DUF4032 - PFAM28P - GREMLIN Contacts

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DUF4032 - Domain of unknown function (DUF4032)

PFAM:	PF13224	Sequences: RLWDELTREEVFGPDERWRIEERIRRLNDLGFDVDELELVTDGDGTRLRLQPKVVDAGHHRRRLLRLTGLDVEENQARRLLNDLDSYRAWLEGRPVDEEVAAHRWLTEVFEPVVAAVPPELRGKLEPAELFHEVLEHRWYLSERAGRDVGLEEAVRSYVATVL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	163 (162)
Sequences:	2541 (1410)
Seq/√Len:	110.8
META:	0.876

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_E	26_R	4.376	1.00
4_D	8_R	3.712	1.00
16_E	19_R	3.511	1.00
157_S	161_T	2.994	1.00
150_G	153_E	2.826	1.00
88_R	101_A	2.763	1.00
28_N	82_N	2.689	1.00
109_V	131_F	2.686	1.00
104_R	108_E	2.546	1.00
137_H	157_S	2.426	1.00
63_R	85_D	2.317	1.00
65_L	71_D	2.247	1.00
155_V	159_V	2.218	1.00
129_E	133_E	2.214	1.00
72_V	128_A	2.173	1.00
97_D	100_V	2.117	1.00
134_V	155_V	2.100	1.00
21_E	25_R	2.082	1.00
110_F	128_A	2.029	1.00
113_V	134_V	2.013	1.00
75_N	78_R	1.944	1.00
13_G	16_E	1.912	1.00
156_R	160_A	1.819	1.00
141_L	157_S	1.812	1.00
116_A	156_R	1.790	1.00
87_Y	108_E	1.760	1.00
10_E	19_R	1.722	1.00
38_E	49_R	1.667	1.00
92_E	95_P	1.648	1.00
24_I	34_V	1.632	1.00
5_E	8_R	1.622	1.00
142_S	150_G	1.592	1.00
79_R	132_H	1.592	1.00
139_W	143_E	1.572	1.00
63_R	67_L	1.568	1.00
59_H	62_R	1.548	1.00
117_V	130_L	1.509	1.00
145_A	153_E	1.459	1.00
85_D	98_E	1.441	1.00
96_V	101_A	1.439	1.00
136_E	143_E	1.435	1.00
136_E	139_W	1.433	1.00
63_R	98_E	1.427	1.00
93_G	96_V	1.391	1.00
5_E	23_R	1.367	1.00
85_D	88_R	1.364	1.00
94_R	100_V	1.364	1.00
152_E	155_V	1.361	1.00
117_V	159_V	1.334	1.00
96_V	100_V	1.330	1.00
140_Y	143_E	1.328	1.00
75_N	129_E	1.309	0.99
52_P	55_V	1.305	0.99
42_D	45_G	1.296	0.99
152_E	156_R	1.275	0.99
93_G	104_R	1.245	0.99
88_R	98_E	1.212	0.99
42_D	47_R	1.196	0.99
141_L	149_V	1.166	0.99
60_H	64_L	1.151	0.99
125_L	133_E	1.141	0.99
134_V	158_Y	1.131	0.98
12_F	19_R	1.122	0.98
10_E	23_R	1.120	0.98
111_E	115_A	1.117	0.98
141_L	145_A	1.109	0.98
19_R	22_E	1.098	0.98
56_D	65_L	1.081	0.98
157_S	160_A	1.066	0.98
143_E	150_G	1.057	0.98
17_R	21_E	1.052	0.98
39_L	48_L	1.037	0.97
57_A	73_E	1.034	0.97
144_R	161_T	1.028	0.97
91_L	95_P	1.026	0.97
12_F	16_E	1.022	0.97
142_S	149_V	1.018	0.97
11_V	49_R	1.003	0.97
149_V	154_A	0.997	0.97
145_A	149_V	0.995	0.97
9_E	51_Q	0.962	0.96
87_Y	104_R	0.942	0.95
61_R	65_L	0.940	0.95
116_A	155_V	0.940	0.95
150_G	154_A	0.932	0.95
107_T	111_E	0.926	0.95
91_L	96_V	0.924	0.95
129_E	136_E	0.921	0.95
106_L	111_E	0.907	0.94
142_S	145_A	0.901	0.94
110_F	114_V	0.894	0.94
16_E	22_E	0.893	0.94
156_R	159_V	0.891	0.94
28_N	59_H	0.885	0.93
58_G	62_R	0.885	0.93
95_P	101_A	0.883	0.93
103_H	107_T	0.871	0.93
41_T	45_G	0.869	0.93
70_L	110_F	0.859	0.92
135_L	138_R	0.854	0.92
136_E	158_Y	0.843	0.92
20_I	34_V	0.841	0.92
5_E	10_E	0.841	0.92
97_D	103_H	0.840	0.92
79_R	140_Y	0.829	0.91
9_E	49_R	0.827	0.91
12_F	21_E	0.822	0.91
134_V	151_L	0.820	0.91
138_R	151_L	0.817	0.90
11_V	47_R	0.814	0.90
53_K	71_D	0.805	0.90
18_W	25_R	0.805	0.90
111_E	127_P	0.802	0.90
99_E	107_T	0.797	0.89
40_V	49_R	0.794	0.89
39_L	42_D	0.790	0.89
136_E	140_Y	0.786	0.89
33_D	56_D	0.781	0.88
35_D	53_K	0.778	0.88
61_R	71_D	0.777	0.88
56_D	71_D	0.770	0.88
79_R	135_L	0.760	0.87
