DUF4271 - PFAM28P - GREMLIN Contacts

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DUF4271 - Domain of unknown function (DUF4271)

PFAM:	PF14093	Sequences: ITILLLLLLLLLALLKLLFPKRFSDLFRSFFNTKYRQQLFREQNLLFSRFSLLLNLLFILSLSLFIYLLLSYFGLLLSISLISGFLLFLIILLILLLFYLLKFLLLKLLGWIFNIKKLISEYLFNKFLYNKLLGLLLLPLLLLLAYSPLSSKIILIIILILLLLLFLLRYIRRLFIIFKLIKFSLFYFILYLCALEILPLLILYKLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	207 (202)
Sequences:	6003 (5128)
Seq/√Len:	360.8
META:	0.911

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_S	92_L	4.871	1.00
189_I	193_C	3.118	1.00
61_S	141_L	3.074	1.00
156_I	159_L	2.804	1.00
88_F	92_L	2.626	1.00
3_I	7_L	2.562	1.00
172_R	176_I	2.388	1.00
156_I	160_I	2.385	1.00
38_Q	41_R	2.188	1.00
62_L	95_L	2.119	1.00
173_R	177_I	2.108	1.00
8_L	61_S	2.104	1.00
55_N	131_K	2.038	1.00
110_G	119_I	2.001	1.00
65_F	159_L	1.978	1.00
16_K	20_P	1.955	1.00
106_L	119_I	1.926	1.00
166_F	169_R	1.909	1.00
58_F	130_N	1.909	1.00
90_I	94_I	1.873	1.00
129_Y	165_L	1.848	1.00
65_F	141_L	1.841	1.00
59_I	92_L	1.840	1.00
67_Y	71_S	1.824	1.00
103_F	127_F	1.769	1.00
67_Y	84_G	1.725	1.00
166_F	170_Y	1.722	1.00
85_F	89_L	1.666	1.00
202_I	205_K	1.605	1.00
69_L	73_F	1.601	1.00
107_K	120_S	1.598	1.00
59_I	96_L	1.596	1.00
14_L	18_L	1.585	1.00
63_S	91_I	1.582	1.00
66_I	91_I	1.577	1.00
107_K	111_W	1.565	1.00
165_L	169_R	1.559	1.00
103_F	123_L	1.557	1.00
174_L	177_I	1.550	1.00
200_L	204_Y	1.539	1.00
8_L	57_L	1.522	1.00
57_L	134_G	1.506	1.00
68_L	145_A	1.500	1.00
58_F	62_L	1.488	1.00
5_L	141_L	1.484	1.00
153_I	159_L	1.464	1.00
102_K	106_L	1.421	1.00
64_L	88_F	1.396	1.00
201_L	205_K	1.392	1.00
2_T	146_Y	1.392	1.00
51_S	131_K	1.363	1.00
67_Y	91_I	1.358	1.00
66_I	95_L	1.321	1.00
153_I	156_I	1.319	1.00
68_L	72_Y	1.310	1.00
189_I	192_L	1.309	1.00
151_S	154_I	1.301	1.00
126_K	130_N	1.296	1.00
194_A	198_L	1.280	1.00
62_L	66_I	1.278	1.00
35_Y	39_L	1.266	1.00
5_L	142_L	1.260	1.00
155_L	158_I	1.249	1.00
86_L	89_L	1.248	1.00
162_L	166_F	1.248	1.00
44_N	47_F	1.245	1.00
170_Y	173_R	1.242	1.00
154_I	158_I	1.230	1.00
86_L	90_I	1.223	1.00
58_F	61_S	1.215	1.00
32_N	35_Y	1.211	1.00
36_R	41_R	1.208	1.00
139_P	143_L	1.201	1.00
157_I	161_L	1.184	1.00
12_L	57_L	1.180	1.00
59_I	63_S	1.179	1.00
149_L	152_K	1.166	1.00
101_L	105_L	1.158	1.00
107_K	123_L	1.149	1.00
84_G	88_F	1.147	1.00
147_S	150_S	1.141	1.00
152_K	156_I	1.140	1.00
169_R	176_I	1.139	1.00
143_L	147_S	1.137	1.00
16_K	23_F	1.121	1.00
53_L	57_L	1.107	1.00
115_I	119_I	1.098	1.00
115_I	118_L	1.090	1.00
50_F	54_L	1.077	1.00
21_K	25_D	1.077	1.00
154_I	157_I	1.074	1.00
70_L	75_L	1.074	1.00
151_S	159_L	1.070	1.00
