DUF1336 - PFAM28P - GREMLIN Contacts

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DUF1336 - Protein of unknown function (DUF1336)

PFAM:	PF07059	Sequences: WSEPDGSTFKVRGPNYLKDKKKVPAAGDALYKLVGVDWFKSDKKIDHIARRPEPLPAQSKASGKLPFIFVVNLQVPGPGYSLVLYFKATEDEPLPDGSLKVKLFALKRFVNGDDAFRNSRFKLIPRIVNGPWIVKKAVGEKPVLLGKALQCNYFRGPEFNYLEIDVDIGSSSVIARKILGLVLGYLKSLVVDLGFLIEGQTEEELPERLLGCVRLNKID	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	219 (208)
Sequences:	803 (520)
Seq/√Len:	36.0
META:	0.352

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
194_G	209_L	4.428	1.00
192_D	214_R	4.063	1.00
49_A	70_V	4.037	1.00
15_N	19_D	3.978	1.00
46_D	74_Q	3.635	1.00
13_G	23_V	3.235	1.00
69_F	164_I	3.224	1.00
47_H	161_Y	3.081	1.00
12_R	16_Y	2.999	1.00
168_I	175_A	2.964	1.00
199_G	205_L	2.738	1.00
13_G	19_D	2.700	1.00
124_I	196_L	2.628	1.00
71_V	195_F	2.541	1.00
74_Q	81_S	2.458	1.00
120_R	204_E	2.367	1.00
31_Y	65_L	2.324	0.99
49_A	165_D	2.192	0.99
35_G	85_Y	2.166	0.99
11_V	124_I	2.123	0.99
44_K	74_Q	2.028	0.99
37_D	85_Y	2.017	0.98
11_V	23_V	1.931	0.98
47_H	165_D	1.918	0.98
116_F	120_R	1.911	0.98
29_A	209_L	1.878	0.98
34_V	68_I	1.845	0.97
13_G	16_Y	1.734	0.96
12_R	22_K	1.701	0.96
162_L	197_I	1.701	0.96
73_L	168_I	1.693	0.95
36_V	213_V	1.683	0.95
194_G	212_C	1.664	0.95
33_L	86_F	1.641	0.95
9_F	194_G	1.592	0.94
14_P	202_E	1.568	0.93
36_V	84_L	1.545	0.93
16_Y	198_E	1.522	0.92
22_K	122_K	1.517	0.92
145_L	166_V	1.486	0.91
168_I	179_L	1.474	0.91
114_D	117_R	1.437	0.90
88_A	96_D	1.436	0.90
108_R	204_E	1.432	0.89
29_A	78_P	1.416	0.89
59_S	71_V	1.415	0.89
85_Y	185_Y	1.398	0.88
38_W	82_L	1.367	0.87
11_V	209_L	1.360	0.87
136_K	139_G	1.360	0.87
92_E	95_P	1.325	0.85
117_R	153_Y	1.324	0.85
17_L	199_G	1.317	0.85
139_G	145_L	1.312	0.85
59_S	63_G	1.309	0.85
16_Y	22_K	1.291	0.84
142_P	148_A	1.277	0.83
156_G	160_N	1.276	0.83
106_L	109_F	1.271	0.83
12_R	122_K	1.266	0.83
42_D	128_V	1.264	0.83
3_E	32_K	1.245	0.82
146_G	153_Y	1.239	0.81
48_I	165_D	1.233	0.81
146_G	171_S	1.216	0.80
118_N	153_Y	1.210	0.80
20_K	141_K	1.206	0.79
127_I	130_G	1.188	0.78
6_G	210_L	1.186	0.78
48_I	162_L	1.176	0.78
131_P	134_V	1.171	0.77
171_S	178_I	1.162	0.77
27_G	38_W	1.151	0.76
127_I	191_V	1.144	0.76
122_K	142_P	1.136	0.75
31_Y	171_S	1.119	0.74
66_P	76_P	1.112	0.74
12_R	142_P	1.100	0.73
215_L	219_D	1.100	0.73
72_N	127_I	1.098	0.73
143_V	148_A	1.095	0.72
77_G	169_G	1.084	0.72
75_V	126_R	1.084	0.72
45_I	74_Q	1.081	0.71
10_K	24_P	1.078	0.71
18_K	50_R	1.075	0.71
32_K	166_V	1.072	0.71
111_N	155_R	1.060	0.70
154_F	161_Y	1.057	0.70
72_N	81_S	1.056	0.70
69_F	162_L	1.051	0.69
86_F	211_G	1.047	0.69
130_G	134_V	1.036	0.68
35_G	72_N	1.033	0.68
129_N	132_W	1.033	0.68
74_Q	165_D	1.029	0.68
