DUF4173 - PFAM28P - GREMLIN Contacts

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DUF4173 - Domain of unknown function (DUF4173)

PFAM:	PF13777	Sequences: VLLNLLFLLFVAVQFAYLFGGFALVLLPAGLTYAEYARRGFFELVAVALLALLLLLAAFRLARRETARDRRLLRVLAGLLIALTLVLLASALLRMRLYIDAYGLTRLRLYVLVFMLWLAVGLVLLLVKILRRRRWLARAALVAALVVLLALNLVNPDALIARYNVARYEGGKLDVAYLASLSADAVPALD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	190 (187)
Sequences:	6618 (4895)
Seq/√Len:	357.9
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
39_R	43_E	3.272	1.00
78_G	130_L	3.190	1.00
124_L	139_A	2.782	1.00
157_D	182_S	2.781	1.00
107_L	111_V	2.726	1.00
99_I	112_L	2.648	1.00
106_R	157_D	2.594	1.00
158_A	162_R	2.509	1.00
111_V	115_M	2.415	1.00
95_M	112_L	2.344	1.00
154_V	159_L	2.230	1.00
173_L	178_L	2.211	1.00
95_M	111_V	2.190	1.00
38_R	42_F	2.073	1.00
78_G	126_L	2.032	1.00
81_I	122_L	1.984	1.00
55_L	77_A	1.957	1.00
104_L	163_Y	1.938	1.00
33_Y	102_Y	1.844	1.00
120_V	143_A	1.843	1.00
75_V	79_L	1.816	1.00
4_N	83_L	1.779	1.00
146_V	150_A	1.772	1.00
4_N	80_L	1.767	1.00
51_A	84_T	1.765	1.00
117_W	143_A	1.755	1.00
121_G	140_A	1.735	1.00
88_L	119_A	1.735	1.00
166_A	169_E	1.722	1.00
162_R	188_A	1.710	1.00
3_L	54_L	1.708	1.00
71_R	75_V	1.681	1.00
117_W	144_A	1.678	1.00
114_F	118_L	1.659	1.00
170_G	173_L	1.650	1.00
93_L	96_R	1.617	1.00
72_L	75_V	1.556	1.00
90_S	94_R	1.552	1.00
106_R	160_I	1.531	1.00
95_M	115_M	1.514	1.00
161_A	185_A	1.501	1.00
67_A	71_R	1.499	1.00
34_A	102_Y	1.495	1.00
92_L	112_L	1.487	1.00
113_V	147_V	1.478	1.00
7_F	51_A	1.474	1.00
33_Y	101_A	1.464	1.00
123_V	127_V	1.458	1.00
161_A	165_V	1.399	1.00
113_V	151_L	1.390	1.00
81_I	126_L	1.343	1.00
96_R	100_D	1.324	1.00
136_L	140_A	1.320	1.00
109_L	159_L	1.318	1.00
99_I	163_Y	1.310	1.00
93_L	97_L	1.309	1.00
80_L	87_L	1.302	1.00
109_L	156_P	1.297	1.00
163_Y	166_A	1.296	1.00
99_I	104_L	1.295	1.00
85_L	119_A	1.289	1.00
4_N	8_L	1.263	1.00
176_A	179_A	1.256	1.00
11_V	83_L	1.249	1.00
55_L	81_I	1.243	1.00
162_R	166_A	1.238	1.00
183_A	186_V	1.236	1.00
4_N	76_L	1.230	1.00
155_N	158_A	1.215	1.00
155_N	184_D	1.208	1.00
85_L	89_A	1.204	1.00
111_V	114_F	1.195	1.00
52_L	122_L	1.186	1.00
73_L	77_A	1.180	1.00
110_Y	151_L	1.166	1.00
165_V	169_E	1.158	1.00
158_A	188_A	1.152	1.00
163_Y	167_R	1.145	1.00
120_V	147_V	1.143	1.00
48_A	122_L	1.142	1.00
25_V	28_P	1.136	1.00
174_D	177_Y	1.125	1.00
35_E	39_R	1.119	1.00
104_L	112_L	1.111	1.00
161_A	188_A	1.108	1.00
