DUF1837 - PFAM28P - GREMLIN Contacts

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DUF1837 - Domain of unknown function (DUF1837)

PFAM:	PF08878	Sequences: DDLAEFLRDNIPEYALSRSEIEELKKEDASLLLKEAAKKFRKDKKGKRGELGELLLYLLLEEFLGAPPILSKIYLKTNSNDEVKGADGVHIVVDDDGLFELWLGESKFYKDIKDAIDDAFKSIKKHLSKDYLKRELSLITNKIDLEDEELAEKLKKLLDPNTSLDDIKVRIAIPILLGYDSDIYKKHTKSTDEYKEEIKKEIKERAKKFFKKIKKPKLDGISFHLFLLPF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	230 (229)
Sequences:	2115 (1743)
Seq/√Len:	115.2
META:	0.765

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_D	84_K	6.529	1.00
56_L	104_G	3.104	1.00
3_L	55_L	2.948	1.00
199_K	203_K	2.911	1.00
196_E	199_K	2.883	1.00
192_D	196_E	2.709	1.00
53_E	87_D	2.690	1.00
50_E	76_K	2.387	1.00
85_G	107_K	2.360	1.00
87_D	105_E	2.327	1.00
119_A	122_S	2.314	1.00
152_E	156_K	2.280	1.00
85_G	105_E	2.270	1.00
196_E	200_K	2.256	1.00
113_K	208_K	2.230	1.00
193_E	197_E	2.223	1.00
147_D	150_L	2.206	1.00
148_E	152_E	2.067	1.00
111_D	114_D	2.046	1.00
9_D	31_L	2.041	1.00
201_E	205_R	2.017	1.00
87_D	107_K	2.001	1.00
209_F	225_L	1.992	1.00
118_D	121_K	1.940	1.00
49_G	105_E	1.922	1.00
20_E	35_E	1.916	1.00
72_K	135_E	1.909	1.00
193_E	196_E	1.903	1.00
121_K	125_K	1.884	1.00
208_K	211_K	1.873	1.00
156_K	162_T	1.868	1.00
191_T	194_Y	1.866	1.00
53_E	105_E	1.774	1.00
190_S	193_E	1.756	1.00
195_K	199_K	1.749	1.00
49_G	87_D	1.721	1.00
212_K	215_K	1.688	1.00
37_A	41_R	1.679	1.00
205_R	208_K	1.673	1.00
29_A	32_L	1.658	1.00
53_E	107_K	1.608	1.00
194_Y	201_E	1.578	1.00
64_L	226_F	1.574	1.00
207_K	211_K	1.573	1.00
37_A	40_F	1.573	1.00
121_K	124_K	1.561	1.00
64_L	67_P	1.560	1.00
29_A	33_L	1.551	1.00
28_D	31_L	1.548	1.00
49_G	53_E	1.523	1.00
6_F	10_N	1.501	1.00
198_I	202_I	1.497	1.00
194_Y	198_I	1.489	1.00
68_P	90_H	1.489	1.00
105_E	122_S	1.481	1.00
109_Y	115_A	1.473	1.00
200_K	203_K	1.472	1.00
127_L	173_I	1.467	1.00
191_T	195_K	1.466	1.00
100_E	172_A	1.454	1.00
76_K	83_V	1.432	1.00
57_Y	66_A	1.403	1.00
206_A	210_F	1.386	1.00
109_Y	118_D	1.359	1.00
50_E	82_E	1.357	1.00
60_L	174_P	1.345	1.00
92_V	102_W	1.335	1.00
44_K	48_R	1.333	1.00
131_Y	136_L	1.318	1.00
25_K	28_D	1.313	1.00
78_N	81_D	1.304	1.00
49_G	107_K	1.300	1.00
49_G	52_G	1.296	1.00
94_D	100_E	1.292	1.00
203_K	207_K	1.286	0.99
197_E	201_E	1.286	0.99
69_I	91_I	1.282	0.99
223_F	229_P	1.273	0.99
111_D	117_D	1.271	0.99
177_L	227_L	1.270	0.99
22_E	25_K	1.257	0.99
200_K	204_E	1.256	0.99
204_E	208_K	1.250	0.99
22_E	26_K	1.248	0.99
25_K	29_A	1.243	0.99
21_I	24_L	1.229	0.99
108_F	178_G	1.217	0.99
52_G	87_D	1.216	0.99
45_K	48_R	1.209	0.99
50_E	90_H	1.207	0.99
123_I	175_I	1.204	0.99
59_L	228_L	1.204	0.99
26_K	30_S	1.160	0.99
191_T	209_F	1.156	0.99
53_E	85_G	1.140	0.99
46_G	49_G	1.139	0.99
222_S	225_L	1.133	0.99
43_D	46_G	1.120	0.99
76_K	105_E	1.117	0.99
66_A	92_V	1.110	0.98
112_I	205_R	1.101	0.98
49_G	85_G	1.098	0.98
42_K	134_R	1.089	0.98
172_A	222_S	1.087	0.98
7_L	54_L	1.085	0.98
