DUF2589 - PFAM28P - GREMLIN Contacts

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DUF2589 - Protein of unknown function (DUF2589)

PFAM:	PF11655	Sequences: PLEDLIGGPLNAAVEAQAQAAQATVDFIKEVGFDKDDDGTETRMVPFTYTRPVPDGDGGEEEVTLEVPLLTLVPIPSLRIDEVDIDFDMEVKSSESSKSSTDSSASASAEASGGWGPVSVKGSVSSKKESTRTDGSKTDNSAKYHVKVKAKQDEPPEGLARLLDILEKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	169 (164)
Sequences:	1976 (1595)
Seq/√Len:	124.5
META:	0.839

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
82_E	149_K	5.157	1.00
86_D	147_K	5.027	1.00
84_D	147_K	4.601	1.00
88_D	145_H	4.471	1.00
81_D	151_K	4.284	1.00
13_A	83_V	3.557	1.00
84_D	149_K	2.989	1.00
86_D	145_H	2.865	1.00
55_D	59_G	2.562	1.00
3_E	15_E	2.452	1.00
110_E	119_S	2.201	1.00
46_P	66_E	2.196	1.00
34_D	38_D	2.070	1.00
34_D	39_G	2.003	1.00
26_D	30_E	1.962	1.00
14_V	20_A	1.898	1.00
50_T	62_E	1.877	1.00
18_A	23_A	1.867	1.00
47_F	51_R	1.778	1.00
113_G	117_P	1.712	1.00
79_R	153_D	1.695	1.00
48_T	66_E	1.669	1.00
32_G	70_L	1.667	1.00
55_D	58_G	1.660	1.00
50_T	60_E	1.643	1.00
50_T	66_E	1.569	1.00
22_Q	26_D	1.558	1.00
13_A	80_I	1.521	1.00
79_R	151_K	1.497	1.00
36_D	39_G	1.495	1.00
111_A	114_G	1.486	1.00
48_T	62_E	1.479	1.00
2_L	7_G	1.442	1.00
56_G	59_G	1.423	1.00
11_N	15_E	1.421	1.00
81_D	149_K	1.406	1.00
111_A	117_P	1.403	1.00
6_I	148_V	1.399	1.00
28_I	32_G	1.356	1.00
87_F	146_V	1.324	1.00
83_V	150_A	1.321	1.00
155_P	160_A	1.315	1.00
34_D	37_D	1.305	1.00
89_M	142_A	1.298	1.00
13_A	150_A	1.294	1.00
156_P	163_L	1.282	1.00
160_A	164_D	1.274	1.00
102_D	127_K	1.260	1.00
50_T	64_T	1.247	1.00
82_E	147_K	1.214	0.99
157_E	160_A	1.211	0.99
35_K	38_D	1.211	0.99
35_K	39_G	1.209	0.99
161_R	164_D	1.200	0.99
48_T	64_T	1.200	0.99
157_E	161_R	1.184	0.99
45_V	51_R	1.171	0.99
156_P	159_L	1.162	0.99
114_G	117_P	1.159	0.99
91_V	142_A	1.152	0.99
46_P	64_T	1.145	0.99
39_G	42_T	1.131	0.99
44_M	66_E	1.131	0.99
112_S	115_W	1.127	0.99
5_L	144_Y	1.115	0.99
4_D	8_G	1.112	0.99
138_T	141_S	1.098	0.99
72_L	162_L	1.094	0.99
74_P	152_Q	1.092	0.99
44_M	47_F	1.085	0.99
2_L	89_M	1.079	0.99
110_E	118_V	1.079	0.99
9_P	144_Y	1.043	0.98
46_P	51_R	1.034	0.98
3_E	119_S	1.031	0.98
74_P	79_R	1.026	0.98
92_K	123_S	1.016	0.98
123_S	127_K	1.014	0.98
54_P	58_G	1.011	0.98
51_R	63_V	1.010	0.98
24_T	76_P	1.006	0.98
113_G	116_G	0.998	0.98
88_D	143_K	0.996	0.98
82_E	151_K	0.989	0.97
132_R	139_D	0.979	0.97
53_V	61_E	0.978	0.97
129_E	132_R	0.954	0.97
100_S	127_K	0.953	0.97
111_A	116_G	0.952	0.97
90_E	143_K	0.950	0.97
15_E	19_Q	0.938	0.97
11_N	19_Q	0.930	0.96
24_T	77_S	0.926	0.96
21_A	24_T	0.924	0.96
24_T	32_G	0.920	0.96
118_V	124_V	0.915	0.96
108_S	121_K	0.910	0.96
151_K	154_E	0.909	0.96
122_G	125_S	0.884	0.95
79_R	152_Q	0.874	0.95
46_P	49_Y	0.874	0.95
24_T	27_F	0.872	0.95
140_N	143_K	0.860	0.94
36_D	40_T	0.857	0.94
47_F	53_V	0.843	0.94
13_A	17_Q	0.842	0.94
25_V	73_V	0.839	0.94
54_P	57_D	0.831	0.93
53_V	56_G	0.821	0.93
157_E	164_D	0.821	0.93
139_D	143_K	0.818	0.93
96_S	137_K	0.808	0.92
5_L	89_M	0.798	0.92
17_Q	166_L	0.791	0.92
11_N	91_V	0.786	0.91
1_P	4_D	0.784	0.91
126_S	130_S	0.778	0.91
7_G	14_V	0.777	0.91
24_T	28_I	0.775	0.91
7_G	10_L	0.771	0.90
127_K	130_S	0.760	0.90
34_D	42_T	0.759	0.90
28_I	75_I	0.757	0.90
