DUF3379 - PFAM28P - GREMLIN Contacts

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DUF3379 - Protein of unknown function (DUF3379)

PFAM:	PF11859	Sequences: MNCLEFRRRLLADPRSRDPELLAHRASCPACAAFADELLALDARLARALAVPVPEGLADRILLRQSLAARARRRRRRRRWLALAASVALAVGLGVGLWLAGPSYDSLAAEVVAHVYHEPPAALATDEPVSLAQLNAVLASFGVRLDPDLGLVTYANSCPFRGHRVPHLVVQTEQGPVTVLLLPHESVADAREDFSEDGYRGVIVPVGGGSIAIVGESGEDLDQVAERLRQAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	232 (230)
Sequences:	1461 (1217)
Seq/√Len:	80.2
META:	0.856

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_H	28_C	5.204	1.00
28_C	31_C	4.597	1.00
24_H	31_C	4.387	1.00
194_F	201_G	3.957	1.00
3_C	24_H	3.900	1.00
4_L	8_R	3.477	1.00
41_L	45_L	3.424	1.00
3_C	31_C	3.207	1.00
3_C	28_C	3.137	1.00
172_T	219_E	2.990	1.00
10_L	21_L	2.884	1.00
10_L	35_A	2.724	1.00
13_D	16_S	2.677	1.00
25_R	35_A	2.572	1.00
172_T	175_G	2.501	1.00
34_F	38_L	2.346	1.00
35_A	39_L	2.208	1.00
115_V	214_V	2.160	1.00
153_T	171_Q	2.106	1.00
83_L	86_S	2.090	1.00
17_R	21_L	1.982	1.00
116_Y	196_E	1.916	1.00
6_F	25_R	1.884	1.00
119_P	122_A	1.884	1.00
46_A	50_A	1.814	1.00
122_A	125_T	1.795	1.00
42_D	45_L	1.795	1.00
119_P	123_L	1.794	1.00
114_H	167_H	1.772	1.00
209_G	212_A	1.756	1.00
56_G	59_D	1.736	1.00
10_L	38_L	1.733	1.00
151_L	171_Q	1.714	1.00
120_P	123_L	1.677	1.00
23_A	27_S	1.672	1.00
2_N	5_E	1.662	1.00
172_T	177_V	1.651	1.00
5_E	9_R	1.642	1.00
6_F	35_A	1.610	1.00
11_L	38_L	1.598	1.00
9_R	18_D	1.576	1.00
6_F	10_L	1.569	1.00
59_D	64_R	1.558	1.00
64_R	68_A	1.554	1.00
15_R	46_A	1.536	0.99
123_L	126_D	1.498	0.99
160_F	180_L	1.495	0.99
29_P	32_A	1.482	0.99
63_L	67_L	1.479	0.99
129_V	134_L	1.472	0.99
10_L	34_F	1.472	0.99
6_F	21_L	1.471	0.99
17_R	22_L	1.467	0.99
118_E	180_L	1.449	0.99
153_T	176_P	1.420	0.99
160_F	178_T	1.382	0.99
187_V	213_I	1.382	0.99
182_L	210_S	1.381	0.99
56_G	60_R	1.378	0.99
215_G	221_L	1.357	0.99
107_L	161_R	1.335	0.98
200_R	218_G	1.324	0.98
57_L	60_R	1.318	0.98
138_L	172_T	1.315	0.98
32_A	36_D	1.315	0.98
57_L	62_L	1.307	0.98
9_R	21_L	1.302	0.98
15_R	42_D	1.300	0.98
131_L	135_N	1.298	0.98
58_A	61_I	1.285	0.98
94_G	98_W	1.270	0.98
67_L	70_R	1.263	0.98
89_L	94_G	1.259	0.98
115_V	194_F	1.252	0.98
5_E	8_R	1.250	0.98
66_S	69_A	1.242	0.98
4_L	7_R	1.241	0.98
94_G	97_L	1.241	0.98
106_S	109_A	1.232	0.97
205_P	209_G	1.224	0.97
57_L	61_I	1.220	0.97
25_R	32_A	1.211	0.97
15_R	39_L	1.190	0.97
111_V	212_A	1.187	0.97
33_A	37_E	1.182	0.97
157_S	166_P	1.165	0.96
99_L	102_P	1.158	0.96
16_S	21_L	1.145	0.96
20_E	23_A	1.140	0.96
121_A	125_T	1.138	0.96
95_V	98_W	1.130	0.96
1_M	5_E	1.124	0.96
171_Q	176_P	1.114	0.95
118_E	154_Y	1.104	0.95
157_S	164_R	1.102	0.95
182_L	212_A	1.086	0.95
161_R	185_E	1.058	0.94
114_H	118_E	1.053	0.94
122_A	154_Y	1.047	0.93
77_R	80_W	1.046	0.93
83_L	90_A	1.046	0.93
203_I	212_A	1.033	0.93
112_V	196_E	1.028	0.93
62_L	65_Q	1.017	0.92
9_R	16_S	1.016	0.92
154_Y	178_T	1.012	0.92
169_V	178_T	1.009	0.92