148_L	152_N	1.103	1.00
34_A	38_R	1.101	1.00
8_L	83_L	1.071	1.00
5_L	9_L	1.065	1.00
19_F	90_S	1.063	1.00
85_L	123_V	1.056	1.00
176_A	180_S	1.048	1.00
11_V	87_L	1.042	1.00
96_R	112_L	1.041	1.00
8_L	12_A	1.028	1.00
117_W	147_V	1.024	1.00
4_N	79_L	1.019	1.00
42_F	46_A	1.018	1.00
23_A	27_L	1.016	1.00
16_A	20_G	1.008	1.00
31_L	39_R	1.007	1.00
17_Y	43_E	1.006	1.00
10_F	14_Q	0.984	1.00
64_R	70_R	0.957	1.00
151_L	156_P	0.957	1.00
48_A	118_L	0.957	1.00
82_A	86_V	0.955	1.00
113_V	116_L	0.954	1.00
88_L	122_L	0.950	1.00
66_T	69_D	0.941	1.00
92_L	116_L	0.939	1.00
57_A	61_L	0.939	1.00
135_W	138_R	0.936	1.00
71_R	74_R	0.928	1.00
140_A	143_A	0.925	1.00
9_L	12_A	0.925	1.00
52_L	125_L	0.915	1.00
168_Y	173_L	0.911	1.00
132_R	137_A	0.909	1.00
70_R	74_R	0.893	1.00
13_V	17_Y	0.893	1.00
2_L	6_L	0.883	1.00
48_A	84_T	0.883	1.00
116_L	120_V	0.881	1.00
41_F	114_F	0.880	1.00
19_F	86_V	0.876	1.00
106_R	110_Y	0.869	1.00
11_V	86_V	0.866	1.00
42_F	45_V	0.863	1.00
159_L	163_Y	0.859	1.00
17_Y	36_Y	0.857	1.00
157_D	181_L	0.850	1.00
77_A	129_I	0.843	1.00
161_A	178_L	0.837	1.00
68_R	71_R	0.836	1.00
143_A	147_V	0.834	1.00
11_V	14_Q	0.833	1.00
159_L	162_R	0.827	1.00
128_K	136_L	0.819	1.00
142_V	145_L	0.819	1.00
48_A	88_L	0.818	1.00
104_L	159_L	0.811	1.00
49_L	53_L	0.805	1.00
59_F	128_K	0.804	1.00
28_P	31_L	0.802	1.00
132_R	135_W	0.801	1.00
136_L	139_A	0.797	1.00
157_D	160_I	0.788	1.00
32_T	35_E	0.784	1.00
181_L	185_A	0.783	1.00
177_Y	181_L	0.782	1.00
34_A	98_Y	0.781	1.00
67_A	70_R	0.777	1.00
168_Y	171_G	0.777	1.00
79_L	83_L	0.777	1.00
47_V	84_T	0.775	1.00
124_L	136_L	0.771	1.00
121_G	125_L	0.771	1.00
124_L	143_A	0.766	1.00
62_A	73_L	0.761	1.00
21_G	25_V	0.755	1.00
22_F	26_L	0.753	1.00
103_G	167_R	0.753	1.00
36_Y	40_G	0.750	1.00
34_A	174_D	0.744	1.00
145_L	152_N	0.740	1.00
141_L	145_L	0.738	1.00
150_A	154_V	0.734	1.00
92_L	96_R	0.733	1.00
88_L	115_M	0.730	1.00
85_L	88_L	0.726	1.00
68_R	72_L	0.721	0.99
15_F	20_G	0.719	0.99
131_R	135_W	0.716	0.99
12_A	16_A	0.707	0.99
64_R	74_R	0.705	0.99
34_A	37_A	0.704	0.99
52_L	121_G	0.703	0.99
74_R	129_I	0.702	0.99
109_L	160_I	0.702	0.99
34_A	103_G	0.700	0.99
63_R	70_R	0.697	0.99
179_A	183_A	0.683	0.99
72_L	76_L	0.680	0.99
119_A	123_V	0.680	0.99
99_I	105_T	0.679	0.99
146_V	149_L	0.677	0.99
98_Y	105_T	0.675	0.99
75_V	78_G	0.674	0.99
78_G	82_A	0.672	0.99
110_Y	114_F	0.671	0.99
175_V	179_A	0.670	0.99
109_L	154_V	0.668	0.99
56_L	60_R	0.666	0.99
