Ependymin - PFAM28P - GREMLIN Contacts

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Ependymin - Ependymin

PFAM:	PF00811	Sequences: NNKTEFFDVLLLYKEGVMYEIDLKTKTCTKSPLTGPFRPFCIPPNATFLGEFTIGSSSVPGEGLLVNTWSGRFPDGKGTYVGTVTEDGCIPVSETFFSNKTGFVTTSFFNVVLGISDPNVFIPPSEC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (121)
Sequences:	671 (577)
Seq/√Len:	52.5
META:	0.58

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_V	30_K	6.091	1.00
18_M	31_S	3.666	1.00
21_I	126_E	3.037	1.00
12_L	15_E	3.031	1.00
66_V	92_V	2.892	1.00
51_E	67_N	2.751	1.00
85_T	92_V	2.689	1.00
124_P	127_C	2.641	1.00
119_N	122_I	2.356	1.00
12_L	123_P	2.195	1.00
114_G	117_D	2.066	1.00
21_I	124_P	2.010	1.00
54_I	109_F	2.010	1.00
42_I	89_C	1.867	0.99
10_L	21_I	1.830	0.99
10_L	123_P	1.799	0.99
48_F	69_W	1.771	0.99
43_P	46_A	1.723	0.99
55_G	89_C	1.719	0.99
22_D	25_T	1.678	0.99
51_E	86_E	1.668	0.99
49_L	70_S	1.592	0.98
9_V	21_I	1.561	0.98
5_E	22_D	1.528	0.97
93_S	107_S	1.496	0.97
85_T	88_G	1.476	0.97
42_I	84_V	1.471	0.97
71_G	84_V	1.309	0.94
35_G	111_V	1.305	0.94
54_I	93_S	1.297	0.93
20_E	29_T	1.295	0.93
112_V	118_P	1.285	0.93
37_F	111_V	1.268	0.93
89_C	111_V	1.242	0.92
69_W	111_V	1.230	0.91
27_T	101_T	1.226	0.91
43_P	89_C	1.211	0.91
121_F	124_P	1.170	0.89
21_I	125_S	1.166	0.89
13_Y	99_N	1.146	0.88
56_S	113_L	1.127	0.87
23_L	122_I	1.122	0.87
33_L	61_G	1.116	0.87
47_T	97_F	1.110	0.86
64_L	76_G	1.110	0.86
9_V	20_E	1.107	0.86
43_P	80_Y	1.104	0.86
11_L	14_K	1.096	0.86
52_F	109_F	1.095	0.86
37_F	42_I	1.093	0.86
27_T	48_F	1.079	0.85
12_L	41_C	1.067	0.84
55_G	85_T	1.063	0.84
39_P	117_D	1.046	0.83
53_T	110_N	1.031	0.82
18_M	108_F	1.017	0.81
41_C	91_P	1.012	0.81
50_G	108_F	1.012	0.81
11_L	18_M	1.007	0.81
52_F	68_T	1.006	0.80
85_T	89_C	0.987	0.79
121_F	127_C	0.971	0.78
46_A	72_R	0.951	0.77
111_V	121_F	0.942	0.76
73_F	76_G	0.924	0.74
85_T	117_D	0.922	0.74
13_Y	22_D	0.905	0.73
87_D	110_N	0.904	0.73
38_R	64_L	0.893	0.72
67_N	86_E	0.892	0.72
63_G	90_I	0.887	0.71
42_I	67_N	0.887	0.71
81_V	107_S	0.884	0.71
89_C	115_I	0.883	0.71
26_K	82_G	0.869	0.70
26_K	126_E	0.856	0.69
17_V	32_P	0.854	0.68
75_D	78_G	0.853	0.68
19_Y	30_K	0.850	0.68
123_P	126_E	0.850	0.68
38_R	94_E	0.843	0.67
91_P	114_G	0.840	0.67
5_E	9_V	0.839	0.67
37_F	69_W	0.827	0.66
28_C	127_C	0.826	0.66
44_P	125_S	0.825	0.66
16_G	32_P	0.821	0.65
13_Y	29_T	0.817	0.65
69_W	85_T	0.815	0.65
42_I	92_V	0.812	0.65
80_Y	96_F	0.808	0.64
84_V	115_I	0.798	0.63
29_T	108_F	0.795	0.63