198_I	201_E	1.075	0.98
7_L	55_L	1.064	0.98
76_K	107_K	1.064	0.98
86_A	126_H	1.052	0.98
178_G	230_F	1.051	0.98
106_S	122_S	1.041	0.98
112_I	177_L	1.027	0.97
18_R	22_E	1.027	0.97
59_L	226_F	1.021	0.97
162_T	166_D	1.020	0.97
205_R	209_F	1.018	0.97
121_K	196_E	1.006	0.97
28_D	33_L	1.002	0.97
114_D	117_D	0.997	0.97
36_A	41_R	0.992	0.97
182_D	186_K	0.992	0.97
195_K	198_I	0.982	0.97
172_A	224_H	0.981	0.97
77_T	84_K	0.975	0.97
92_V	100_E	0.973	0.96
106_S	170_R	0.965	0.96
113_K	204_E	0.963	0.96
72_K	87_D	0.960	0.96
190_S	209_F	0.957	0.96
52_G	106_S	0.949	0.96
115_A	177_L	0.948	0.96
205_R	210_F	0.947	0.96
76_K	85_G	0.943	0.96
202_I	205_R	0.941	0.96
202_I	206_A	0.938	0.96
198_I	205_R	0.931	0.95
195_K	202_I	0.931	0.95
44_K	47_K	0.918	0.95
117_D	212_K	0.915	0.95
28_D	32_L	0.914	0.95
94_D	97_G	0.896	0.94
68_P	71_S	0.895	0.94
15_A	73_I	0.895	0.94
58_L	62_E	0.894	0.94
72_K	105_E	0.893	0.94
89_V	139_I	0.892	0.94
97_G	170_R	0.890	0.94
53_E	72_K	0.888	0.94
27_E	32_L	0.875	0.94
207_K	210_F	0.873	0.94
56_L	72_K	0.872	0.94
128_S	156_K	0.858	0.93
66_A	90_H	0.856	0.93
201_E	208_K	0.853	0.93
119_A	175_I	0.850	0.93
211_K	216_P	0.840	0.92
187_H	191_T	0.838	0.92
65_G	92_V	0.835	0.92
130_D	133_K	0.835	0.92
68_P	179_Y	0.835	0.92
114_D	118_D	0.834	0.92
131_Y	135_E	0.825	0.92
21_I	33_L	0.822	0.91
190_S	198_I	0.818	0.91
70_L	138_L	0.814	0.91
75_L	130_D	0.811	0.91
52_G	105_E	0.810	0.91
206_A	209_F	0.804	0.91
151_A	155_K	0.802	0.90
30_S	33_L	0.802	0.90
5_E	27_E	0.801	0.90
200_K	211_K	0.794	0.90
25_K	32_L	0.791	0.90
24_L	30_S	0.789	0.90
5_E	26_K	0.788	0.90
35_E	137_S	0.787	0.90
48_R	86_A	0.786	0.90
61_E	67_P	0.782	0.89
24_L	34_K	0.778	0.89
9_D	30_S	0.775	0.89
76_K	87_D	0.774	0.89
142_K	145_L	0.772	0.89
10_N	13_E	0.764	0.88
89_V	154_L	0.760	0.88
218_L	221_I	0.760	0.88
101_L	182_D	0.758	0.88
185_K	188_T	0.753	0.87
212_K	216_P	0.751	0.87
201_E	209_F	0.748	0.87
5_E	34_K	0.748	0.87
97_G	153_K	0.748	0.87
21_I	28_D	0.745	0.87
200_K	207_K	0.744	0.87
182_D	185_K	0.742	0.87
117_D	208_K	0.738	0.86
73_I	77_T	0.730	0.86
77_T	83_V	0.729	0.86
14_Y	83_V	0.727	0.86
103_L	126_H	0.726	0.85
201_E	204_E	0.724	0.85
57_Y	61_E	0.724	0.85
216_P	219_D	0.724	0.85
16_L	20_E	0.722	0.85
78_N	138_L	0.720	0.85
107_K	122_S	0.720	0.85
190_S	197_E	0.710	0.84
190_S	195_K	0.708	0.84
186_K	207_K	0.708	0.84
77_T	138_L	0.701	0.83
2_D	5_E	0.701	0.83
149_E	154_L	0.691	0.83
148_E	151_A	0.684	0.82
187_H	197_E	0.684	0.82
67_P	178_G	0.682	0.82
76_K	122_S	0.682	0.82
186_K	197_E	0.676	0.81
174_P	178_G	0.675	0.81
83_V	122_S	0.670	0.81
204_E	207_K	0.670	0.81
24_L	27_E	0.669	0.81
70_L	173_I	0.668	0.80
191_T	202_I	0.665	0.80
57_Y	71_S	0.662	0.80
24_L	29_A	0.662	0.80
213_I	222_S	0.656	0.79
55_L	178_G	0.656	0.79
9_D	29_A	0.656	0.79
174_P	177_L	0.653	0.79
181_S	201_E	0.652	0.79
48_R	82_E	0.651	0.79
60_L	88_G	0.651	0.79
35_E	38_K	0.650	0.79
204_E	219_D	0.648	0.78
70_L	85_G	0.648	0.78
197_E	200_K	0.646	0.78
77_T	81_D	0.644	0.78
76_K	89_V	0.644	0.78
