Chorein_N - PFAM28P - GREMLIN Contacts

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Chorein_N - N-terminal region of Chorein or VPS13

PFAM:	PF12624	Sequences: FESLVASLLNRYLGKYVENLDKDQLKVSLWSGDVELENLELKPDALDELGLPFEVKSGFIGKLTLKIPWSNLGSEPVVVEIEDVYLLLEPKDDSEKYDEEEEEKREQAAKQEKLEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	116 (108)
Sequences:	2126 (1681)
Seq/√Len:	161.8
META:	0.492

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_G	83_D	6.424	1.00
18_E	40_E	3.878	1.00
37_E	62_K	3.178	1.00
71_N	75_E	3.160	1.00
62_K	82_E	3.055	1.00
56_K	89_E	2.817	1.00
33_D	64_T	2.516	1.00
35_E	62_K	2.423	1.00
35_E	64_T	2.239	1.00
66_K	78_V	2.216	1.00
33_D	66_K	2.192	1.00
104_K	108_A	2.072	1.00
54_E	89_E	2.064	1.00
60_I	84_V	2.016	1.00
71_N	74_S	1.985	1.00
21_D	24_Q	1.693	1.00
55_V	88_L	1.502	1.00
18_E	42_K	1.499	1.00
39_L	58_G	1.462	1.00
105_R	109_A	1.457	1.00
106_E	109_A	1.425	1.00
30_W	69_W	1.423	1.00
40_E	57_S	1.370	1.00
17_V	39_L	1.363	1.00
64_T	80_E	1.332	1.00
15_K	48_E	1.297	1.00
8_L	12_Y	1.294	1.00
65_L	79_V	1.259	1.00
103_E	107_Q	1.234	1.00
66_K	80_E	1.190	1.00
6_A	10_N	1.169	1.00
101_E	105_R	1.166	1.00
43_P	47_D	1.163	1.00
30_W	70_S	1.156	1.00
32_G	69_W	1.138	1.00
61_G	85_Y	1.120	1.00
45_A	55_V	1.091	1.00
56_K	87_L	1.090	1.00
103_E	108_A	1.058	0.99
100_E	104_K	1.047	0.99
40_E	59_F	1.038	0.99
46_L	55_V	1.026	0.99
104_K	107_Q	1.024	0.99
17_V	60_I	1.010	0.99
36_L	39_L	1.005	0.99
18_E	43_P	0.998	0.99
56_K	59_F	0.995	0.99
54_E	91_K	0.995	0.99
105_R	108_A	0.991	0.99
5_V	77_V	0.986	0.99
72_L	77_V	0.980	0.99
6_A	22_K	0.978	0.99
61_G	82_E	0.971	0.99
75_E	78_V	0.969	0.99
47_D	55_V	0.957	0.99
66_K	75_E	0.956	0.99
102_E	106_E	0.952	0.99
58_G	86_L	0.951	0.99
34_V	65_L	0.939	0.99
2_E	26_K	0.937	0.99
23_D	93_D	0.925	0.98
96_K	99_E	0.907	0.98
5_V	12_Y	0.889	0.98
69_W	77_V	0.883	0.98
67_I	72_L	0.864	0.97
26_K	45_A	0.861	0.97
16_Y	19_N	0.860	0.97
10_N	22_K	0.850	0.97
99_E	103_E	0.843	0.97
24_Q	38_N	0.843	0.97
38_N	61_G	0.829	0.97
98_D	101_E	0.821	0.97
95_E	98_D	0.820	0.97
7_S	11_R	0.811	0.96
18_E	53_F	0.808	0.96
28_S	31_S	0.805	0.96
17_V	41_L	0.804	0.96
14_G	25_L	0.804	0.96
46_L	49_L	0.802	0.96
9_L	12_Y	0.800	0.96
103_E	106_E	0.799	0.96
3_S	7_S	0.798	0.96