65_L	123_P	0.793	0.63
117_D	120_V	0.784	0.62
112_V	117_D	0.779	0.61
35_G	125_S	0.752	0.59
48_F	100_K	0.747	0.58
82_G	110_N	0.745	0.58
62_E	67_N	0.741	0.57
53_T	57_S	0.728	0.56
39_P	69_W	0.721	0.55
55_G	64_L	0.720	0.55
52_F	66_V	0.719	0.55
50_G	68_T	0.716	0.55
66_V	71_G	0.715	0.55
87_D	111_V	0.712	0.54
42_I	46_A	0.711	0.54
21_I	42_I	0.704	0.54
34_T	119_N	0.698	0.53
20_E	105_T	0.697	0.53
45_N	56_S	0.696	0.53
30_K	104_V	0.689	0.52
80_Y	84_V	0.688	0.52
13_Y	47_T	0.683	0.51
89_C	114_G	0.682	0.51
10_L	57_S	0.673	0.50
28_C	124_P	0.668	0.50
26_K	110_N	0.668	0.50
65_L	86_E	0.668	0.50
32_P	125_S	0.663	0.49
69_W	74_P	0.662	0.49
46_A	90_I	0.660	0.49
41_C	84_V	0.659	0.49
43_P	85_T	0.658	0.49
22_D	37_F	0.654	0.48
64_L	78_G	0.652	0.48
115_I	125_S	0.646	0.48
67_N	73_F	0.639	0.47
74_P	96_F	0.631	0.46
52_F	72_R	0.630	0.46
9_V	16_G	0.628	0.46
48_F	67_N	0.627	0.46
8_D	12_L	0.622	0.45
35_G	121_F	0.613	0.44
66_V	90_I	0.613	0.44
7_F	11_L	0.611	0.44
41_C	56_S	0.609	0.44
24_K	68_T	0.609	0.44
20_E	69_W	0.606	0.43
57_S	66_V	0.602	0.43
54_I	57_S	0.600	0.43
98_S	101_T	0.600	0.43
6_F	9_V	0.599	0.43
24_K	79_T	0.598	0.43
51_E	83_T	0.598	0.43
63_G	76_G	0.596	0.42
53_T	65_L	0.591	0.42
46_A	116_S	0.588	0.42
66_V	91_P	0.587	0.41
20_E	92_V	0.586	0.41
112_V	116_S	0.585	0.41
54_I	111_V	0.585	0.41
46_A	80_Y	0.575	0.40
68_T	109_F	0.573	0.40
66_V	104_V	0.565	0.39
54_I	110_N	0.561	0.39
25_T	93_S	0.557	0.38
62_E	110_N	0.556	0.38
53_T	56_S	0.554	0.38
42_I	85_T	0.554	0.38
45_N	98_S	0.552	0.38
56_S	69_W	0.549	0.38
44_P	100_K	0.540	0.37
17_V	101_T	0.539	0.37
26_K	46_A	0.537	0.36
10_L	13_Y	0.537	0.36
69_W	103_F	0.534	0.36
13_Y	21_I	0.534	0.36
45_N	122_I	0.523	0.35
18_M	51_E	0.523	0.35
93_S	109_F	0.520	0.35
29_T	36_P	0.519	0.35
60_P	115_I	0.518	0.35
26_K	120_V	0.516	0.34
46_A	94_E	0.514	0.34
56_S	62_E	0.513	0.34
27_T	122_I	0.510	0.34
26_K	32_P	0.505	0.33
48_F	57_S	0.502	0.33
65_L	69_W	0.502	0.33
48_F	119_N	0.500	0.33

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
3bmzA	2	0.9134	19.8	0.899	Contact Map
2ab9A	1	0.2441	12.9	0.907	Contact Map
4ixjA	1	0.4331	2.3	0.935	Contact Map
4mxtA	2	0.9055	2.1	0.936	Contact Map
3zleA	3	0.9685	2.1	0.936	Contact Map
1vazA	1	0.5433	1.9	0.938	Contact Map
2yzyA	1	0.8031	1.8	0.939	Contact Map
3gfuC	1	0.2441	1.7	0.94	Contact Map
3emwA	1	0.4252	1.5	0.941	Contact Map
4yivA	1	0.9685	1.4	0.942	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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