Rrp15p - PFAM28P - GREMLIN Contacts

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Rrp15p - Rrp15p

PFAM:	PF07890	Sequences: FADAMSKILSTKLPTSKRADPILSRSKKAAKKLEDEKLEAKAKKKLRAEKKEAEEKGRVKDVLGDLERERRLRKIATRGVVKLFNAVRKAQKKAEEALKEAGKSEGGKKKREKVVKEMSKEGFLDLLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	128 (128)
Sequences:	558 (405)
Seq/√Len:	35.8
META:	0.242

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_A	87_V	2.769	1.00
61_D	64_G	2.651	1.00
38_L	42_A	2.593	1.00
39_E	43_K	2.564	1.00
61_D	78_R	2.406	1.00
77_T	82_K	2.258	0.99
2_A	17_K	2.134	0.99
14_P	118_M	2.043	0.99
86_A	124_L	2.040	0.99
8_I	13_L	1.929	0.98
8_I	11_T	1.911	0.98
119_S	124_L	1.892	0.98
31_K	34_E	1.889	0.98
5_M	9_L	1.873	0.97
28_K	32_K	1.861	0.97
77_T	81_V	1.833	0.97
4_A	8_I	1.720	0.96
44_K	47_R	1.696	0.95
15_T	18_R	1.688	0.95
96_E	99_K	1.667	0.95
5_M	88_R	1.645	0.95
114_V	122_G	1.598	0.94
26_S	31_K	1.596	0.94
27_K	34_E	1.560	0.93
67_E	70_R	1.541	0.92
3_D	10_S	1.525	0.92
86_A	91_Q	1.481	0.91
115_V	124_L	1.467	0.90
11_T	16_S	1.448	0.90
36_E	40_A	1.443	0.90
109_K	116_K	1.441	0.90
102_G	105_E	1.382	0.88
118_M	124_L	1.369	0.87
70_R	125_D	1.366	0.87
107_G	127_L	1.356	0.87
5_M	8_I	1.352	0.86
98_L	114_V	1.342	0.86
61_D	65_D	1.333	0.86
3_D	7_K	1.324	0.85
102_G	127_L	1.323	0.85
58_R	82_K	1.318	0.85
21_P	24_S	1.288	0.84
13_L	18_R	1.276	0.83
53_A	56_K	1.266	0.82
23_L	80_V	1.238	0.81
14_P	19_A	1.237	0.81
63_L	77_T	1.217	0.80
120_K	123_F	1.203	0.79
114_V	119_S	1.200	0.79
41_K	56_K	1.197	0.79
64_G	77_T	1.181	0.78
41_K	50_K	1.180	0.78
69_E	76_A	1.175	0.77
95_E	99_K	1.172	0.77
93_K	117_E	1.158	0.76
95_E	100_E	1.147	0.76
18_R	25_R	1.147	0.76
113_K	117_E	1.136	0.75
113_K	118_M	1.135	0.75
2_A	87_V	1.134	0.75
54_E	71_R	1.128	0.74
52_E	70_R	1.118	0.74
87_V	91_Q	1.114	0.74
75_I	95_E	1.108	0.73
28_K	62_V	1.106	0.73
3_D	9_L	1.105	0.73
93_K	96_E	1.105	0.73
22_I	53_A	1.094	0.72
12_K	18_R	1.092	0.72
50_K	117_E	1.079	0.71
97_A	100_E	1.070	0.70
89_K	92_K	1.062	0.70
66_L	73_R	1.057	0.70
46_L	74_K	1.049	0.69
94_A	97_A	1.043	0.68
95_E	98_L	1.030	0.68
3_D	87_V	1.025	0.67
44_K	50_K	1.018	0.67
66_L	106_G	1.006	0.66
11_T	14_P	1.000	0.65
44_K	68_R	0.973	0.63
17_K	120_K	0.962	0.62
2_A	110_K	0.960	0.62
80_V	85_N	0.943	0.61
22_I	35_D	0.942	0.60
15_T	99_K	0.934	0.60
90_A	94_A	0.915	0.58
8_I	14_P	0.909	0.58
65_D	110_K	0.903	0.57
63_L	67_E	0.891	0.56
52_E	56_K	0.890	0.56
50_K	56_K	0.874	0.55
40_A	93_K	0.869	0.54
33_L	37_K	0.859	0.53
85_N	123_F	0.837	0.52
81_V	84_F	0.833	0.51
123_F	127_L	0.831	0.51
77_T	83_L	0.823	0.50
