DUF3800 - PFAM28P - GREMLIN Contacts

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DUF3800 - Protein of unknown function (DUF3800)

PFAM:	PF12686	Sequences: IIYIDESGDLGLDFSDPSSPYFVLGGVIVPEEDWRELEKEIRELKRKLFGKDEVEPRELHASKIRKGKGEFRGLSDEKRRRLLKDLLDLLAKLDFLIFAAVIVKKKLLDKYALDNEDPHDPWYFYKYALRLLLERLELFLEGPDERGIIIFDSRGKKEDRKLEEYLRRLILRGTRYDRLRRIIEDIFFVDSKESPGLQLADLVAGAIRRKYERKDKSKAKEQKNRLFEIIKPKFY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	235 (209)
Sequences:	14232 (12764)
Seq/√Len:	882.9
META:	0.888

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_G	204_A	4.792	1.00
61_A	205_G	3.883	1.00
208_R	212_E	2.804	1.00
47_K	85_D	2.794	1.00
79_R	82_L	2.431	1.00
152_D	191_S	2.327	1.00
189_V	194_S	2.313	1.00
104_K	107_L	2.298	1.00
23_V	204_A	2.296	1.00
23_V	208_R	2.276	1.00
190_D	193_E	2.275	1.00
2_I	28_I	2.223	1.00
42_R	195_P	2.133	1.00
89_L	93_L	2.067	1.00
189_V	197_L	2.064	1.00
45_K	195_P	2.053	1.00
33_D	36_E	1.939	1.00
40_E	93_L	1.935	1.00
38_E	195_P	1.926	1.00
7_S	23_V	1.896	1.00
2_I	26_G	1.893	1.00
75_S	78_K	1.842	1.00
38_E	42_R	1.794	1.00
103_V	106_K	1.790	1.00
27_V	200_A	1.786	1.00
2_I	147_G	1.756	1.00
74_L	78_K	1.739	1.00
103_V	107_L	1.739	1.00
78_K	81_R	1.689	1.00
30_P	33_D	1.662	1.00
36_E	40_E	1.647	1.00
71_F	74_L	1.647	1.00
48_L	85_D	1.633	1.00
162_L	166_L	1.617	1.00
44_L	48_L	1.603	1.00
60_H	64_I	1.600	1.00
118_P	121_P	1.590	1.00
74_L	79_R	1.576	1.00
39_K	43_E	1.550	1.00
131_L	134_E	1.547	1.00
159_D	163_E	1.539	1.00
76_D	80_R	1.537	1.00
75_S	82_L	1.529	1.00
101_V	104_K	1.524	1.00
61_A	65_R	1.482	1.00
173_G	176_Y	1.480	1.00
127_Y	131_L	1.430	1.00
4_I	26_G	1.429	1.00
155_G	159_D	1.428	1.00
158_E	161_K	1.396	1.00
155_G	158_E	1.389	1.00
97_I	103_V	1.385	1.00
75_S	79_R	1.380	1.00
60_H	63_K	1.378	1.00
43_E	47_K	1.378	1.00
130_R	134_E	1.352	1.00
205_G	209_R	1.351	1.00
153_S	159_D	1.328	1.00
105_K	108_L	1.321	1.00
100_A	103_V	1.315	1.00
154_R	159_D	1.312	1.00
156_K	159_D	1.309	1.00
61_A	64_I	1.303	1.00
40_E	43_E	1.302	1.00
40_E	92_K	1.289	1.00
170_I	173_G	1.288	1.00
44_L	47_K	1.272	1.00
154_R	158_E	1.256	1.00
34_W	38_E	1.255	1.00
148_I	185_D	1.251	1.00
59_L	64_I	1.247	1.00
83_L	87_L	1.246	1.00
114_D	117_D	1.214	1.00
115_N	118_P	1.208	1.00
85_D	88_D	1.206	1.00
99_A	104_K	1.191	1.00
148_I	187_F	1.188	1.00
78_K	82_L	1.180	1.00
184_E	187_F	1.178	1.00
41_I	45_K	1.177	1.00
171_L	174_T	1.172	1.00
156_K	160_R	1.169	1.00
45_K	48_L	1.169	1.00
136_L	147_G	1.166	1.00
96_L	104_K	1.160	1.00
64_I	68_K	1.150	1.00
131_L	135_R	1.148	1.00
100_A	104_K	1.147	1.00
85_D	89_L	1.145	1.00
50_G	54_V	1.139	1.00
77_E	81_R	1.137	1.00
27_V	203_V	1.134	1.00
9_D	19_S	1.123	1.00
146_R	184_E	1.122	1.00
125_Y	129_L	1.122	1.00
109_D	112_A	1.120	1.00
