ORF6C - PFAM28P - GREMLIN Contacts

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ORF6C - ORF6C domain

PFAM:	PF10552	Sequences: QLKLLLQAIEELDERIDEVEERVEELENNMTLDPGQQRELQKAVKKRVVELLGGKDSNAYKDKSLRRKVFSDIYRDLKRRFGVPSYKDIPRKDFDEALEFIENWEPPTNLKEEI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	114 (106)
Sequences:	1076 (867)
Seq/√Len:	84.2
META:	0.653

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_R	27_E	6.039	1.00
15_R	20_E	4.307	1.00
19_V	23_V	3.046	1.00
12_L	16_I	3.027	1.00
83_V	89_I	2.756	1.00
77_L	89_I	2.659	1.00
93_D	96_E	2.366	1.00
5_L	9_I	2.342	1.00
6_L	10_E	2.283	1.00
44_V	74_Y	2.063	1.00
9_I	12_L	1.992	1.00
5_L	8_A	1.802	1.00
90_P	93_D	1.787	1.00
8_A	13_D	1.782	1.00
16_I	19_V	1.766	1.00
23_V	26_L	1.761	1.00
41_Q	45_K	1.607	1.00
76_D	80_R	1.593	1.00
74_Y	86_Y	1.511	0.99
48_V	70_F	1.505	0.99
6_L	9_I	1.478	0.99
34_P	37_Q	1.473	0.99
39_E	94_F	1.411	0.99
34_P	88_D	1.408	0.99
8_A	12_L	1.377	0.99
43_A	98_L	1.364	0.99
43_A	102_E	1.332	0.99
62_D	66_R	1.321	0.99
5_L	11_E	1.303	0.98
54_G	57_S	1.282	0.98
20_E	27_E	1.262	0.98
44_V	77_L	1.256	0.98
47_R	50_E	1.239	0.98
74_Y	77_L	1.214	0.98
57_S	60_Y	1.188	0.97
84_P	88_D	1.160	0.97
73_I	101_I	1.146	0.97
10_E	13_D	1.132	0.96
5_L	13_D	1.130	0.96
13_D	17_D	1.120	0.96
47_R	51_L	1.116	0.96
31_T	88_D	1.111	0.96
77_L	97_A	1.091	0.95
54_G	60_Y	1.040	0.94
44_V	73_I	1.033	0.94
5_L	12_L	1.031	0.94
35_G	88_D	1.018	0.93
75_R	79_R	1.002	0.93
8_A	11_E	1.000	0.93
105_E	111_K	0.995	0.93
40_L	101_I	0.989	0.92
100_F	109_N	0.989	0.92
6_L	12_L	0.968	0.92
36_Q	91_R	0.963	0.91
94_F	98_L	0.953	0.91
37_Q	85_S	0.949	0.91
31_T	34_P	0.929	0.90
85_S	88_D	0.923	0.89
74_Y	78_K	0.915	0.89
45_K	48_V	0.908	0.89
33_D	36_Q	0.906	0.89
78_K	84_P	0.894	0.88
66_R	70_F	0.888	0.88
76_D	104_W	0.882	0.87
40_L	97_A	0.879	0.87
76_D	100_F	0.858	0.86
38_R	87_K	0.857	0.86
47_R	101_I	0.855	0.86
24_E	28_N	0.849	0.85
37_Q	88_D	0.849	0.85
9_I	13_D	0.848	0.85
42_K	79_R	0.842	0.85
10_E	14_E	0.842	0.85
5_L	10_E	0.838	0.84
43_A	46_K	0.830	0.84
51_L	106_P	0.827	0.84
72_D	104_W	0.824	0.83
45_K	70_F	0.820	0.83
72_D	79_R	0.817	0.83
36_Q	94_F	0.813	0.83
108_T	111_K	0.801	0.82
40_L	89_I	0.798	0.81
38_R	42_K	0.797	0.81
81_F	97_A	0.795	0.81
84_P	87_K	0.759	0.78
7_Q	10_E	0.750	0.77
81_F	96_E	0.739	0.76
78_K	85_S	0.735	0.76
76_D	79_R	0.731	0.75
31_T	37_Q	0.727	0.75
40_L	74_Y	0.714	0.74
38_R	85_S	0.706	0.73
95_D	99_E	0.700	0.72
99_E	103_N	0.698	0.72
53_G	60_Y	0.698	0.72
74_Y	85_S	0.688	0.71
7_Q	13_D	0.677	0.70
41_Q	74_Y	0.676	0.70
15_R	19_V	0.669	0.69
49_V	52_L	0.660	0.68
7_Q	11_E	0.651	0.67
107_P	110_L	0.650	0.67
11_E	16_I	0.649	0.66
52_L	60_Y	0.644	0.66
12_L	19_V	0.638	0.65
78_K	86_Y	0.627	0.64
98_L	102_E	0.627	0.64
95_D	98_L	0.624	0.63
32_L	40_L	0.622	0.63
43_A	101_I	0.622	0.63
20_E	24_E	0.619	0.63
37_Q	87_K	0.617	0.63
53_G	59_A	0.616	0.62
10_E	16_I	0.615	0.62
41_Q	78_K	0.615	0.62
32_L	37_Q	0.612	0.62
52_L	57_S	0.611	0.62
86_Y	110_L	0.610	0.62
17_D	20_E	0.610	0.62
9_I	17_D	0.609	0.62
67_R	70_F	0.609	0.62
53_G	57_S	0.600	0.60
100_F	104_W	0.597	0.60
8_A	17_D	0.596	0.60
67_R	71_S	0.594	0.60
45_K	87_K	0.588	0.59
9_I	16_I	0.586	0.59
77_L	83_V	0.581	0.58
73_I	106_P	0.577	0.57
22_R	25_E	0.577	0.57
54_G	59_A	0.572	0.57
21_E	24_E	0.570	0.57
50_E	102_E	0.569	0.56
107_P	111_K	0.566	0.56
56_D	61_K	0.564	0.56
40_L	94_F	0.562	0.55
10_E	17_D	0.560	0.55
72_D	107_P	0.555	0.55
48_V	104_W	0.551	0.54
44_V	89_I	0.550	0.54
89_I	101_I	0.542	0.53
29_N	91_R	0.540	0.53
24_E	27_E	0.540	0.53
100_F	103_N	0.535	0.52
81_F	100_F	0.535	0.52
35_G	82_G	0.531	0.51
36_Q	90_P	0.529	0.51
51_L	108_T	0.527	0.51
44_V	48_V	0.526	0.51
21_E	105_E	0.523	0.50
96_E	99_E	0.523	0.50
84_P	105_E	0.522	0.50
38_R	41_Q	0.518	0.50
69_V	110_L	0.518	0.50
6_L	15_R	0.511	0.49
52_L	55_K	0.509	0.48
89_I	97_A	0.508	0.48
11_E	17_D	0.504	0.48
10_E	15_R	0.500	0.47

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
4y66B	1	0.8509	47.2	0.862	Contact Map
3wprA	3	0.307	25.2	0.881	Contact Map
3wp8A	3	0.2719	23.5	0.883	Contact Map
3rrkA	1	0.4386	22.1	0.884	Contact Map
2yo0A	3	0.2895	21.4	0.885	Contact Map
3ziaJ	1	0.0088	21.3	0.885	Contact Map
3ci9A	5	0.2719	13.6	0.895	Contact Map
4hjbC	3	0.2368	10.8	0.899	Contact Map
1gcvB	1	0.7018	10.5	0.9	Contact Map
3mtuE	2	0.4474	10.3	0.9	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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