SWIRM-assoc_1 - PFAM28P - GREMLIN Contacts

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SWIRM-assoc_1 - SWIRM-associated region 1

PFAM:	PF16495	Sequences: ATALAAAAAKAKLLADQEEREIQRLVASLVELQLKKLELKLKQFEELEAILEAERRQLERQRQQLFLERLALKKRVLEVQEKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	83 (79)
Sequences:	657 (452)
Seq/√Len:	50.8
META:	0.298

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_A	9_A	4.848	1.00
64_Q	68_E	3.351	1.00
21_E	29_L	3.173	1.00
21_E	24_R	2.989	1.00
43_Q	46_E	1.865	0.99
57_Q	73_K	1.760	0.99
12_K	16_D	1.733	0.99
74_K	78_E	1.695	0.99
48_E	54_E	1.676	0.98
76_V	79_V	1.638	0.98
4_L	7_A	1.625	0.98
10_K	23_Q	1.580	0.98
52_E	56_R	1.543	0.97
44_F	71_A	1.515	0.97
52_E	61_Q	1.490	0.97
42_K	53_A	1.476	0.96
41_L	63_Q	1.450	0.96
31_E	35_K	1.404	0.95
53_A	56_R	1.364	0.94
60_R	63_Q	1.361	0.94
56_R	76_V	1.360	0.94
67_L	70_L	1.348	0.94
58_L	71_A	1.327	0.94
8_A	15_A	1.321	0.93
59_E	65_L	1.307	0.93
27_A	30_V	1.250	0.91
3_A	29_L	1.182	0.89
31_E	34_L	1.152	0.88
55_R	58_L	1.150	0.87
57_Q	67_L	1.138	0.87
7_A	10_K	1.134	0.87
21_E	33_Q	1.126	0.86
11_A	47_L	1.119	0.86
34_L	42_K	1.118	0.86
75_R	78_E	1.115	0.86
36_K	48_E	1.085	0.84
40_K	68_E	1.073	0.83
23_Q	34_L	1.043	0.82
39_L	42_K	1.025	0.81
25_L	36_K	1.022	0.80
48_E	65_L	1.022	0.80
59_E	62_R	1.018	0.80
23_Q	29_L	1.013	0.80
8_A	11_A	1.003	0.79
10_K	20_R	1.000	0.79
44_F	50_I	0.986	0.78
39_L	44_F	0.983	0.78
66_F	72_L	0.967	0.77
9_A	12_K	0.958	0.76
33_Q	78_E	0.957	0.76
41_L	45_E	0.930	0.74
26_V	64_Q	0.903	0.71
22_I	33_Q	0.878	0.69
32_L	52_E	0.858	0.68
22_I	29_L	0.850	0.67
26_V	32_L	0.838	0.66
18_E	25_L	0.832	0.65
63_Q	66_F	0.831	0.65
30_V	52_E	0.825	0.64
18_E	24_R	0.824	0.64
57_Q	61_Q	0.822	0.64
10_K	25_L	0.818	0.64
9_A	56_R	0.803	0.62
36_K	69_R	0.780	0.60
26_V	29_L	0.765	0.59
59_E	63_Q	0.761	0.58
51_L	64_Q	0.759	0.58
16_D	20_R	0.744	0.56
55_R	59_E	0.726	0.55
50_I	54_E	0.720	0.54
38_E	53_A	0.713	0.53
27_A	44_F	0.712	0.53
44_F	59_E	0.699	0.52
60_R	70_L	0.694	0.51
33_Q	58_L	0.683	0.50
39_L	51_L	0.673	0.49
72_L	76_V	0.673	0.49
5_A	25_L	0.661	0.48
30_V	34_L	0.660	0.48
72_L	78_E	0.659	0.48
56_R	67_L	0.655	0.47
31_E	66_F	0.647	0.47
12_K	23_Q	0.647	0.47
67_L	79_V	0.644	0.46
67_L	71_A	0.640	0.46
23_Q	27_A	0.637	0.45
47_L	58_L	0.636	0.45
77_L	80_Q	0.634	0.45
40_K	47_L	0.633	0.45
10_K	63_Q	0.618	0.44
67_L	72_L	0.614	0.43
24_R	38_E	0.612	0.43
20_R	24_R	0.610	0.43
49_A	60_R	0.607	0.42
71_A	75_R	0.606	0.42
11_A	32_L	0.606	0.42
25_L	62_R	0.605	0.42
14_L	68_E	0.595	0.41
58_L	62_R	0.593	0.41
73_K	77_L	0.582	0.40
20_R	66_F	0.568	0.39
3_A	14_L	0.567	0.38
6_A	10_K	0.560	0.38
17_Q	62_R	0.560	0.38
12_K	79_V	0.560	0.38
30_V	56_R	0.560	0.38
12_K	21_E	0.557	0.37
37_L	46_E	0.555	0.37
5_A	8_A	0.547	0.37
33_Q	37_L	0.533	0.35
38_E	42_K	0.524	0.34
13_L	34_L	0.519	0.34
16_D	22_I	0.516	0.34
33_Q	61_Q	0.510	0.33
3_A	6_A	0.510	0.33
37_L	40_K	0.505	0.33
35_K	80_Q	0.502	0.32
21_E	76_V	0.500	0.32

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
4cgkA	3	1	4.5	0.873	Contact Map
2jeeA	2	0.8916	2.6	0.888	Contact Map
2qagB	1	0.0964	2.3	0.891	Contact Map
3vkgA	2	0.9036	2.2	0.892	Contact Map
4r3zA	1	0.7229	1.8	0.897	Contact Map
4iloA	3	0.759	1.8	0.898	Contact Map
2wt7B	1	0.8193	1.8	0.898	Contact Map
2xv5A	2	0.6265	1.6	0.901	Contact Map
3q8tA	2	1	1.6	0.901	Contact Map
1gk6A	2	0.5663	1.5	0.902	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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