112_V	198_G	1.005	0.92
96_G	99_L	1.002	0.92
158_C	167_H	0.999	0.92
65_Q	69_A	0.990	0.91
198_G	205_P	0.985	0.91
26_A	32_A	0.981	0.91
89_L	96_G	0.978	0.91
33_A	36_D	0.970	0.91
93_L	102_P	0.967	0.90
118_E	160_F	0.963	0.90
159_P	164_R	0.950	0.90
45_L	230_Q	0.931	0.89
78_R	81_L	0.928	0.89
114_H	158_C	0.926	0.88
121_A	124_A	0.919	0.88
141_F	166_P	0.916	0.88
152_V	170_V	0.914	0.88
39_L	140_S	0.913	0.88
155_A	201_G	0.903	0.87
115_V	118_E	0.902	0.87
87_V	92_G	0.891	0.86
122_A	126_D	0.883	0.86
23_A	26_A	0.881	0.86
225_A	229_R	0.878	0.86
75_R	79_R	0.878	0.86
27_S	36_D	0.877	0.86
143_V	166_P	0.862	0.85
187_V	212_A	0.856	0.84
18_D	21_L	0.855	0.84
97_L	101_G	0.854	0.84
187_V	210_S	0.854	0.84
81_L	88_A	0.852	0.84
38_L	41_L	0.850	0.84
16_S	45_L	0.849	0.84
87_V	90_A	0.846	0.83
155_A	181_L	0.845	0.83
127_E	130_S	0.837	0.83
165_V	183_P	0.837	0.83
3_C	7_R	0.833	0.83
82_A	86_S	0.832	0.82
18_D	134_L	0.826	0.82
90_A	93_L	0.822	0.82
65_Q	68_A	0.820	0.82
61_I	65_Q	0.812	0.81
56_G	61_I	0.811	0.81
184_H	208_G	0.807	0.80
8_R	11_L	0.804	0.80
215_G	219_E	0.801	0.80
97_L	103_S	0.798	0.80
90_A	102_P	0.798	0.80
111_V	180_L	0.797	0.80
33_A	50_A	0.790	0.79
213_I	225_A	0.781	0.78
41_L	44_R	0.780	0.78
96_G	100_A	0.779	0.78
14_P	114_H	0.777	0.78
125_T	129_V	0.772	0.77
2_N	7_R	0.770	0.77
111_V	203_I	0.767	0.77
137_V	166_P	0.761	0.76
58_A	63_L	0.760	0.76
89_L	93_L	0.758	0.76
210_S	213_I	0.756	0.76
66_S	70_R	0.754	0.76
16_S	22_L	0.753	0.76
10_L	25_R	0.753	0.76
157_S	165_V	0.753	0.76
204_V	211_I	0.751	0.75
174_Q	219_E	0.750	0.75
17_R	35_A	0.750	0.75
39_L	42_D	0.748	0.75
21_L	34_F	0.744	0.75
58_A	89_L	0.742	0.75
134_L	168_L	0.741	0.75
92_G	136_A	0.737	0.74
88_A	105_D	0.734	0.74
56_G	62_L	0.734	0.74
3_C	30_A	0.729	0.73
99_L	104_Y	0.728	0.73
31_C	34_F	0.724	0.73
209_G	214_V	0.723	0.73
194_F	199_Y	0.721	0.73
81_L	86_S	0.719	0.72
87_V	216_E	0.719	0.72
61_I	64_R	0.719	0.72
168_L	179_V	0.718	0.72
60_R	63_L	0.714	0.72
125_T	134_L	0.712	0.72
222_D	226_E	0.712	0.72
53_V	66_S	0.712	0.72
79_R	82_A	0.711	0.71
134_L	170_V	0.711	0.71
191_R	215_G	0.708	0.71
97_L	102_P	0.707	0.71
125_T	153_T	0.706	0.71
11_L	42_D	0.703	0.71
145_L	227_R	0.702	0.70
92_G	217_S	0.700	0.70
112_V	116_Y	0.700	0.70
155_A	167_H	0.698	0.70
187_V	203_I	0.695	0.70
22_L	35_A	0.690	0.69
204_V	207_G	0.690	0.69
224_V	227_R	0.689	0.69
139_A	142_G	0.684	0.69
22_L	26_A	0.683	0.68
81_L	163_H	0.683	0.68
75_R	78_R	0.683	0.68
12_A	143_V	0.682	0.68
19_P	32_A	0.681	0.68
177_V	215_G	0.679	0.68
30_A	37_E	0.675	0.67
176_P	182_L	0.675	0.67
111_V	182_L	0.673	0.67
198_G	216_E	0.668	0.67
47_R	52_P	0.668	0.67
79_R	170_V	0.666	0.66
125_T	154_Y	0.662	0.66
116_Y	198_G	0.662	0.66
168_L	181_L	0.661	0.66
169_V	176_P	0.659	0.66
139_A	143_V	0.654	0.65
137_V	155_A	0.653	0.65
51_V	54_P	0.653	0.65
54_P	57_L	0.652	0.65
3_C	8_R	0.651	0.65
147_P	150_G	0.650	0.65
33_A	146_D	0.649	0.64
94_G	207_G	0.648	0.64
45_L	49_L	0.646	0.64
167_H	178_T	0.643	0.64
91_V	94_G	0.643	0.64