22_F	28_P	0.665	0.99
36_Y	94_R	0.665	0.99
156_P	160_I	0.663	0.99
81_I	85_L	0.662	0.99
174_D	178_L	0.661	0.99
169_E	172_K	0.655	0.99
122_L	125_L	0.654	0.99
147_V	150_A	0.652	0.99
112_L	116_L	0.652	0.99
88_L	92_L	0.650	0.99
135_W	139_A	0.649	0.99
47_V	87_L	0.646	0.99
6_L	9_L	0.644	0.99
165_V	168_Y	0.641	0.99
11_V	15_F	0.640	0.99
66_T	70_R	0.637	0.99
45_V	114_F	0.634	0.99
161_A	181_L	0.634	0.99
42_F	95_M	0.632	0.99
13_V	20_G	0.632	0.99
125_L	136_L	0.629	0.99
148_L	151_L	0.629	0.99
96_R	99_I	0.623	0.98
53_L	57_A	0.619	0.98
45_V	49_L	0.618	0.98
13_V	18_L	0.612	0.98
147_V	151_L	0.611	0.98
59_F	64_R	0.611	0.98
13_V	33_Y	0.609	0.98
15_F	18_L	0.606	0.98
143_A	150_A	0.603	0.98
114_F	117_W	0.602	0.98
37_A	42_F	0.599	0.98
22_F	29_A	0.592	0.98
32_T	102_Y	0.584	0.98
10_F	43_E	0.580	0.98
81_I	129_I	0.575	0.97
176_A	183_A	0.575	0.97
92_L	115_M	0.574	0.97
149_L	153_L	0.574	0.97
38_R	111_V	0.572	0.97
46_A	49_L	0.571	0.97
165_V	178_L	0.571	0.97
4_N	7_F	0.571	0.97
45_V	111_V	0.569	0.97
165_V	188_A	0.569	0.97
59_F	77_A	0.564	0.97
40_G	94_R	0.563	0.97
64_R	73_L	0.560	0.97
18_L	37_A	0.560	0.97
60_R	63_R	0.558	0.97
37_A	111_V	0.557	0.97
63_R	66_T	0.557	0.97
95_M	107_L	0.554	0.97
112_L	115_M	0.554	0.97
74_R	78_G	0.551	0.97
117_W	121_G	0.550	0.97
110_Y	156_P	0.545	0.97
78_G	129_I	0.545	0.97
23_A	26_L	0.544	0.96
172_K	176_A	0.542	0.96
55_L	125_L	0.541	0.96
5_L	8_L	0.540	0.96
85_L	126_L	0.540	0.96
10_F	41_F	0.538	0.96
11_V	19_F	0.537	0.96
22_F	27_L	0.536	0.96
109_L	113_V	0.536	0.96
106_R	177_Y	0.536	0.96
51_A	80_L	0.535	0.96
25_V	93_L	0.528	0.96
86_V	89_A	0.527	0.96
134_R	138_R	0.526	0.96
14_Q	19_F	0.525	0.96
58_A	77_A	0.524	0.96
75_V	127_V	0.522	0.96
13_V	90_S	0.522	0.96
17_Y	20_G	0.521	0.96
144_A	151_L	0.517	0.95
178_L	189_L	0.516	0.95
51_A	54_L	0.514	0.95
81_I	125_L	0.510	0.95
120_V	124_L	0.506	0.95
111_V	118_L	0.504	0.95
9_L	13_V	0.502	0.95
142_V	146_V	0.500	0.94

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
2xgrA	1	0.1632	3.8	0.955	Contact Map
3j9pD	4	0.7474	3.4	0.956	Contact Map
1jmuA	3	0.1368	3.3	0.956	Contact Map
2rddB	1	0.1947	1.9	0.961	Contact Map
1bzkA	1	0.2105	1.8	0.962	Contact Map
4il3A	1	0.9632	1.7	0.962	Contact Map
1rz2A	1	0.1684	1.7	0.962	Contact Map
4aw6A	2	0.9579	1.6	0.963	Contact Map
4l0nA	2	0.1	1.5	0.963	Contact Map
4o6yA	2	0.4684	1.4	0.964	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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