DUF3683 - PFAM28P - GREMLIN Contacts

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DUF3683 - Protein of unknown function (DUF3683)

PFAM:	PF12447	Sequences: QRLREIPYNYTSFSDREIVIRLLGEEAWELLEELRGERRTGRSARMLYEVLGDIWVVQRNPYLQDDLLDNPKRRRALIEALRHRLDEIEKRRERDAKVGELLAAARAAVDRFE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	113 (112)
Sequences:	2531 (803)
Seq/√Len:	75.8
META:	0.922

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_E	97_K	3.523	1.00
22_L	58_Q	3.300	1.00
107_A	111_R	3.229	1.00
27_A	104_A	3.074	1.00
89_E	106_R	3.064	1.00
26_E	100_E	2.929	1.00
80_A	83_H	2.908	1.00
27_A	30_L	2.693	1.00
87_E	90_K	2.654	1.00
29_E	32_E	2.430	1.00
82_R	110_D	2.362	1.00
92_R	99_G	2.300	1.00
82_R	106_R	2.101	1.00
16_R	20_I	2.006	1.00
75_R	79_E	1.937	1.00
110_D	113_E	1.898	1.00
65_D	69_D	1.817	1.00
14_S	17_E	1.780	1.00
86_D	106_R	1.676	1.00
22_L	54_I	1.658	1.00
26_E	29_E	1.653	1.00
82_R	113_E	1.641	1.00
98_V	102_L	1.637	1.00
29_E	33_E	1.479	0.99
25_E	29_E	1.438	0.99
50_V	109_V	1.419	0.99
37_E	97_K	1.417	0.99
74_R	78_I	1.413	0.99
100_E	104_A	1.373	0.98
85_L	109_V	1.372	0.98
28_W	35_R	1.318	0.98
50_V	105_A	1.300	0.98
74_R	81_L	1.297	0.98
58_Q	111_R	1.293	0.98
30_L	97_K	1.269	0.97
31_L	42_R	1.235	0.97
79_E	86_D	1.233	0.97
51_L	55_W	1.223	0.97
54_I	108_A	1.189	0.96
103_A	107_A	1.179	0.96
53_D	80_A	1.160	0.96
49_E	84_R	1.146	0.95
19_V	28_W	1.146	0.95
18_I	55_W	1.133	0.95
105_A	109_V	1.089	0.94
97_K	100_E	1.047	0.92
87_E	98_V	1.019	0.91
20_I	27_A	0.997	0.91
30_L	104_A	0.990	0.90
86_D	89_E	0.989	0.90
89_E	92_R	0.975	0.90
23_L	51_L	0.969	0.89
107_A	110_D	0.969	0.89
26_E	104_A	0.951	0.88
104_A	107_A	0.944	0.88
100_E	103_A	0.936	0.88
4_R	7_P	0.936	0.88
13_F	64_Q	0.924	0.87
77_L	80_A	0.914	0.86
42_R	48_Y	0.909	0.86
53_D	76_A	0.891	0.85
100_E	107_A	0.887	0.85
94_R	99_G	0.887	0.85
79_E	82_R	0.882	0.84
71_P	75_R	0.877	0.84
30_L	100_E	0.847	0.82
87_E	92_R	0.845	0.82
14_S	49_E	0.836	0.81
106_R	110_D	0.834	0.81
42_R	81_L	0.826	0.80
82_R	86_D	0.808	0.79
70_N	80_A	0.803	0.78
78_I	82_R	0.798	0.78
45_R	63_L	0.797	0.78
86_D	90_K	0.789	0.77
46_M	55_W	0.789	0.77
25_E	32_E	0.788	0.77
18_I	53_D	0.776	0.76
70_N	81_L	0.767	0.75
45_R	83_H	0.761	0.74
39_R	64_Q	0.759	0.74
105_A	110_D	0.757	0.74
22_L	27_A	0.757	0.74
99_G	103_A	0.754	0.74
85_L	102_L	0.748	0.73
