DUF4573 - PFAM28P - GREMLIN Contacts

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DUF4573 - Domain of unknown function (DUF4573)

PFAM:	PF15140	Sequences: AVDPVGPVEPVDPVEPVEPVEPVQPVGPVDPVEPVEPVEPVEPVTPVEPVKPVAPVEPVGPVAPVEPVRPVEPVDPVGPVEPVEPVQPVGPVEPVGPVEPVEPVEPVEPVEPVEPVGPVEPVQPVEPVEPVEPVSPVVEPVQPVEPVEPVQPVEPVGPVEPVQPVEPVPKENET	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	174 (161)
Sequences:	565 (480)
Seq/√Len:	37.9
META:	0.558

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_G	96_G	2.592	1.00
69_R	105_E	2.460	1.00
39_E	57_E	2.344	1.00
60_G	96_G	2.287	1.00
93_E	111_E	2.162	0.99
54_A	72_E	2.098	0.99
87_Q	105_E	2.059	0.99
111_E	129_E	1.995	0.99
84_E	120_E	1.994	0.99
96_G	114_E	1.994	0.99
69_R	87_Q	1.932	0.98
89_V	107_V	1.920	0.98
51_K	69_R	1.914	0.98
60_G	78_G	1.900	0.98
53_V	107_V	1.858	0.98
42_E	96_G	1.832	0.98
75_D	93_E	1.815	0.97
45_T	99_E	1.786	0.97
66_E	84_E	1.776	0.97
33_E	51_K	1.648	0.95
99_E	117_G	1.622	0.95
72_E	90_G	1.603	0.95
77_V	113_V	1.597	0.95
24_Q	42_E	1.596	0.95
48_E	66_E	1.592	0.94
60_G	114_E	1.574	0.94
85_P	103_P	1.564	0.94
102_E	120_E	1.558	0.94
79_P	97_P	1.547	0.94
84_E	102_E	1.546	0.94
95_V	131_V	1.543	0.94
55_P	91_P	1.538	0.93
45_T	63_A	1.535	0.93
81_E	99_E	1.508	0.93
114_E	132_E	1.452	0.91
57_E	111_E	1.444	0.91
37_P	55_P	1.440	0.91
42_E	60_G	1.440	0.91
96_G	132_E	1.430	0.91
57_E	75_D	1.423	0.90
50_V	104_V	1.401	0.90
64_P	118_P	1.400	0.90
107_V	125_V	1.388	0.89
105_E	123_Q	1.387	0.89
61_P	115_P	1.372	0.89
87_Q	123_Q	1.369	0.89
39_E	93_E	1.364	0.88
69_R	123_Q	1.364	0.88
57_E	93_E	1.363	0.88
77_V	95_V	1.363	0.88
58_P	76_P	1.321	0.87
63_A	81_E	1.303	0.86
78_G	114_E	1.300	0.86
81_E	117_G	1.289	0.85
68_V	86_V	1.285	0.85
103_P	121_P	1.281	0.85
58_P	112_P	1.267	0.84
62_V	80_V	1.258	0.84
27_G	63_A	1.243	0.83
30_D	66_E	1.228	0.82
100_P	118_P	1.228	0.82
51_K	123_Q	1.216	0.82
67_P	103_P	1.216	0.82
76_P	112_P	1.209	0.81
40_P	58_P	1.199	0.81
72_E	108_E	1.199	0.81
44_V	80_V	1.185	0.80
90_G	126_E	1.184	0.80
48_E	102_E	1.176	0.80
91_P	109_P	1.167	0.79
118_P	136_P	1.165	0.79
142_Q	160_E	1.160	0.79
73_P	91_P	1.159	0.79
68_V	104_V	1.152	0.78
52_P	106_P	1.149	0.78
43_P	61_P	1.133	0.77
48_E	120_E	1.130	0.77
106_P	124_P	1.109	0.75
59_V	95_V	1.097	0.75
36_E	90_G	1.082	0.74
74_V	110_V	1.066	0.72
108_E	126_E	1.065	0.72
55_P	109_P	1.063	0.72
95_V	113_V	1.060	0.72
51_K	105_E	1.057	0.72
21_E	57_E	1.041	0.71
52_P	124_P	1.035	0.70
20_V	38_V	1.031	0.70
39_E	129_E	1.028	0.70
86_V	104_V	1.024	0.69
61_P	79_P	1.024	0.69
42_E	114_E	1.010	0.68
54_A	135_S	1.008	0.68
51_K	87_Q	1.006	0.68
66_E	102_E	1.002	0.68
70_P	88_P	0.996	0.67
69_R	78_G	0.995	0.67
47_V	83_V	0.994	0.67
75_D	111_E	0.988	0.67
49_P	67_P	0.979	0.66
98_V	116_V	0.975	0.65
25_P	43_P	0.975	0.65
97_P	115_P	0.972	0.65
64_P	100_P	0.966	0.65
71_V	125_V	0.965	0.65
78_G	132_E	0.961	0.64
51_K	78_G	0.942	0.63
33_E	69_R	0.940	0.63
26_V	44_V	0.931	0.62
104_V	122_V	0.928	0.62
73_P	109_P	0.925	0.61
80_V	98_V	0.923	0.61
53_V	71_V	0.920	0.61
64_P	91_P	0.917	0.61
71_V	89_V	0.905	0.60
30_D	48_E	0.902	0.59
49_P	103_P	0.897	0.59
46_P	64_P	0.891	0.58
44_V	98_V	0.882	0.58
89_V	125_V	0.881	0.58
92_V	110_V	0.879	0.57
