DUF4433 - PFAM28P - GREMLIN Contacts

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DUF4433 - Domain of unknown function (DUF4433)

PFAM:	PF14487	Sequences: YHITHIDNLPSILENGGLLSRNELEERGLNYTDIGDPEIQDRRLTRPVPVPPGGTLHDYVPFYFCPRSPMLYNIRHRGNVPEYRGGQEDIVILVIDLEVLVELGFVFTDGNAASSYTEFYSDLDDLDEKIDWDAIFARDWRDDDEDPDRKRRKQAEFLVPDSVPWELIEGIGVYNEAVKERVEALLAAAGFHRPPVEVRPDWYF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	204 (201)
Sequences:	4648 (4061)
Seq/√Len:	286.5
META:	0.867

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
179_K	183_E	5.326	1.00
130_I	135_I	4.802	1.00
110_G	117_T	3.203	1.00
4_T	12_I	3.085	1.00
110_G	151_R	3.056	1.00
22_N	58_D	2.961	1.00
9_L	182_V	2.785	1.00
23_E	26_E	2.784	1.00
170_G	197_E	2.781	1.00
94_V	170_G	2.684	1.00
17_G	162_S	2.582	1.00
23_E	161_D	2.388	1.00
131_D	152_R	2.310	1.00
23_E	27_R	2.309	1.00
176_E	179_K	2.224	1.00
109_D	118_E	2.118	1.00
104_G	160_P	2.057	1.00
120_Y	129_K	2.053	1.00
117_T	151_R	1.941	1.00
109_D	120_Y	1.891	1.00
178_V	181_R	1.883	1.00
65_C	153_K	1.882	1.00
125_D	129_K	1.867	1.00
131_D	134_A	1.850	1.00
95_I	163_V	1.824	1.00
96_D	169_E	1.776	1.00
40_Q	57_H	1.761	1.00
36_D	73_N	1.749	1.00
99_V	169_E	1.705	1.00
93_L	168_I	1.651	1.00
62_F	163_V	1.612	1.00
7_D	32_T	1.612	1.00
4_T	8_N	1.612	1.00
175_N	178_V	1.596	1.00
99_V	102_E	1.568	1.00
173_V	182_V	1.542	1.00
41_D	45_T	1.537	1.00
88_E	175_N	1.531	1.00
10_P	185_L	1.498	1.00
55_T	58_D	1.486	1.00
122_D	125_D	1.482	1.00
88_E	174_Y	1.471	1.00
14_E	189_A	1.462	1.00
15_N	27_R	1.447	1.00
165_W	168_I	1.420	1.00
148_D	152_R	1.387	1.00
15_N	29_L	1.373	1.00
110_G	114_S	1.369	1.00
15_N	19_L	1.358	1.00
142_D	149_R	1.348	1.00
2_H	18_L	1.336	1.00
94_V	172_G	1.331	1.00
148_D	151_R	1.296	1.00
54_G	59_Y	1.294	1.00
103_L	164_P	1.285	1.00
108_T	119_F	1.277	1.00
39_I	113_A	1.269	1.00
71_L	90_I	1.264	1.00
54_G	161_D	1.263	1.00
93_L	171_I	1.252	1.00
19_L	24_L	1.246	1.00
108_T	117_T	1.240	1.00
83_Y	86_G	1.193	1.00
68_S	71_L	1.186	1.00
164_P	167_L	1.183	1.00
24_L	29_L	1.179	1.00
54_G	160_P	1.177	1.00
171_I	182_V	1.171	1.00
135_I	153_K	1.170	1.00
73_N	77_R	1.168	1.00
159_V	163_V	1.167	1.00
176_E	180_E	1.134	1.00
105_F	157_F	1.131	1.00
69_P	153_K	1.131	1.00
59_Y	106_V	1.123	1.00
114_S	151_R	1.123	1.00
85_G	89_D	1.119	1.00
101_V	123_L	1.109	1.00
75_R	78_G	1.101	1.00
174_Y	178_V	1.086	1.00
152_R	155_A	1.081	1.00
134_A	152_R	1.077	1.00
46_R	115_S	1.071	1.00
95_I	168_I	1.068	1.00
9_L	171_I	1.056	1.00
170_G	199_R	1.055	1.00
60_V	163_V	1.052	1.00
114_S	117_T	1.043	1.00
19_L	23_E	1.042	1.00
134_A	137_A	1.039	1.00
174_Y	200_P	1.037	1.00
9_L	93_L	1.036	1.00