16_E	21_E	0.755	0.87
80_L	99_E	0.755	0.87
114_V	130_L	0.754	0.86
52_P	59_H	0.752	0.86
80_L	133_E	0.747	0.86
52_P	126_E	0.746	0.86
11_V	17_R	0.738	0.85
70_L	73_E	0.736	0.85
22_E	25_R	0.736	0.85
148_D	153_E	0.734	0.85
83_D	138_R	0.730	0.85
18_W	22_E	0.729	0.85
146_G	150_G	0.728	0.84
17_R	22_E	0.727	0.84
5_E	30_L	0.725	0.84
84_L	107_T	0.725	0.84
147_R	153_E	0.723	0.84
63_R	66_R	0.716	0.83
91_L	101_A	0.694	0.82
2_L	7_T	0.694	0.82
145_A	148_D	0.693	0.81
74_E	78_R	0.686	0.81
41_T	46_T	0.685	0.81
58_G	137_H	0.683	0.81
58_G	118_P	0.683	0.81
128_A	132_H	0.682	0.80
103_H	111_E	0.680	0.80
24_I	79_R	0.676	0.80
67_L	102_A	0.675	0.80
17_R	148_D	0.675	0.80
36_E	80_L	0.673	0.80
118_P	124_K	0.661	0.78
21_E	48_L	0.657	0.78
130_L	158_Y	0.655	0.78
70_L	106_L	0.654	0.78
151_L	158_Y	0.653	0.77
12_F	18_W	0.652	0.77
33_D	98_E	0.651	0.77
96_V	104_R	0.651	0.77
14_P	19_R	0.649	0.77
114_V	159_V	0.647	0.77
58_G	132_H	0.646	0.77
100_V	103_H	0.645	0.77
37_L	101_A	0.645	0.77
86_S	138_R	0.644	0.77
46_T	57_A	0.643	0.76
122_R	127_P	0.643	0.76
152_E	159_V	0.637	0.76
64_L	72_V	0.632	0.75
88_R	91_L	0.632	0.75
51_Q	57_A	0.632	0.75
8_R	42_D	0.629	0.75
39_L	50_L	0.624	0.74
121_L	124_K	0.620	0.74
64_L	77_A	0.620	0.74
137_H	141_L	0.618	0.74
53_K	65_L	0.617	0.73
126_E	129_E	0.617	0.73
23_R	26_R	0.616	0.73
75_N	84_L	0.615	0.73
151_L	155_V	0.611	0.73
91_L	94_R	0.605	0.72
34_V	50_L	0.605	0.72
148_D	154_A	0.600	0.71
92_E	96_V	0.598	0.71
141_L	151_L	0.598	0.71
133_E	155_V	0.595	0.71
53_K	66_R	0.590	0.70
24_I	56_D	0.588	0.70
144_R	157_S	0.588	0.70
10_E	21_E	0.587	0.70
118_P	125_L	0.586	0.70
13_G	22_E	0.585	0.69
8_R	14_P	0.585	0.69
55_V	138_R	0.584	0.69
91_L	104_R	0.584	0.69
93_G	101_A	0.583	0.69
107_T	152_E	0.583	0.69
20_I	24_I	0.581	0.69
136_E	157_S	0.576	0.68
63_R	81_L	0.574	0.68
55_V	59_H	0.572	0.68
61_R	70_L	0.569	0.67
64_L	80_L	0.564	0.67
14_P	17_R	0.561	0.66
72_V	79_R	0.560	0.66
110_F	117_V	0.560	0.66
39_L	46_T	0.560	0.66
98_E	103_H	0.555	0.65
43_G	46_T	0.554	0.65
118_P	132_H	0.553	0.65
132_H	140_Y	0.551	0.65
137_H	140_Y	0.548	0.64
59_H	133_E	0.545	0.64
36_E	69_G	0.545	0.64
32_F	78_R	0.543	0.64
94_R	101_A	0.543	0.64
128_A	133_E	0.543	0.64
38_E	87_Y	0.542	0.64
9_E	73_E	0.540	0.63
37_L	61_R	0.540	0.63
74_E	155_V	0.538	0.63
60_H	77_A	0.538	0.63
144_R	147_R	0.534	0.62
106_L	126_E	0.534	0.62
28_N	56_D	0.534	0.62
90_W	110_F	0.531	0.62
6_L	12_F	0.528	0.62
40_V	47_R	0.527	0.61
66_R	103_H	0.527	0.61
139_W	142_S	0.525	0.61
33_D	59_H	0.525	0.61
113_V	155_V	0.525	0.61
21_E	86_S	0.521	0.61
10_E	13_G	0.518	0.60
113_V	152_E	0.515	0.60
87_Y	91_L	0.515	0.60
100_V	104_R	0.514	0.60
118_P	123_G	0.514	0.60
124_K	127_P	0.513	0.59
63_R	74_E	0.500	0.58

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
3gfzA	2	0.6564	26.4	0.948	Contact Map
3mc9A	2	0	21.4	0.95	Contact Map
3q6bA	1	0.3436	13.9	0.954	Contact Map
1x9zA	4	0.7362	10.1	0.957	Contact Map
2ltaA	1	0.5399	8.2	0.959	Contact Map
2x8xX	1	0.362	7.9	0.959	Contact Map
2wxyC	2	0.8896	6.8	0.96	Contact Map
2fi0A	1	0.2331	6.3	0.961	Contact Map
3dp7A	2	0.3252	5.6	0.962	Contact Map
4q6jA	4	0.6319	5.4	0.962	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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