77_L	112_F	0.747	0.73
89_E	103_A	0.739	0.72
95_D	99_G	0.736	0.72
96_A	107_A	0.730	0.71
88_I	92_R	0.728	0.71
23_L	55_W	0.718	0.70
89_E	102_L	0.717	0.70
54_I	57_V	0.716	0.70
26_E	30_L	0.713	0.69
76_A	80_A	0.712	0.69
64_Q	78_I	0.709	0.69
85_L	92_R	0.702	0.68
77_L	81_L	0.697	0.68
88_I	102_L	0.694	0.67
89_E	99_G	0.685	0.66
32_E	48_Y	0.685	0.66
76_A	79_E	0.684	0.66
42_R	85_L	0.683	0.66
53_D	70_N	0.681	0.66
22_L	48_Y	0.680	0.66
88_I	105_A	0.679	0.66
48_Y	95_D	0.674	0.65
17_E	21_R	0.672	0.65
42_R	54_I	0.670	0.65
66_D	81_L	0.667	0.64
64_Q	80_A	0.659	0.63
13_F	49_E	0.656	0.63
9_N	12_S	0.644	0.62
92_R	98_V	0.643	0.61
35_R	44_A	0.635	0.60
42_R	65_D	0.633	0.60
62_Y	87_E	0.632	0.60
35_R	56_V	0.629	0.60
12_S	15_D	0.622	0.59
21_R	84_R	0.622	0.59
57_V	66_D	0.619	0.59
71_P	74_R	0.618	0.58
96_A	110_D	0.613	0.58
68_L	74_R	0.611	0.58
42_R	45_R	0.611	0.58
37_E	88_I	0.608	0.57
30_L	39_R	0.606	0.57
63_L	76_A	0.605	0.57
38_R	44_A	0.600	0.56
102_L	106_R	0.598	0.56
77_L	83_H	0.598	0.56
37_E	95_D	0.595	0.56
6_I	9_N	0.591	0.55
46_M	64_Q	0.585	0.54
49_E	66_D	0.583	0.54
55_W	84_R	0.582	0.54
58_Q	76_A	0.580	0.54
5_E	35_R	0.578	0.53
41_G	59_R	0.577	0.53
75_R	113_E	0.574	0.53
40_T	43_S	0.571	0.53
27_A	31_L	0.568	0.52
31_L	47_L	0.568	0.52
13_F	17_E	0.565	0.52
96_A	99_G	0.561	0.51
19_V	31_L	0.559	0.51
82_R	89_E	0.554	0.50
57_V	81_L	0.551	0.50
49_E	105_A	0.549	0.50
93_E	96_A	0.548	0.50
8_Y	53_D	0.547	0.50
78_I	113_E	0.544	0.49
40_T	44_A	0.541	0.49
17_E	84_R	0.541	0.49
17_E	49_E	0.538	0.48
67_L	74_R	0.534	0.48
81_L	91_R	0.533	0.48
88_I	98_V	0.532	0.48
103_A	110_D	0.531	0.48
49_E	57_V	0.523	0.47
10_Y	47_L	0.520	0.46
19_V	27_A	0.518	0.46
29_E	94_R	0.516	0.46
41_G	60_N	0.514	0.45
13_F	84_R	0.513	0.45
5_E	38_R	0.508	0.45
4_R	9_N	0.506	0.44
83_H	87_E	0.500	0.44

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
4dndA	1	0.6018	20.6	0.942	Contact Map
2y1nA	1	0.7168	14.8	0.945	Contact Map
2c5kT	1	0.6549	13.1	0.947	Contact Map
4j2cA	1	0.6726	11.3	0.948	Contact Map
3u0rA	1	0.8673	8.5	0.951	Contact Map
1jqnA	3	0.9469	6.8	0.953	Contact Map
4pz1A	2	0.292	6.6	0.953	Contact Map
2zaeA	1	0.5221	5.9	0.954	Contact Map
4r8aA	1	0.8319	5.8	0.954	Contact Map
3l4jA	1	0.9823	5.1	0.956	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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