134_L	155_A	0.642	0.64
175_G	215_G	0.641	0.64
18_D	22_L	0.640	0.63
140_S	159_P	0.639	0.63
202_V	222_D	0.638	0.63
154_Y	169_V	0.637	0.63
180_L	214_V	0.637	0.63
89_L	92_G	0.637	0.63
78_R	134_L	0.632	0.62
147_P	152_V	0.631	0.62
90_A	97_L	0.631	0.62
155_A	168_L	0.629	0.62
114_H	166_P	0.626	0.62
44_R	180_L	0.625	0.62
160_F	165_V	0.624	0.61
118_E	178_T	0.622	0.61
114_H	175_G	0.619	0.61
113_A	174_Q	0.618	0.61
11_L	41_L	0.618	0.61
196_E	199_Y	0.617	0.61
135_N	139_A	0.615	0.60
110_E	113_A	0.615	0.60
74_R	78_R	0.615	0.60
137_V	156_N	0.610	0.60
34_F	215_G	0.609	0.60
71_A	75_R	0.604	0.59
110_E	161_R	0.602	0.59
18_D	113_A	0.602	0.59
122_A	176_P	0.601	0.59
86_S	92_G	0.601	0.59
156_N	168_L	0.598	0.58
55_E	74_R	0.596	0.58
154_Y	157_S	0.596	0.58
163_H	183_P	0.595	0.58
155_A	212_A	0.594	0.58
124_A	128_P	0.591	0.57
138_L	179_V	0.591	0.57
95_V	103_S	0.588	0.57
211_I	214_V	0.584	0.56
19_P	23_A	0.583	0.56
77_R	81_L	0.583	0.56
161_R	196_E	0.578	0.56
91_V	190_A	0.576	0.55
42_D	46_A	0.573	0.55
43_A	87_V	0.572	0.55
165_V	212_A	0.570	0.55
28_C	205_P	0.570	0.55
149_L	184_H	0.570	0.55
94_G	100_A	0.569	0.54
226_E	229_R	0.568	0.54
153_T	168_L	0.564	0.54
218_G	221_L	0.564	0.54
46_A	195_S	0.563	0.54
58_A	62_L	0.563	0.54
126_D	130_S	0.562	0.54
92_G	97_L	0.562	0.54
68_A	71_A	0.560	0.53
64_R	69_A	0.560	0.53
93_L	97_L	0.558	0.53
173_E	223_Q	0.555	0.53
154_Y	185_E	0.552	0.52
61_I	188_A	0.551	0.52
31_C	205_P	0.551	0.52
129_V	172_T	0.550	0.52
160_F	182_L	0.550	0.52
20_E	36_D	0.549	0.52
38_L	134_L	0.549	0.52
91_V	150_G	0.546	0.52
61_I	89_L	0.546	0.52
154_Y	160_F	0.545	0.51
196_E	214_V	0.540	0.51
122_A	127_E	0.539	0.51
12_A	184_H	0.539	0.51
148_D	170_V	0.534	0.50
26_A	35_A	0.533	0.50
62_L	111_V	0.533	0.50
52_P	72_R	0.528	0.49
128_P	136_A	0.527	0.49
60_R	136_A	0.526	0.49
81_L	229_R	0.526	0.49
182_L	213_I	0.526	0.49
31_C	209_G	0.525	0.49
36_D	189_D	0.523	0.49
110_E	163_H	0.522	0.48
44_R	140_S	0.522	0.48
160_F	196_E	0.521	0.48
161_R	165_V	0.520	0.48
216_E	227_R	0.520	0.48
60_R	64_R	0.520	0.48
182_L	185_E	0.520	0.48
111_V	168_L	0.520	0.48
36_D	39_L	0.518	0.48
115_V	199_Y	0.517	0.48
92_G	96_G	0.514	0.47
137_V	209_G	0.512	0.47
10_L	129_V	0.512	0.47
63_L	72_R	0.511	0.47
98_W	101_G	0.511	0.47
16_S	32_A	0.511	0.47
154_Y	171_Q	0.509	0.47
11_L	34_F	0.509	0.47
111_V	116_Y	0.508	0.47
9_R	31_C	0.507	0.46
2_N	24_H	0.502	0.46
89_L	95_V	0.502	0.46
1_M	37_E	0.500	0.46

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
3hugB	2	0.2198	95.6	0.897	Contact Map
2q1zB	1	0.7198	94.7	0.903	Contact Map
4nqwB	1	0.2629	93.5	0.908	Contact Map
1or7C	1	0.2759	33.1	0.947	Contact Map
2lcoA	1	0.0819	16.1	0.954	Contact Map
1qb3A	2	0.1293	11.1	0.957	Contact Map
2jz2A	1	0.2284	8.1	0.96	Contact Map
4nphA	1	0.4397	7.4	0.96	Contact Map
4v3iA	2	0.2328	7.2	0.961	Contact Map
3vmaA	1	0.6078	6.1	0.962	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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