40_A	109_K	0.822	0.50
69_E	74_K	0.818	0.50
48_A	68_R	0.817	0.50
112_E	116_K	0.805	0.49
1_F	21_P	0.803	0.49
69_E	72_L	0.797	0.48
114_V	118_M	0.793	0.48
28_K	37_K	0.780	0.47
18_R	21_P	0.778	0.46
45_K	74_K	0.774	0.46
22_I	32_K	0.768	0.46
13_L	21_P	0.764	0.45
12_K	101_A	0.760	0.45
113_K	116_K	0.750	0.44
9_L	25_R	0.745	0.44
28_K	31_K	0.745	0.44
13_L	32_K	0.744	0.43
121_E	125_D	0.737	0.43
97_A	101_A	0.736	0.43
83_L	123_F	0.736	0.43
26_S	81_V	0.725	0.42
55_E	106_G	0.725	0.42
27_K	51_K	0.717	0.41
30_A	70_R	0.716	0.41
45_K	49_E	0.711	0.41
35_D	57_G	0.710	0.41
43_K	47_R	0.710	0.41
121_E	128_K	0.697	0.40
34_E	58_R	0.689	0.39
15_T	20_D	0.689	0.39
51_K	122_G	0.685	0.39
8_I	28_K	0.685	0.39
101_A	104_S	0.677	0.38
67_E	71_R	0.670	0.37
40_A	83_L	0.667	0.37
15_T	22_I	0.656	0.36
29_A	33_L	0.653	0.36
77_T	127_L	0.649	0.36
17_K	34_E	0.648	0.36
55_E	121_E	0.647	0.35
12_K	20_D	0.645	0.35
104_S	109_K	0.643	0.35
84_F	91_Q	0.638	0.35
8_I	29_A	0.636	0.35
4_A	11_T	0.636	0.35
48_A	99_K	0.635	0.35
47_R	90_A	0.635	0.35
69_E	79_G	0.632	0.34
95_E	114_V	0.630	0.34
25_R	33_L	0.629	0.34
36_E	46_L	0.626	0.34
28_K	82_K	0.621	0.33
94_A	102_G	0.619	0.33
4_A	25_R	0.615	0.33
39_E	60_K	0.610	0.33
66_L	98_L	0.610	0.33
55_E	59_V	0.607	0.32
113_K	124_L	0.606	0.32
32_K	44_K	0.605	0.32
5_M	10_S	0.604	0.32
102_G	107_G	0.592	0.31
58_R	67_E	0.591	0.31
77_T	92_K	0.584	0.31
70_R	113_K	0.582	0.30
64_G	90_A	0.582	0.30
50_K	73_R	0.582	0.30
70_R	101_A	0.582	0.30
25_R	97_A	0.580	0.30
30_A	97_A	0.566	0.29
22_I	44_K	0.559	0.29
6_S	14_P	0.558	0.29
72_L	76_A	0.553	0.28
66_L	70_R	0.551	0.28
56_K	97_A	0.549	0.28
79_G	123_F	0.548	0.28
33_L	110_K	0.546	0.28
50_K	74_K	0.545	0.28
81_V	123_F	0.545	0.28
49_E	120_K	0.543	0.28
13_L	71_R	0.537	0.27
49_E	100_E	0.528	0.27
42_A	51_K	0.525	0.26
100_E	103_K	0.523	0.26
7_K	17_K	0.520	0.26
32_K	86_A	0.514	0.26
48_A	52_E	0.513	0.26
72_L	82_K	0.511	0.26
56_K	104_S	0.511	0.26
70_R	85_N	0.510	0.25
6_S	31_K	0.510	0.25
42_A	46_L	0.506	0.25
116_K	120_K	0.502	0.25
36_E	43_K	0.501	0.25
98_L	112_E	0.500	0.25

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
2dodA	1	0.2188	4.4	0.934	Contact Map
2doeA	1	0.2188	3.3	0.937	Contact Map
4oydB	1	0.6797	3.2	0.938	Contact Map
1tt5E	1	0.1016	2.6	0.941	Contact Map
4q9vA	2	0.5	2.3	0.942	Contact Map
1sn9A	2	0.1016	2.2	0.943	Contact Map
2oy9A	2	0.3203	1.9	0.945	Contact Map
2ibfB	1	0.1172	1.8	0.946	Contact Map
2kpaA	1	0.0859	1.7	0.947	Contact Map
1syqB	1	0.1328	1.6	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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