55_P	73_P	0.876	0.57
43_P	97_P	0.874	0.57
61_P	97_P	0.872	0.57
68_V	95_V	0.869	0.56
74_V	92_V	0.868	0.56
39_E	75_D	0.861	0.56
85_P	121_P	0.861	0.56
45_T	81_E	0.859	0.56
50_V	86_V	0.847	0.55
79_P	115_P	0.846	0.54
65_V	83_V	0.839	0.54
80_V	134_V	0.839	0.54
32_V	50_V	0.839	0.54
76_P	94_P	0.826	0.53
46_P	100_P	0.822	0.52
25_P	79_P	0.819	0.52
33_E	105_E	0.812	0.51
24_Q	60_G	0.811	0.51
75_D	129_E	0.811	0.51
110_V	128_V	0.810	0.51
46_P	73_P	0.809	0.51
101_V	119_V	0.804	0.51
18_E	36_E	0.800	0.50
50_V	68_V	0.794	0.50
82_P	100_P	0.792	0.50
57_E	120_E	0.782	0.49
108_E	142_Q	0.781	0.49
100_P	136_P	0.777	0.48
90_G	117_G	0.776	0.48
63_A	99_E	0.772	0.48
82_P	118_P	0.763	0.47
36_E	99_E	0.762	0.47
49_P	85_P	0.755	0.46
21_E	39_E	0.750	0.46
27_G	45_T	0.744	0.45
60_G	87_Q	0.744	0.45
36_E	126_E	0.733	0.44
33_E	87_Q	0.727	0.44
75_D	102_E	0.726	0.44
38_V	128_V	0.725	0.44
19_P	55_P	0.723	0.44
28_P	91_P	0.722	0.43
88_P	124_P	0.713	0.43
45_T	117_G	0.703	0.42
52_P	70_P	0.703	0.42
12_D	111_E	0.701	0.42
63_A	117_G	0.698	0.41
34_P	52_P	0.696	0.41
64_P	109_P	0.693	0.41
12_D	30_D	0.682	0.40
44_V	62_V	0.681	0.40
18_E	108_E	0.677	0.40
41_V	77_V	0.676	0.39
113_V	131_V	0.675	0.39
70_P	97_P	0.673	0.39
37_P	91_P	0.671	0.39
44_V	116_V	0.670	0.39
41_V	59_V	0.667	0.39
93_E	120_E	0.667	0.39
93_E	129_E	0.666	0.39
70_P	106_P	0.662	0.38
123_Q	139_E	0.662	0.38
64_P	82_P	0.658	0.38
126_E	142_Q	0.658	0.38
57_E	129_E	0.658	0.38
24_Q	51_K	0.656	0.38
109_P	127_P	0.655	0.38
88_P	106_P	0.654	0.38
43_P	133_P	0.654	0.38
54_A	90_G	0.649	0.37
86_V	122_V	0.647	0.37
73_P	100_P	0.642	0.37
42_E	78_G	0.633	0.36
91_P	127_P	0.631	0.36
47_V	65_V	0.627	0.35
33_E	78_G	0.622	0.35
28_P	82_P	0.621	0.35
90_G	135_S	0.612	0.34
94_P	112_P	0.611	0.34
66_E	129_E	0.609	0.34
40_P	94_P	0.608	0.34
33_E	96_G	0.606	0.34
38_V	74_V	0.600	0.33
36_E	108_E	0.592	0.33
46_P	109_P	0.586	0.32
48_E	154_E	0.585	0.32
59_V	77_V	0.582	0.32
47_V	74_V	0.574	0.31
60_G	123_Q	0.574	0.31
50_V	131_V	0.574	0.31
117_G	135_S	0.569	0.31
57_E	63_A	0.569	0.31
54_A	126_E	0.566	0.31
68_V	122_V	0.566	0.31
51_K	148_E	0.565	0.31
27_G	81_E	0.562	0.30
81_E	135_S	0.560	0.30
105_E	132_E	0.557	0.30
28_P	46_P	0.551	0.29
49_P	112_P	0.548	0.29
96_G	148_E	0.546	0.29
71_V	107_V	0.543	0.29
32_V	86_V	0.543	0.29
53_V	89_V	0.543	0.29
44_V	89_V	0.532	0.28
39_E	84_E	0.529	0.28
67_P	121_P	0.529	0.28
46_P	118_P	0.527	0.28
69_R	139_E	0.527	0.28
92_V	128_V	0.526	0.28
45_T	108_E	0.524	0.27
27_G	135_S	0.523	0.27
90_G	108_E	0.522	0.27
62_V	98_V	0.521	0.27
22_P	76_P	0.521	0.27
60_G	132_E	0.521	0.27
31_P	67_P	0.516	0.27
124_P	140_P	0.512	0.27
48_E	75_D	0.507	0.26
88_P	140_P	0.506	0.26
87_Q	99_E	0.500	0.26

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
2lcmA	1	0.1379	1.2	0.942	Contact Map
1mskA	1	0.3678	0.6	0.953	Contact Map
3bulA	1	0.3333	0.6	0.953	Contact Map
2lu2A	1	0.4655	0.5	0.954	Contact Map
3b23C	1	0.0172	0.4	0.958	Contact Map
4ggdC	1	0.046	0.4	0.958	Contact Map
4x2uA	1	0.3621	0.3	0.963	Contact Map
2jrhA	1	0.2471	0.3	0.963	Contact Map
4ujqF	1	0.4483	0.3	0.964	Contact Map
4ep8C	3	0.3851	0.3	0.965	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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