37_D	72_N	1.024	0.67
177_K	198_E	1.019	0.67
121_F	195_F	1.005	0.66
47_H	154_F	0.997	0.65
134_V	185_Y	0.995	0.65
34_V	53_E	0.987	0.64
132_W	139_G	0.975	0.63
190_V	214_R	0.972	0.63
149_L	153_Y	0.967	0.63
89_T	95_P	0.959	0.62
134_V	181_L	0.957	0.62
120_R	160_N	0.955	0.62
86_F	185_Y	0.955	0.62
130_G	139_G	0.954	0.62
77_G	161_Y	0.948	0.61
15_N	23_V	0.947	0.61
73_L	137_A	0.929	0.60
138_V	145_L	0.925	0.59
74_Q	169_G	0.924	0.59
198_E	207_E	0.920	0.59
36_V	215_L	0.919	0.59
111_N	121_F	0.916	0.59
127_I	134_V	0.913	0.58
127_I	138_V	0.911	0.58
81_S	165_D	0.911	0.58
167_D	192_D	0.904	0.58
52_P	85_Y	0.900	0.57
5_D	70_V	0.899	0.57
80_Y	183_L	0.898	0.57
30_L	37_D	0.898	0.57
48_I	83_V	0.896	0.57
35_G	182_V	0.891	0.56
47_H	50_R	0.883	0.56
68_I	87_K	0.883	0.56
18_K	62_S	0.882	0.56
14_P	36_V	0.881	0.56
22_K	142_P	0.870	0.55
124_I	129_N	0.870	0.55
118_N	161_Y	0.868	0.54
175_A	178_I	0.866	0.54
144_L	200_Q	0.863	0.54
18_K	202_E	0.861	0.54
39_F	45_I	0.857	0.53
39_F	120_R	0.857	0.53
17_L	78_P	0.847	0.53
52_P	199_G	0.845	0.52
81_S	168_I	0.844	0.52
129_N	134_V	0.841	0.52
72_N	167_D	0.840	0.52
45_I	68_I	0.837	0.52
41_S	90_E	0.836	0.52
11_V	173_V	0.834	0.51
106_L	110_V	0.831	0.51
2_S	210_L	0.829	0.51
1_W	11_V	0.820	0.50
108_R	112_G	0.819	0.50
189_L	217_K	0.795	0.48
30_L	180_G	0.793	0.48
130_G	135_K	0.791	0.48
189_L	192_D	0.782	0.47
33_L	170_S	0.779	0.47
146_G	169_G	0.779	0.47
50_R	164_I	0.775	0.46
69_F	123_L	0.774	0.46
13_G	172_S	0.772	0.46
38_W	148_A	0.764	0.45
130_G	138_V	0.759	0.45
161_Y	165_D	0.759	0.45
13_G	210_L	0.758	0.45
125_P	146_G	0.758	0.45
16_Y	122_K	0.758	0.45
117_R	171_S	0.753	0.44
6_G	209_L	0.746	0.44
59_S	62_S	0.741	0.43
156_G	162_L	0.739	0.43
71_V	86_F	0.733	0.43
127_I	189_L	0.733	0.43
37_D	176_R	0.726	0.42
28_D	142_P	0.718	0.41
4_P	192_D	0.717	0.41
63_G	68_I	0.712	0.41
49_A	144_L	0.707	0.41
135_K	138_V	0.706	0.40
105_A	109_F	0.704	0.40
186_L	191_V	0.701	0.40
128_V	192_D	0.699	0.40
131_P	135_K	0.697	0.40
156_G	161_Y	0.691	0.39
150_Q	153_Y	0.688	0.39
33_L	36_V	0.687	0.39
134_V	171_S	0.685	0.39
26_A	97_G	0.682	0.38
46_D	75_V	0.681	0.38
77_G	80_Y	0.680	0.38
30_L	84_L	0.680	0.38
213_V	219_D	0.679	0.38
125_P	180_G	0.678	0.38
176_R	187_K	0.676	0.38
105_A	166_V	0.676	0.38
20_K	27_G	0.676	0.38
9_F	212_C	0.676	0.38
84_L	193_L	0.675	0.38
39_F	73_L	0.671	0.38
90_E	94_L	0.667	0.37
15_N	18_K	0.666	0.37
138_V	175_A	0.666	0.37
169_G	173_V	0.664	0.37
22_K	198_E	0.663	0.37
183_L	193_L	0.656	0.36
201_T	211_G	0.655	0.36
173_V	176_R	0.655	0.36
39_F	164_I	0.655	0.36
135_K	170_S	0.653	0.36
169_G	176_R	0.652	0.36
123_L	178_I	0.649	0.36
90_E	95_P	0.649	0.36
79_G	171_S	0.648	0.36
83_V	123_L	0.648	0.36
35_G	73_L	0.647	0.36
156_G	217_K	0.646	0.36