128_L	132_L	1.068	1.00
153_I	157_I	1.066	1.00
24_S	28_R	1.060	1.00
88_F	91_I	1.055	1.00
173_R	176_I	1.055	1.00
21_K	24_S	1.054	1.00
110_G	196_E	1.053	1.00
59_I	95_L	1.043	1.00
13_A	17_L	1.043	1.00
106_L	126_K	1.041	1.00
99_Y	126_K	1.041	1.00
172_R	177_I	1.033	1.00
39_L	42_E	1.025	1.00
70_L	74_G	1.023	1.00
38_Q	42_E	1.021	1.00
178_F	188_F	1.019	1.00
35_Y	38_Q	1.017	1.00
163_L	166_F	1.016	1.00
106_L	122_Y	1.015	1.00
16_K	19_F	1.003	1.00
57_L	61_S	1.003	1.00
4_L	88_F	0.997	1.00
103_F	107_K	0.996	1.00
97_L	101_L	0.992	1.00
29_S	128_L	0.979	1.00
29_S	34_K	0.977	1.00
68_L	71_S	0.970	1.00
13_A	16_K	0.969	1.00
34_K	43_Q	0.968	1.00
15_L	54_L	0.948	1.00
54_L	57_L	0.940	1.00
160_I	164_L	0.935	1.00
102_K	196_E	0.931	1.00
70_L	87_L	0.930	1.00
133_L	165_L	0.926	1.00
101_L	104_L	0.913	1.00
202_I	206_L	0.910	1.00
89_L	93_L	0.907	1.00
176_I	180_L	0.905	1.00
177_I	180_L	0.893	1.00
174_L	178_F	0.893	1.00
8_L	60_L	0.891	1.00
67_Y	88_F	0.890	1.00
68_L	141_L	0.887	1.00
127_F	131_K	0.885	1.00
102_K	126_K	0.877	1.00
46_L	51_S	0.875	1.00
162_L	165_L	0.865	1.00
36_R	42_E	0.861	1.00
70_L	91_I	0.860	1.00
74_G	77_L	0.859	1.00
173_R	179_K	0.857	1.00
178_F	181_I	0.856	1.00
58_F	134_G	0.851	1.00
175_F	188_F	0.848	1.00
181_I	185_L	0.842	1.00
8_L	11_L	0.839	1.00
55_N	127_F	0.836	1.00
108_L	112_I	0.836	1.00
150_S	153_I	0.833	1.00
160_I	163_L	0.828	1.00
111_W	116_K	0.825	1.00
106_L	123_L	0.823	1.00
102_K	130_N	0.822	1.00
181_I	188_F	0.820	1.00
85_F	88_F	0.813	1.00
38_Q	43_Q	0.810	1.00
98_F	126_K	0.809	1.00
122_Y	126_K	0.802	1.00
34_K	38_Q	0.801	1.00
44_N	48_S	0.800	1.00
79_I	83_S	0.798	1.00
195_L	198_L	0.798	1.00
63_S	88_F	0.792	1.00
127_F	130_N	0.792	1.00
4_L	8_L	0.791	1.00
3_I	10_L	0.789	1.00
126_K	129_Y	0.786	1.00
16_K	24_S	0.779	1.00
32_N	36_R	0.775	1.00
134_G	141_L	0.774	1.00
192_L	200_L	0.772	1.00
164_L	168_L	0.770	1.00
58_F	99_Y	0.768	1.00
126_K	188_F	0.767	1.00
22_R	25_D	0.764	1.00
198_L	202_I	0.762	1.00
55_N	59_I	0.760	1.00
76_L	79_I	0.759	1.00
181_I	184_S	0.757	1.00
170_Y	188_F	0.749	1.00
136_L	165_L	0.746	1.00
125_N	129_Y	0.744	1.00
185_L	189_I	0.740	1.00
126_K	169_R	0.738	1.00
61_S	65_F	0.736	1.00
99_Y	200_L	0.733	1.00
69_L	72_Y	0.733	1.00
22_R	39_L	0.732	1.00
93_L	97_L	0.732	1.00
128_L	182_K	0.728	1.00
164_L	167_L	0.727	1.00
183_F	188_F	0.725	1.00
196_E	200_L	0.725	1.00
86_L	108_L	0.722	1.00
185_L	190_L	0.721	0.99
163_L	170_Y	0.715	0.99
190_L	195_L	0.713	0.99
43_Q	124_F	0.713	0.99
59_I	99_Y	0.713	0.99
7_L	11_L	0.712	0.99
33_T	37_Q	0.711	0.99
104_L	108_L	0.711	0.99
73_F	76_L	0.711	0.99
11_L	78_S	0.707	0.99
20_P	24_S	0.706	0.99
37_Q	40_F	0.705	0.99