8_N	31_Y	1.030	1.00
18_L	60_V	1.030	1.00
21_R	40_Q	1.028	1.00
123_L	126_L	1.027	1.00
44_L	57_H	1.027	1.00
180_E	183_E	1.020	1.00
172_G	202_W	1.012	1.00
18_L	21_R	1.005	1.00
35_G	40_Q	0.997	1.00
3_I	92_I	0.993	1.00
34_I	70_M	0.991	1.00
107_F	122_D	0.983	1.00
176_E	198_V	0.983	1.00
19_L	162_S	0.976	1.00
9_L	91_V	0.976	1.00
67_R	71_L	0.976	1.00
39_I	42_R	0.974	1.00
189_A	192_H	0.973	1.00
51_P	121_S	0.972	1.00
63_Y	154_Q	0.971	1.00
47_P	55_T	0.964	1.00
132_W	135_I	0.958	1.00
89_D	181_R	0.958	1.00
4_T	31_Y	0.942	1.00
3_I	90_I	0.940	1.00
56_L	111_N	0.940	1.00
108_T	112_A	0.940	1.00
59_Y	160_P	0.927	1.00
177_A	181_R	0.924	1.00
54_G	58_D	0.924	1.00
141_R	146_D	0.921	1.00
35_G	57_H	0.920	1.00
20_S	23_E	0.919	1.00
6_I	178_V	0.905	1.00
69_P	150_K	0.900	1.00
146_D	152_R	0.897	1.00
20_S	161_D	0.896	1.00
72_Y	77_R	0.891	1.00
65_C	68_S	0.885	1.00
10_P	14_E	0.880	1.00
100_L	159_V	0.880	1.00
38_E	82_E	0.877	1.00
20_S	24_L	0.877	1.00
134_A	149_R	0.850	1.00
1_Y	66_P	0.847	1.00
110_G	148_D	0.845	1.00
36_D	39_I	0.844	1.00
33_D	37_P	0.842	1.00
5_H	89_D	0.831	1.00
95_I	99_V	0.830	1.00
111_N	154_Q	0.828	1.00
21_R	24_L	0.828	1.00
101_V	105_F	0.824	1.00
181_R	184_A	0.824	1.00
183_E	187_A	0.818	1.00
73_N	79_N	0.816	1.00
138_R	201_D	0.813	1.00
71_L	92_I	0.808	0.99
63_Y	68_S	0.807	0.99
132_W	136_F	0.806	0.99
94_V	169_E	0.806	0.99
100_L	163_V	0.804	0.99
186_L	195_P	0.800	0.99
56_L	61_P	0.794	0.99
11_S	15_N	0.793	0.99
146_D	149_R	0.789	0.99
181_R	185_L	0.785	0.99
13_L	165_W	0.780	0.99
42_R	113_A	0.773	0.99
116_Y	151_R	0.772	0.99
72_Y	75_R	0.771	0.99
65_C	92_I	0.766	0.99
24_L	31_Y	0.761	0.99
105_F	159_V	0.758	0.99
18_L	22_N	0.755	0.99
76_H	80_V	0.752	0.99
69_P	154_Q	0.752	0.99
67_R	92_I	0.751	0.99
68_S	92_I	0.751	0.99
3_I	34_I	0.749	0.99
50_V	106_V	0.748	0.99
92_I	172_G	0.747	0.99
73_N	150_K	0.747	0.99
51_P	106_V	0.746	0.99
182_V	196_V	0.745	0.99
137_A	149_R	0.742	0.99
165_W	192_H	0.741	0.99
180_E	184_A	0.737	0.99
48_V	119_F	0.737	0.99
99_V	167_L	0.732	0.99
21_R	33_D	0.730	0.99
182_V	185_L	0.729	0.99
133_D	137_A	0.723	0.99
76_H	79_N	0.721	0.99
173_V	179_K	0.715	0.99
41_D	44_L	0.711	0.99
67_R	72_Y	0.708	0.99
102_E	167_L	0.704	0.99
89_D	178_V	0.703	0.99
131_D	135_I	0.703	0.99
64_F	107_F	0.696	0.98
77_R	80_V	0.693	0.98
91_V	173_V	0.693	0.98
97_L	123_L	0.684	0.98
100_L	157_F	0.683	0.98
65_C	135_I	0.679	0.98
145_E	149_R	0.679	0.98
46_R	113_A	0.677	0.98
187_A	190_G	0.673	0.98
39_I	57_H	0.672	0.98
107_F	126_L	0.669	0.98
190_G	193_R	0.669	0.98
22_N	26_E	0.666	0.98
110_G	155_A	0.665	0.98
50_V	119_F	0.664	0.98
49_P	52_P	0.663	0.98
86_G	89_D	0.663	0.98