28_S	67_I	0.796	0.96
43_P	57_S	0.786	0.96
13_L	36_L	0.782	0.95
101_E	107_Q	0.779	0.95
44_D	47_D	0.769	0.95
57_S	87_L	0.767	0.95
38_N	59_F	0.763	0.95
8_L	11_R	0.755	0.95
15_K	86_L	0.754	0.94
12_Y	15_K	0.741	0.94
29_L	34_V	0.738	0.94
53_F	88_L	0.736	0.94
25_L	34_V	0.726	0.93
47_D	91_K	0.725	0.93
98_D	102_E	0.719	0.93
7_S	16_Y	0.708	0.92
7_S	10_N	0.696	0.92
91_K	94_S	0.689	0.91
47_D	53_F	0.676	0.91
39_L	60_I	0.673	0.90
15_K	44_D	0.671	0.90
10_N	30_W	0.669	0.90
20_L	39_L	0.668	0.90
99_E	109_A	0.665	0.90
36_L	40_E	0.665	0.90
97_Y	100_E	0.664	0.90
2_E	22_K	0.659	0.89
51_L	88_L	0.657	0.89
39_L	63_L	0.640	0.88
43_P	54_E	0.638	0.88
82_E	85_Y	0.634	0.88
8_L	17_V	0.631	0.87
100_E	108_A	0.629	0.87
5_V	30_W	0.625	0.87
94_S	98_D	0.623	0.87
98_D	103_E	0.620	0.86
103_E	109_A	0.616	0.86
5_V	13_L	0.616	0.86
81_I	85_Y	0.609	0.85
96_K	100_E	0.609	0.85
4_L	11_R	0.607	0.85
102_E	108_A	0.606	0.85
3_S	40_E	0.603	0.85
28_S	32_G	0.601	0.85
69_W	72_L	0.600	0.85
12_Y	65_L	0.599	0.85
4_L	7_S	0.599	0.85
68_P	75_E	0.595	0.84
41_L	64_T	0.590	0.84
14_G	20_L	0.584	0.83
60_I	63_L	0.583	0.83
81_I	84_V	0.580	0.83
96_K	102_E	0.579	0.83
30_W	77_V	0.578	0.82
81_I	107_Q	0.577	0.82
42_K	58_G	0.577	0.82
13_L	24_Q	0.566	0.81
63_L	81_I	0.563	0.81
3_S	22_K	0.558	0.80
27_V	34_V	0.557	0.80
101_E	104_K	0.550	0.79
73_G	77_V	0.549	0.79
94_S	97_Y	0.548	0.79
68_P	71_N	0.534	0.77
28_S	34_V	0.531	0.77
15_K	65_L	0.526	0.76
26_K	34_V	0.520	0.75
30_W	33_D	0.519	0.75
102_E	105_R	0.517	0.75
5_V	26_K	0.517	0.75
25_L	33_D	0.517	0.75
29_L	73_G	0.517	0.75
41_L	54_E	0.515	0.75
9_L	14_G	0.511	0.74
49_L	52_P	0.510	0.74
35_E	78_V	0.507	0.74
11_R	22_K	0.505	0.73
17_V	20_L	0.504	0.73
20_L	24_Q	0.502	0.73
7_S	73_G	0.500	0.73

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
3tqmA	1	0.6724	4.1	0.914	Contact Map
4bpeC	1	0.8621	3.8	0.915	Contact Map
1fcqA	1	0.1638	3.1	0.919	Contact Map
4ddpA	1	0.681	2.9	0.92	Contact Map
4d2uA	3	0.3362	2.8	0.92	Contact Map
4heiA	1	0.6638	2.8	0.92	Contact Map
4lkbF	4	0.3879	2.5	0.923	Contact Map
3v26X	1	0.681	2.1	0.925	Contact Map
2jn4A	1	0.4741	2.1	0.925	Contact Map
3bsoA	1	0.1724	2.1	0.925	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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