Conotoxin - PFAM28P - GREMLIN Contacts

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Conotoxin - Conotoxin

PFAM:	PF02950	Sequences: MKLTVVLIVALLLLTTLATLQLDGDQPADRPAKRLQDRKSDERSKLTRRCTPPGGYCADRDRRCCSGWCDCPCCI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (72)
Sequences:	590 (371)
Seq/√Len:	43.7
META:	0.014

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_T	55_G	2.962	1.00
1_M	5_V	2.408	1.00
19_T	22_L	2.297	1.00
1_M	4_T	2.124	1.00
8_I	12_L	2.024	0.99
17_L	21_Q	1.996	0.99
17_L	22_L	1.938	0.99
51_T	63_R	1.900	0.99
5_V	8_I	1.828	0.98
31_P	34_R	1.768	0.98
10_A	14_L	1.711	0.98
66_S	72_P	1.570	0.96
62_R	66_S	1.543	0.96
20_L	24_G	1.528	0.95
30_R	33_K	1.488	0.95
18_A	21_Q	1.438	0.94
35_L	38_R	1.437	0.94
66_S	71_C	1.426	0.93
19_T	23_D	1.406	0.93
52_P	55_G	1.387	0.92
61_D	72_P	1.334	0.91
5_V	15_T	1.296	0.89
21_Q	24_G	1.287	0.89
69_C	74_C	1.269	0.88
50_C	57_C	1.217	0.86
62_R	67_G	1.184	0.85
64_C	74_C	1.183	0.85
4_T	10_A	1.168	0.84
63_R	66_S	1.168	0.84
19_T	24_G	1.152	0.83
59_D	62_R	1.130	0.82
17_L	20_L	1.101	0.80
18_A	22_L	1.095	0.80
52_P	70_D	1.093	0.80
48_R	55_G	1.071	0.78
39_K	43_R	1.066	0.78
55_G	73_C	1.054	0.77
11_L	15_T	1.051	0.77
30_R	36_Q	1.039	0.76
51_T	62_R	1.016	0.74
55_G	62_R	1.016	0.74
44_S	47_T	0.984	0.72
56_Y	62_R	0.967	0.71
66_S	70_D	0.956	0.70
68_W	72_P	0.954	0.70
18_A	25_D	0.947	0.69
20_L	23_D	0.943	0.69
61_D	66_S	0.928	0.67
41_D	45_K	0.927	0.67
27_P	32_A	0.904	0.65
17_L	23_D	0.898	0.65
60_R	63_R	0.874	0.63
8_I	14_L	0.864	0.62
49_R	62_R	0.859	0.61
56_Y	71_C	0.843	0.60
10_A	15_T	0.841	0.60
25_D	29_D	0.840	0.60
61_D	73_C	0.839	0.60
6_V	24_G	0.837	0.59
60_R	67_G	0.830	0.59
1_M	8_I	0.816	0.57
39_K	44_S	0.811	0.57
15_T	27_P	0.794	0.55
4_T	14_L	0.790	0.55
60_R	72_P	0.784	0.54
12_L	21_Q	0.778	0.54
49_R	63_R	0.769	0.53
56_Y	59_D	0.757	0.52
25_D	30_R	0.750	0.51
41_D	47_T	0.750	0.51
45_K	48_R	0.749	0.51
8_I	15_T	0.749	0.51
56_Y	61_D	0.748	0.51
59_D	68_W	0.720	0.48
38_R	41_D	0.716	0.48
50_C	64_C	0.696	0.46
51_T	56_Y	0.696	0.46
67_G	70_D	0.683	0.45
22_L	25_D	0.654	0.42
63_R	68_W	0.652	0.42
9_V	37_D	0.650	0.42
31_P	38_R	0.632	0.40
67_G	71_C	0.632	0.40
8_I	11_L	0.631	0.40
70_D	73_C	0.627	0.40
22_L	26_Q	0.626	0.39
40_S	44_S	0.615	0.38
39_K	42_E	0.614	0.38
54_G	68_W	0.611	0.38
51_T	67_G	0.606	0.38
6_V	25_D	0.576	0.35
2_K	10_A	0.569	0.34
52_P	56_Y	0.564	0.34
48_R	60_R	0.561	0.34
27_P	35_L	0.558	0.33
20_L	26_Q	0.555	0.33
61_D	68_W	0.553	0.33
28_A	40_S	0.552	0.33
34_R	39_K	0.549	0.33
53_P	56_Y	0.547	0.32
21_Q	26_Q	0.534	0.31
2_K	69_C	0.520	0.30
35_L	41_D	0.515	0.30
31_P	36_Q	0.512	0.30
28_A	36_Q	0.509	0.29
60_R	68_W	0.508	0.29
1_M	6_V	0.507	0.29
41_D	61_D	0.500	0.29

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
1yz2A	1	0.3333	88.9	0.735	Contact Map
1fu3A	1	0.36	88.1	0.739	Contact Map
1g1pA	1	0.36	87.3	0.742	Contact Map
1f3kA	1	0.3333	87.3	0.742	Contact Map
1fygA	1	0.3333	86.9	0.744	Contact Map
1hvwA	1	0.3333	85.7	0.748	Contact Map
1cnnA	1	0.3333	72.8	0.778	Contact Map
1v4qA	1	0.3333	72	0.779	Contact Map
1omcA	1	0.32	44.9	0.814	Contact Map
2m36A	1	0.3467	32	0.828	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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