103_L	162_S	0.661	0.98
185_L	188_A	0.659	0.98
22_N	57_H	0.657	0.98
8_N	11_S	0.655	0.98
74_I	77_R	0.654	0.98
18_L	24_L	0.653	0.98
70_M	74_I	0.652	0.98
35_G	39_I	0.648	0.98
34_I	90_I	0.644	0.97
179_K	198_V	0.641	0.97
106_V	157_F	0.635	0.97
185_L	189_A	0.633	0.97
94_V	197_E	0.628	0.97
1_Y	172_G	0.627	0.97
7_D	89_D	0.627	0.97
31_Y	34_I	0.625	0.97
163_V	168_I	0.625	0.97
184_A	187_A	0.625	0.97
143_D	149_R	0.622	0.97
6_I	181_R	0.621	0.97
140_W	143_D	0.617	0.97
37_P	41_D	0.617	0.97
139_D	143_D	0.616	0.97
32_T	85_G	0.616	0.97
88_E	177_A	0.615	0.97
110_G	152_R	0.614	0.97
172_G	199_R	0.614	0.97
64_F	157_F	0.612	0.97
83_Y	89_D	0.610	0.96
27_R	30_N	0.609	0.96
175_N	200_P	0.607	0.96
96_D	99_V	0.606	0.96
165_W	194_P	0.604	0.96
68_S	153_K	0.602	0.96
2_H	11_S	0.599	0.96
177_A	180_E	0.597	0.96
47_P	53_G	0.596	0.96
31_Y	35_G	0.592	0.96
168_I	194_P	0.589	0.96
105_F	160_P	0.588	0.96
130_I	134_A	0.580	0.95
112_A	158_L	0.579	0.95
72_Y	76_H	0.577	0.95
142_D	150_K	0.576	0.95
39_I	111_N	0.572	0.95
48_V	51_P	0.571	0.95
92_I	203_Y	0.571	0.95
98_E	102_E	0.569	0.95
21_R	61_P	0.569	0.95
62_F	157_F	0.568	0.95
199_R	202_W	0.566	0.95
23_E	162_S	0.566	0.95
123_L	127_D	0.564	0.95
97_L	101_V	0.563	0.95
142_D	145_E	0.562	0.95
124_D	127_D	0.561	0.94
184_A	188_A	0.560	0.94
64_F	130_I	0.560	0.94
47_P	50_V	0.559	0.94
112_A	119_F	0.559	0.94
186_L	196_V	0.558	0.94
21_R	57_H	0.557	0.94
34_I	74_I	0.555	0.94
183_E	196_V	0.555	0.94
71_L	75_R	0.550	0.94
189_A	197_E	0.550	0.94
2_H	12_I	0.547	0.94
76_H	81_P	0.546	0.94
68_S	154_Q	0.545	0.94
7_D	181_R	0.544	0.94
48_V	54_G	0.544	0.94
58_D	160_P	0.542	0.93
110_G	116_Y	0.542	0.93
149_R	153_K	0.540	0.93
63_Y	70_M	0.536	0.93
131_D	149_R	0.535	0.93
42_R	115_S	0.531	0.93
28_G	31_Y	0.530	0.93
106_V	160_P	0.526	0.92
75_R	79_N	0.523	0.92
150_K	154_Q	0.518	0.92
138_R	141_R	0.517	0.92
5_H	8_N	0.517	0.92
139_D	142_D	0.516	0.92
21_R	31_Y	0.515	0.92
171_I	194_P	0.515	0.92
195_P	201_D	0.510	0.91
103_L	159_V	0.509	0.91
48_V	52_P	0.507	0.91
48_V	59_Y	0.504	0.91
95_I	167_L	0.503	0.91
137_A	140_W	0.502	0.91
38_E	42_R	0.500	0.90

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
1wfxA	3	0.4314	81.7	0.901	Contact Map
4m5rA	2	0.1912	3.3	0.955	Contact Map
1brvA	1	0.0931	2.4	0.958	Contact Map
2o0qA	1	0.5441	2.1	0.96	Contact Map
4gelA	2	0.2745	1.8	0.961	Contact Map
1v0wA	1	0.4069	1.7	0.962	Contact Map
4zrlB	1	0.1814	1.4	0.963	Contact Map
2ejbA	6	0.25	1.3	0.964	Contact Map
3u4zA	2	0.2647	1.2	0.965	Contact Map
5aj3R	1	0.3235	1.1	0.966	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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