25_G	203_V	1.114	1.00
108_L	111_Y	1.108	1.00
8_G	208_R	1.105	1.00
40_E	89_L	1.093	1.00
64_I	202_L	1.090	1.00
139_F	143_P	1.078	1.00
99_A	103_V	1.078	1.00
39_K	42_R	1.073	1.00
132_L	136_L	1.066	1.00
160_R	163_E	1.066	1.00
20_P	212_E	1.064	1.00
107_L	111_Y	1.062	1.00
62_S	68_K	1.061	1.00
44_L	89_L	1.052	1.00
125_Y	128_A	1.044	1.00
209_R	213_R	1.037	1.00
38_E	196_G	1.028	1.00
148_I	184_E	1.027	1.00
6_E	22_F	1.024	1.00
42_R	46_R	1.023	1.00
97_I	104_K	1.020	1.00
105_K	109_D	1.003	1.00
35_R	39_K	0.987	1.00
74_L	77_E	0.986	1.00
150_I	187_F	0.981	1.00
128_A	131_L	0.971	1.00
73_G	82_L	0.960	1.00
76_D	79_R	0.959	1.00
37_L	41_I	0.953	1.00
200_A	204_A	0.940	1.00
100_A	207_I	0.938	1.00
150_I	189_V	0.938	1.00
44_L	85_D	0.937	1.00
19_S	208_R	0.935	1.00
160_R	164_E	0.932	1.00
74_L	82_L	0.927	1.00
89_L	92_K	0.925	1.00
77_E	80_R	0.924	1.00
127_Y	130_R	0.923	1.00
170_I	174_T	0.917	1.00
107_L	110_K	0.910	1.00
154_R	157_K	0.908	1.00
162_L	165_Y	0.905	1.00
88_D	91_A	0.904	1.00
189_V	193_E	0.901	1.00
4_I	132_L	0.899	1.00
97_I	100_A	0.891	1.00
87_L	91_A	0.890	1.00
159_D	162_L	0.890	1.00
87_L	90_L	0.889	1.00
34_W	196_G	0.886	1.00
188_F	191_S	0.881	1.00
84_K	87_L	0.874	1.00
158_E	165_Y	0.870	1.00
123_Y	126_K	0.868	1.00
161_K	165_Y	0.867	1.00
182_I	186_I	0.866	1.00
164_E	167_R	0.865	1.00
73_G	78_K	0.862	1.00
3_Y	34_W	0.857	1.00
27_V	199_L	0.857	1.00
77_E	82_L	0.856	1.00
29_V	34_W	0.852	1.00
153_S	158_E	0.849	1.00
102_I	107_L	0.827	1.00
37_L	196_G	0.826	1.00
110_K	113_L	0.824	1.00
98_F	101_V	0.820	1.00
130_R	133_L	0.816	1.00
187_F	190_D	0.812	1.00
103_V	111_Y	0.811	1.00
128_A	135_R	0.809	1.00
121_P	124_F	0.804	1.00
150_I	197_L	0.801	1.00
157_K	163_E	0.797	1.00
163_E	166_L	0.794	1.00
155_G	165_Y	0.792	1.00
185_D	188_F	0.790	1.00
96_L	99_A	0.789	1.00
76_D	82_L	0.784	1.00
84_K	88_D	0.782	1.00
100_A	107_L	0.779	1.00
4_I	151_F	0.775	1.00
161_K	164_E	0.771	1.00
128_A	133_L	0.767	1.00
7_S	208_R	0.766	1.00
26_G	132_L	0.763	1.00
10_L	19_S	0.762	1.00
104_K	108_L	0.748	1.00
112_A	115_N	0.746	1.00
126_K	130_R	0.741	1.00
29_V	37_L	0.738	1.00
2_I	136_L	0.735	1.00
90_L	199_L	0.734	1.00
6_E	24_L	0.734	1.00
75_S	80_R	0.732	1.00
96_L	103_V	0.724	1.00
172_R	176_Y	0.721	1.00
96_L	100_A	0.721	1.00
185_D	189_V	0.720	1.00
51_K	55_E	0.719	1.00
117_D	120_D	0.718	1.00
120_D	123_Y	0.714	1.00
121_P	125_Y	0.709	1.00
72_R	75_S	0.708	1.00
129_L	132_L	0.703	1.00
49_F	54_V	0.702	1.00
74_L	80_R	0.700	1.00
174_T	177_D	0.700	1.00
38_E	41_I	0.698	1.00
96_L	105_K	0.698	1.00
62_S	66_K	0.697	1.00
73_G	76_D	0.697	1.00
50_G	55_E	0.695	1.00
106_K	109_D	0.694	1.00
184_E	188_F	0.690	1.00
9_D	22_F	0.689	1.00
97_I	105_K	0.689	1.00
8_G	19_S	0.681	1.00
98_F	107_L	0.676	1.00
33_D	94_D	0.668	1.00
