32_V	0.984	0.98
69_Y	91_E	0.983	0.98
133_E	136_E	0.967	0.98
103_L	107_L	0.965	0.98
83_E	118_Y	0.962	0.98
100_D	103_L	0.952	0.98
5_Y	11_P	0.950	0.98
106_E	171_F	0.945	0.98
140_F	146_E	0.939	0.98
33_E	60_F	0.919	0.97
97_L	100_D	0.919	0.97
91_E	95_E	0.910	0.97
70_W	76_F	0.908	0.97
31_R	76_F	0.902	0.97
157_L	165_H	0.902	0.97
81_S	84_D	0.894	0.97
130_D	137_I	0.884	0.97
72_E	96_R	0.882	0.96
159_E	163_Y	0.879	0.96
105_R	109_K	0.866	0.96
152_P	155_E	0.865	0.96
69_Y	88_I	0.855	0.96
138_R	163_Y	0.854	0.96
103_L	173_F	0.848	0.96
50_E	54_K	0.839	0.95
150_Y	154_Y	0.832	0.95
129_D	132_E	0.829	0.95
84_D	88_I	0.827	0.95
69_Y	73_K	0.824	0.95
102_E	105_R	0.824	0.95
101_L	105_R	0.823	0.95
48_T	93_L	0.817	0.95
75_Y	91_E	0.815	0.95
70_W	75_Y	0.801	0.94
141_L	168_I	0.795	0.94
47_H	107_L	0.795	0.94
86_Y	112_Y	0.794	0.94
137_I	141_L	0.793	0.94
138_R	160_K	0.793	0.94
8_M	16_L	0.785	0.93
112_Y	125_L	0.783	0.93
139_E	143_N	0.775	0.93
70_W	80_H	0.775	0.93
113_L	119_K	0.774	0.93
158_D	163_Y	0.767	0.93
134_K	138_R	0.761	0.92
90_L	94_E	0.758	0.92
131_K	134_K	0.750	0.92
69_Y	75_Y	0.750	0.92
38_K	80_H	0.745	0.91
44_R	116_E	0.744	0.91
138_R	141_L	0.744	0.91
147_I	162_L	0.737	0.91
135_E	142_K	0.736	0.91
70_W	88_I	0.736	0.91
132_E	136_E	0.731	0.91
22_S	26_I	0.729	0.91
40_Y	63_F	0.725	0.90
51_Y	100_D	0.722	0.90
135_E	139_E	0.720	0.90
109_K	125_L	0.715	0.90
163_Y	166_T	0.714	0.90
138_R	147_I	0.707	0.89
139_E	142_K	0.706	0.89
163_Y	167_H	0.701	0.89
5_Y	124_F	0.700	0.89
97_L	101_L	0.699	0.89
137_I	140_F	0.696	0.88
97_L	104_L	0.693	0.88
51_Y	93_L	0.678	0.87
116_E	122_P	0.672	0.87
23_Y	92_F	0.663	0.86
154_Y	162_L	0.657	0.85
130_D	134_K	0.653	0.85
69_Y	95_E	0.651	0.85
131_K	143_N	0.643	0.84
32_V	76_F	0.640	0.84
137_I	168_I	0.640	0.84
23_Y	35_M	0.637	0.84
43_G	84_D	0.636	0.84
148_P	154_Y	0.634	0.83
151_L	165_H	0.634	0.83
39_Y	66_L	0.633	0.83
82_L	115_R	0.632	0.83
55_K	65_E	0.631	0.83
136_E	139_E	0.630	0.83
9_D	63_F	0.630	0.83
159_E	162_L	0.629	0.83
148_P	155_E	0.628	0.83
106_E	173_F	0.626	0.83
90_L	101_L	0.626	0.83
17_S	24_E	0.626	0.83
160_K	164_K	0.625	0.82
93_L	100_D	0.624	0.82
21_L	29_L	0.621	0.82
51_Y	104_L	0.617	0.82
27_L	31_R	0.617	0.82
3_Y	19_K	0.613	0.81
49_L	53_I	0.611	0.81
161_Q	166_T	0.610	0.81
81_S	112_Y	0.607	0.81
48_T	89_L	0.607	0.81
74_G	77_R	0.606	0.80
94_E	105_R	0.605	0.80
145_E	148_P	0.604	0.80
56_F	92_F	0.602	0.80
26_I	36_L	0.600	0.80
39_Y	70_W	0.600	0.80
48_T	108_L	0.592	0.79
132_E	135_E	0.589	0.79
52_L	56_F	0.587	0.78
112_Y	116_E	0.586	0.78
147_I	151_L	0.585	0.78
15_V	26_I	0.585	0.78
99_E	106_E	0.584	0.78
147_I	150_Y	0.583	0.78
55_K	104_L	0.581	0.78
167_H	171_F	0.580	0.78
128_E	133_E	0.578	0.77
18_T	21_L	0.572	0.77
142_K	159_E	0.570	0.76
65_E	68_D	0.565	0.76
17_S	26_I	0.562	0.75
27_L	30_K	0.561	0.75
65_E	73_K	0.561	0.75
61_D	65_E	0.561	0.75
159_E	170_V	0.559	0.75
162_L	168_I	0.558	0.75
109_K	121_R	0.556	0.75
172_S	175_V	0.554	0.74
59_P	62_F	0.553	0.74
158_D	169_E	0.552	0.74
109_K	113_L	0.549	0.74
33_E	36_L	0.548	0.74
10_Y	17_S	0.547	0.73
133_E	170_V	0.546	0.73
118_Y	121_R	0.543	0.73
149_K	171_F	0.543	0.73
127_R	130_D	0.541	0.73
44_R	119_K	0.535	0.72
65_E	97_L	0.534	0.72
39_Y	119_K	0.528	0.71
129_D	141_L	0.525	0.70
116_E	121_R	0.524	0.70
56_F	63_F	0.524	0.70
7_Y	148_P	0.520	0.70
34_E	66_L	0.519	0.69
113_L	167_H	0.519	0.69
91_E	94_E	0.519	0.69
147_I	154_Y	0.518	0.69
131_K	136_E	0.516	0.69
149_K	152_P	0.516	0.69
63_F	78_I	0.514	0.69
106_E	110_F	0.513	0.69
55_K	101_L	0.507	0.68
83_E	120_P	0.507	0.68
158_D	166_T	0.505	0.67
51_Y	103_L	0.504	0.67
37_E	63_F	0.504	0.67
24_E	27_L	0.503	0.67
34_E	80_H	0.500	0.67
27_L	34_E	0.500	0.67

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
1ercA	1	0.0745	21.7	0.933	Contact Map
2e9xA	1	0.2979	4.6	0.951	Contact Map
3cl6A	3	0.5053	4.5	0.951	Contact Map
3f2kA	1	0.4309	4.3	0.951	Contact Map
4mdaA	1	0.4362	4.2	0.951	Contact Map
4i43B	1	0.9043	3.5	0.953	Contact Map
3s6oA	3	0.4947	3.5	0.953	Contact Map
4jrbA	1	0.8404	3.2	0.954	Contact Map
2xpnB	1	0.0479	3.1	0.955	Contact Map
4jbuA	1	0.4415	2.5	0.957	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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