73_L	127_I	0.644	0.35
44_K	192_D	0.644	0.35
16_Y	43_K	0.638	0.35
129_N	171_S	0.636	0.35
131_P	136_K	0.634	0.35
78_P	179_L	0.634	0.35
161_Y	203_E	0.630	0.34
36_V	82_L	0.630	0.34
141_K	191_V	0.628	0.34
166_V	171_S	0.626	0.34
120_R	200_Q	0.623	0.34
139_G	170_S	0.622	0.34
121_F	144_L	0.622	0.34
107_K	112_G	0.621	0.34
73_L	216_N	0.621	0.34
11_V	196_L	0.618	0.33
143_V	166_V	0.617	0.33
55_L	75_V	0.617	0.33
94_L	97_G	0.617	0.33
125_P	193_L	0.615	0.33
67_F	146_G	0.609	0.33
142_P	207_E	0.609	0.33
50_R	193_L	0.605	0.32
35_G	95_P	0.604	0.32
19_D	182_V	0.601	0.32
145_L	151_C	0.600	0.32
190_V	217_K	0.599	0.32
75_V	179_L	0.599	0.32
109_F	117_R	0.596	0.32
28_D	61_A	0.594	0.32
90_E	96_D	0.589	0.31
96_D	108_R	0.589	0.31
45_I	81_S	0.588	0.31
84_L	213_V	0.586	0.31
20_K	50_R	0.585	0.31
24_P	86_F	0.585	0.31
76_P	195_F	0.584	0.31
1_W	12_R	0.583	0.31
137_A	178_I	0.577	0.30
59_S	203_E	0.577	0.30
79_G	169_G	0.576	0.30
49_A	92_E	0.575	0.30
19_D	205_L	0.573	0.30
30_L	155_R	0.571	0.30
14_P	205_L	0.571	0.30
98_S	168_I	0.570	0.30
19_D	202_E	0.567	0.30
120_R	165_D	0.566	0.29
17_L	144_L	0.560	0.29
149_L	169_G	0.560	0.29
23_V	179_L	0.559	0.29
33_L	213_V	0.559	0.29
166_V	189_L	0.558	0.29
19_D	121_F	0.556	0.29
127_I	173_V	0.554	0.29
126_R	145_L	0.553	0.29
89_T	97_G	0.552	0.28
128_V	167_D	0.551	0.28
197_I	209_L	0.546	0.28
122_K	207_E	0.545	0.28
84_L	219_D	0.543	0.28
109_F	167_D	0.541	0.28
134_V	137_A	0.534	0.27
125_P	130_G	0.534	0.27
3_E	29_A	0.531	0.27
142_P	187_K	0.531	0.27
117_R	139_G	0.531	0.27
127_I	179_L	0.530	0.27
31_Y	66_P	0.530	0.27
75_V	209_L	0.529	0.27
135_K	139_G	0.529	0.27
45_I	197_I	0.529	0.27
116_F	197_I	0.527	0.27
9_F	139_G	0.526	0.27
145_L	176_R	0.524	0.27
168_I	183_L	0.517	0.26
86_F	145_L	0.517	0.26
131_P	190_V	0.516	0.26
30_L	121_F	0.516	0.26
97_G	188_S	0.515	0.26
107_K	199_G	0.514	0.26
61_A	64_K	0.512	0.26
47_H	156_G	0.512	0.26
124_I	194_G	0.512	0.26
94_L	107_K	0.510	0.26
196_L	199_G	0.509	0.26
135_K	180_G	0.509	0.26
46_D	154_F	0.509	0.26
137_A	162_L	0.506	0.25
85_Y	162_L	0.506	0.25
164_I	213_V	0.502	0.25
44_K	119_S	0.501	0.25
167_D	214_R	0.501	0.25
184_G	188_S	0.501	0.25
160_N	169_G	0.500	0.25
117_R	130_G	0.500	0.25

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
4dayC	1	0.0548	21.9	0.954	Contact Map
2jvfA	1	0.3379	2.8	0.97	Contact Map
1r8uA	1	0.1735	2.6	0.97	Contact Map
3epzA	1	0.2329	2.4	0.971	Contact Map
4pgiA	1	0.2055	2.3	0.971	Contact Map
3if8B	1	0.5205	2	0.972	Contact Map
2b9sB	1	0.0639	2	0.972	Contact Map
1p4qA	1	0.2283	2	0.972	Contact Map
2iiiA	2	0.5479	2	0.972	Contact Map
2gj2A	3	0.137	1.9	0.972	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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