25_D	29_S	0.702	0.99
61_S	134_G	0.701	0.99
65_F	144_L	0.698	0.99
110_G	113_F	0.698	0.99
60_L	88_F	0.696	0.99
136_L	139_P	0.696	0.99
113_F	196_E	0.696	0.99
175_F	178_F	0.695	0.99
22_R	43_Q	0.694	0.99
46_L	49_R	0.693	0.99
193_C	197_I	0.692	0.99
65_F	72_Y	0.681	0.99
12_L	16_K	0.681	0.99
102_K	127_F	0.679	0.99
30_F	132_L	0.678	0.99
184_S	188_F	0.677	0.99
28_R	62_L	0.675	0.99
15_L	57_L	0.673	0.99
6_L	10_L	0.673	0.99
143_L	149_L	0.673	0.99
141_L	145_A	0.673	0.99
187_Y	192_L	0.672	0.99
141_L	144_L	0.671	0.99
163_L	167_L	0.667	0.99
183_F	198_L	0.651	0.99
128_L	131_K	0.648	0.99
107_K	116_K	0.646	0.99
27_F	31_F	0.644	0.99
106_L	110_G	0.640	0.99
54_L	58_F	0.637	0.99
79_I	93_L	0.631	0.99
110_G	123_L	0.626	0.99
33_T	176_I	0.626	0.99
45_L	48_S	0.622	0.99
109_L	112_I	0.622	0.99
83_S	86_L	0.621	0.99
6_L	9_L	0.614	0.98
78_S	155_L	0.614	0.98
23_F	27_F	0.607	0.98
135_L	139_P	0.607	0.98
17_L	20_P	0.606	0.98
173_R	178_F	0.604	0.98
74_G	152_K	0.603	0.98
163_L	169_R	0.603	0.98
133_L	136_L	0.593	0.98
122_Y	173_R	0.592	0.98
122_Y	166_F	0.592	0.98
9_L	13_A	0.589	0.98
111_W	114_N	0.582	0.98
89_L	97_L	0.582	0.98
22_R	26_L	0.578	0.98
201_L	204_Y	0.577	0.98
71_S	94_I	0.576	0.98
29_S	39_L	0.570	0.97
27_F	125_N	0.570	0.97
75_L	83_S	0.557	0.97
150_S	155_L	0.554	0.97
120_S	124_F	0.553	0.97
9_L	138_L	0.552	0.97
153_I	158_I	0.550	0.97
188_F	192_L	0.550	0.97
113_F	122_Y	0.549	0.97
167_L	183_F	0.547	0.97
125_N	173_R	0.547	0.97
168_L	172_R	0.547	0.97
28_R	35_Y	0.546	0.97
61_S	138_L	0.546	0.97
129_Y	166_F	0.545	0.97
106_L	195_L	0.544	0.97
40_F	48_S	0.540	0.96
177_I	181_I	0.538	0.96
12_L	135_L	0.536	0.96
65_F	166_F	0.535	0.96
92_L	96_L	0.534	0.96
29_S	33_T	0.532	0.96
15_L	53_L	0.532	0.96
17_L	21_K	0.526	0.96
139_P	142_L	0.521	0.96
52_L	56_L	0.520	0.96
37_Q	43_Q	0.520	0.96
179_K	182_K	0.517	0.95
5_L	9_L	0.516	0.95
170_Y	174_L	0.514	0.95
161_L	165_L	0.512	0.95
171_I	175_F	0.508	0.95
177_I	183_F	0.508	0.95
190_L	193_C	0.508	0.95
169_R	173_R	0.505	0.95
59_I	103_F	0.504	0.95
143_L	146_Y	0.503	0.95
110_G	122_Y	0.502	0.95
18_L	90_I	0.501	0.95
27_F	30_F	0.500	0.95

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
2mv6A	1	0.1401	2.3	0.931	Contact Map
2xq2A	2	0.4396	1.5	0.938	Contact Map
2kncA	1	0.1884	1.3	0.94	Contact Map
3dh4A	3	0.314	1.2	0.941	Contact Map
2m3eA	1	0.1691	0.9	0.945	Contact Map
1g92A	1	0.0531	0.9	0.946	Contact Map
3j01B	1	0.3961	0.8	0.947	Contact Map
2ks1B	1	0.1159	0.7	0.949	Contact Map
3wu2H	1	0.1594	0.7	0.949	Contact Map
2m20A	2	0.2319	0.7	0.95	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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