103_S	107_A	0.751	0.89
124_V	127_K	0.750	0.89
43_R	47_F	0.737	0.88
79_R	154_E	0.735	0.88
19_Q	22_Q	0.733	0.88
7_G	12_A	0.732	0.88
161_R	166_L	0.731	0.88
144_Y	157_E	0.730	0.88
109_A	118_V	0.729	0.88
125_S	128_K	0.726	0.88
45_V	49_Y	0.724	0.88
24_T	29_K	0.716	0.87
122_G	127_K	0.716	0.87
111_A	115_W	0.716	0.87
2_L	13_A	0.708	0.86
16_A	80_I	0.707	0.86
71_T	156_P	0.704	0.86
91_V	144_Y	0.703	0.86
101_T	106_S	0.696	0.85
88_D	141_S	0.694	0.85
17_Q	80_I	0.692	0.85
77_S	146_V	0.691	0.85
52_P	73_V	0.691	0.85
14_V	23_A	0.687	0.85
78_L	83_V	0.686	0.85
106_S	109_A	0.684	0.84
9_P	12_A	0.683	0.84
112_S	116_G	0.677	0.84
63_V	162_L	0.676	0.84
163_L	167_E	0.674	0.84
2_L	5_L	0.672	0.83
26_D	78_L	0.672	0.83
91_V	140_N	0.670	0.83
111_A	118_V	0.669	0.83
158_G	163_L	0.669	0.83
14_V	76_P	0.665	0.83
27_F	76_P	0.663	0.83
52_P	60_E	0.658	0.82
124_V	128_K	0.657	0.82
17_Q	24_T	0.652	0.81
4_D	11_N	0.641	0.80
132_R	138_T	0.641	0.80
15_E	23_A	0.640	0.80
6_I	87_F	0.639	0.80
80_I	148_V	0.639	0.80
45_V	53_V	0.635	0.80
98_K	129_E	0.631	0.79
118_V	126_S	0.626	0.79
110_E	115_W	0.626	0.79
104_S	127_K	0.625	0.79
71_T	167_E	0.622	0.78
77_S	85_I	0.618	0.78
113_G	119_S	0.615	0.78
81_D	152_Q	0.614	0.77
4_D	19_Q	0.613	0.77
85_I	148_V	0.610	0.77
49_Y	53_V	0.609	0.77
89_M	144_Y	0.606	0.77
155_P	163_L	0.604	0.76
25_V	29_K	0.603	0.76
20_A	23_A	0.599	0.76
7_G	21_A	0.598	0.76
37_D	57_D	0.594	0.75
1_P	9_P	0.592	0.75
102_D	106_S	0.588	0.74
123_S	129_E	0.586	0.74
144_Y	155_P	0.586	0.74
10_L	150_A	0.585	0.74
9_P	32_G	0.585	0.74
13_A	85_I	0.584	0.74
141_S	157_E	0.579	0.73
112_S	117_P	0.574	0.73
101_T	112_S	0.574	0.73
36_D	45_V	0.573	0.72
48_T	52_P	0.570	0.72
7_G	51_R	0.570	0.72
10_L	165_I	0.569	0.72
7_G	11_N	0.562	0.71
11_N	16_A	0.561	0.71
38_D	45_V	0.559	0.71
23_A	80_I	0.559	0.71
80_I	85_I	0.556	0.70
60_E	63_V	0.555	0.70
20_A	78_L	0.552	0.70
50_T	53_V	0.551	0.70
77_S	150_A	0.549	0.69
27_F	75_I	0.546	0.69
21_A	152_Q	0.546	0.69
37_D	40_T	0.546	0.69
8_G	12_A	0.546	0.69
44_M	49_Y	0.546	0.69
70_L	158_G	0.543	0.68
88_D	142_A	0.541	0.68
67_V	72_L	0.540	0.68
67_V	162_L	0.537	0.68
1_P	13_A	0.537	0.68
118_V	123_S	0.536	0.67
28_I	45_V	0.535	0.67
49_Y	52_P	0.533	0.67
9_P	165_I	0.532	0.67
90_E	141_S	0.530	0.67
11_N	18_A	0.530	0.67
2_L	146_V	0.530	0.67
119_S	122_G	0.528	0.66
25_V	161_R	0.528	0.66
110_E	121_K	0.522	0.65
121_K	127_K	0.520	0.65
102_D	105_A	0.518	0.65
5_L	77_S	0.517	0.65
38_D	42_T	0.516	0.65
33_F	67_V	0.515	0.64
20_A	74_P	0.515	0.64
84_D	146_V	0.513	0.64
23_A	27_F	0.513	0.64
70_L	87_F	0.512	0.64
113_G	120_V	0.511	0.64
12_A	81_D	0.510	0.64
34_D	41_E	0.508	0.63
14_V	31_V	0.507	0.63
165_I	168_K	0.504	0.63
18_A	32_G	0.503	0.63
45_V	65_L	0.500	0.62
10_L	27_F	0.500	0.62

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
3eojA	3	0.3905	8.5	0.929	Contact Map
2ot3A	1	0.4675	6.3	0.933	Contact Map
2l32A	1	0.1538	4.9	0.936	Contact Map
1xkmA	2	0.1124	3.9	0.94	Contact Map
2izyA	5	0.1006	3.7	0.94	Contact Map
4hrsA	2	0.1598	3	0.943	Contact Map
2k5pA	1	0.1538	2.7	0.944	Contact Map
4anoA	1	0.2959	2.3	0.946	Contact Map
2lvwA	2	0.2012	2.2	0.947	Contact Map
4wyqB	1	0.1893	2.2	0.947	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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