152_E	155_K	0.642	0.78
84_K	107_K	0.640	0.78
198_I	208_K	0.639	0.77
57_Y	86_A	0.638	0.77
50_E	83_V	0.636	0.77
33_L	37_A	0.636	0.77
214_K	219_D	0.635	0.77
61_E	68_P	0.633	0.77
188_T	193_E	0.632	0.77
175_I	225_L	0.632	0.77
122_S	126_H	0.629	0.76
79_S	138_L	0.625	0.76
208_K	212_K	0.624	0.76
35_E	39_K	0.624	0.76
219_D	222_S	0.621	0.75
190_S	201_E	0.621	0.75
39_K	42_K	0.620	0.75
5_E	9_D	0.615	0.75
210_F	222_S	0.615	0.75
39_K	141_N	0.611	0.74
21_I	26_K	0.610	0.74
192_D	200_K	0.609	0.74
13_E	61_E	0.608	0.74
196_E	207_K	0.607	0.74
5_E	29_A	0.606	0.74
30_S	34_K	0.604	0.73
59_L	195_K	0.604	0.73
50_E	78_N	0.599	0.73
60_L	71_S	0.599	0.73
84_K	105_E	0.598	0.73
7_L	51_L	0.593	0.72
191_T	198_I	0.592	0.72
10_N	58_L	0.587	0.71
27_E	34_K	0.587	0.71
4_A	10_N	0.583	0.71
189_K	219_D	0.580	0.70
68_P	75_L	0.577	0.70
83_V	105_E	0.574	0.70
86_A	131_Y	0.573	0.69
220_G	223_F	0.572	0.69
213_I	218_L	0.571	0.69
109_Y	114_D	0.570	0.69
200_K	219_D	0.570	0.69
171_I	174_P	0.569	0.69
225_L	228_L	0.567	0.69
186_K	189_K	0.567	0.69
56_L	143_I	0.566	0.69
198_I	206_A	0.565	0.68
44_K	80_N	0.564	0.68
212_K	217_K	0.564	0.68
110_K	180_D	0.564	0.68
215_K	219_D	0.562	0.68
75_L	164_L	0.562	0.68
64_L	178_G	0.561	0.68
156_K	165_D	0.561	0.68
63_F	172_A	0.559	0.68
15_A	71_S	0.559	0.68
24_L	31_L	0.557	0.67
145_L	151_A	0.556	0.67
17_S	73_I	0.556	0.67
194_Y	205_R	0.555	0.67
77_T	122_S	0.553	0.67
64_L	88_G	0.553	0.67
108_F	119_A	0.550	0.66
40_F	73_I	0.548	0.66
197_E	202_I	0.548	0.66
70_L	105_E	0.548	0.66
20_E	23_E	0.546	0.66
26_K	32_L	0.546	0.66
218_L	223_F	0.545	0.66
195_K	201_E	0.544	0.65
203_K	209_F	0.543	0.65
29_A	34_K	0.543	0.65
65_G	170_R	0.542	0.65
19_S	144_D	0.542	0.65
194_Y	209_F	0.539	0.65
215_K	220_G	0.528	0.63
74_Y	102_W	0.527	0.63
77_T	85_G	0.525	0.63
72_K	104_G	0.525	0.63
53_E	76_K	0.525	0.63
24_L	32_L	0.524	0.63
194_Y	197_E	0.523	0.62
18_R	61_E	0.522	0.62
7_L	58_L	0.521	0.62
51_L	176_L	0.521	0.62
25_K	34_K	0.520	0.62
196_E	203_K	0.520	0.62
100_E	170_R	0.519	0.62
73_I	153_K	0.519	0.62
13_E	32_L	0.518	0.62
112_I	116_I	0.518	0.62
193_E	210_F	0.516	0.61
134_R	137_S	0.514	0.61
206_A	226_F	0.513	0.61
69_I	75_L	0.513	0.61
89_V	167_I	0.512	0.61
181_S	198_I	0.512	0.61
208_K	215_K	0.511	0.61
14_Y	135_E	0.509	0.60
217_K	220_G	0.509	0.60
116_I	120_F	0.508	0.60
136_L	140_T	0.507	0.60
121_K	182_D	0.507	0.60
48_R	84_K	0.507	0.60
214_K	222_S	0.503	0.60
192_D	211_K	0.500	0.59

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
4wlrB	1	0.3522	11.4	0.939	Contact Map
3katA	2	0.2826	4.9	0.949	Contact Map
3j9oB	7	0.3565	4.7	0.949	Contact Map
1ynfA	2	0.2348	4.6	0.949	Contact Map
2lu1A	1	0.2739	4	0.951	Contact Map
1ry2A	1	0.2391	3.7	0.952	Contact Map
2kl5A	1	0.1609	3.5	0.952	Contact Map
3fovA	2	0.4391	2.7	0.955	Contact Map
2kqzA	1	0.4522	2.5	0.955	Contact Map
1s03H	1	0.2565	2.4	0.956	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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