89_L	94_D	0.668	1.00
73_G	80_R	0.667	1.00
64_I	69_G	0.660	1.00
154_R	161_K	0.654	1.00
205_G	208_R	0.652	1.00
191_S	194_S	0.649	1.00
37_L	40_E	0.648	1.00
159_D	165_Y	0.646	1.00
37_L	42_R	0.646	1.00
99_A	207_I	0.642	1.00
157_K	160_R	0.640	1.00
28_I	147_G	0.640	1.00
50_G	53_E	0.639	1.00
49_F	53_E	0.638	1.00
25_G	99_A	0.635	1.00
6_E	125_Y	0.633	1.00
29_V	33_D	0.633	1.00
76_D	81_R	0.630	1.00
83_L	86_L	0.627	1.00
100_A	108_L	0.625	1.00
157_K	161_K	0.621	1.00
124_F	128_A	0.621	1.00
197_L	200_A	0.621	1.00
114_D	118_P	0.620	1.00
113_L	116_E	0.620	1.00
38_E	194_S	0.619	1.00
152_D	190_D	0.618	1.00
153_S	166_L	0.616	1.00
106_K	110_K	0.616	1.00
213_R	216_K	0.615	1.00
126_K	129_L	0.611	1.00
148_I	151_F	0.604	1.00
25_G	207_I	0.602	1.00
88_D	92_K	0.601	1.00
52_D	55_E	0.600	1.00
71_F	75_S	0.596	1.00
183_I	186_I	0.594	1.00
99_A	102_I	0.591	1.00
132_L	135_R	0.590	1.00
74_L	81_R	0.589	1.00
129_L	137_E	0.588	1.00
48_L	51_K	0.587	1.00
63_K	69_G	0.586	1.00
128_A	137_E	0.586	1.00
9_D	18_S	0.584	1.00
113_L	118_P	0.584	1.00
86_L	89_L	0.582	1.00
45_K	198_Q	0.581	1.00
60_H	205_G	0.580	1.00
4_I	149_I	0.579	1.00
173_G	177_D	0.574	1.00
171_L	176_Y	0.572	1.00
64_I	67_G	0.571	1.00
134_E	137_E	0.569	1.00
130_R	137_E	0.566	1.00
191_S	197_L	0.563	1.00
73_G	79_R	0.562	1.00
106_K	111_Y	0.562	1.00
163_E	167_R	0.560	1.00
125_Y	132_L	0.558	1.00
90_L	95_F	0.558	1.00
83_L	91_A	0.557	1.00
36_E	39_K	0.557	1.00
13_D	17_P	0.556	1.00
44_L	86_L	0.553	1.00
66_K	69_G	0.550	1.00
139_F	142_G	0.550	1.00
110_K	114_D	0.548	1.00
128_A	132_L	0.545	1.00
61_A	209_R	0.544	1.00
153_S	156_K	0.544	1.00
43_E	46_R	0.542	1.00
112_A	117_D	0.538	1.00
171_L	175_R	0.536	1.00
125_Y	136_L	0.534	1.00
67_G	79_R	0.527	1.00
153_S	161_K	0.524	1.00
113_L	117_D	0.524	1.00
128_A	136_L	0.523	1.00
72_R	79_R	0.523	1.00
102_I	108_L	0.522	1.00
86_L	202_L	0.521	1.00
14_F	17_P	0.521	1.00
102_I	105_K	0.519	1.00
41_I	199_L	0.519	1.00
133_L	149_I	0.519	1.00
75_S	81_R	0.518	1.00
33_D	95_F	0.514	1.00
159_D	166_L	0.514	1.00
11_G	14_F	0.514	1.00
91_A	95_F	0.512	1.00
112_A	116_E	0.512	1.00
51_K	54_V	0.510	1.00
153_S	157_K	0.509	1.00
204_A	208_R	0.505	1.00
155_G	163_E	0.501	1.00
11_G	19_S	0.500	1.00

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
1ekeA	2	0.8128	13.8	0.914	Contact Map
2d0bA	1	0.766	7.8	0.923	Contact Map
2etjA	1	0.6128	4.1	0.933	Contact Map
1e8pA	1	0.1106	3.8	0.934	Contact Map
2qwvA	2	0.2468	3.3	0.936	Contact Map
1io2A	1	0.7532	2.7	0.939	Contact Map
1xpnA	1	0.2596	2.5	0.94	Contact Map
4yd8A	1	0.1064	2.5	0.94	Contact Map
3qecA	3	0.2596	2.4	0.94	Contact Map
2a7oA	1	0.2213	2.4	0.941	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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