Cys_rich_CPCC - PFAM28P - GREMLIN Contacts

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Cys_rich_CPCC - Cysteine-rich CPCC

PFAM:	PF14206	Sequences: YPCPCCGYLTLDERPGSYEICPVCFWEDDGQQLDDPDVRGGANGVSLREARENFARFGACEERFLKHVRPPLPEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (72)
Sequences:	3613 (2893)
Seq/√Len:	340.9
META:	0.91

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_D	48_R	2.915	1.00
2_P	9_L	2.895	1.00
18_Y	27_E	2.673	1.00
64_F	67_H	2.635	1.00
48_R	51_R	2.084	1.00
52_E	56_R	2.021	1.00
36_P	48_R	2.010	1.00
60_C	64_F	1.995	1.00
13_E	17_S	1.975	1.00
57_F	62_E	1.897	1.00
53_N	57_F	1.679	1.00
62_E	65_L	1.663	1.00
61_E	64_F	1.574	1.00
20_I	27_E	1.550	1.00
45_V	50_A	1.544	1.00
35_D	38_V	1.537	1.00
25_F	59_A	1.531	1.00
10_T	22_P	1.482	1.00
18_Y	30_G	1.474	1.00
45_V	61_E	1.412	1.00
45_V	60_C	1.333	1.00
8_Y	54_F	1.305	1.00
52_E	55_A	1.281	1.00
12_D	19_E	1.277	1.00
31_Q	38_V	1.269	1.00
4_P	11_L	1.239	1.00
56_R	62_E	1.233	1.00
25_F	67_H	1.227	1.00
34_D	39_R	1.226	1.00
25_F	68_V	1.168	1.00
25_F	64_F	1.151	1.00
28_D	33_L	1.115	1.00
16_G	28_D	1.084	1.00
59_A	68_V	1.071	1.00
5_C	47_L	1.068	1.00
7_G	51_R	1.017	1.00
39_R	49_E	0.954	1.00
57_F	65_L	0.945	1.00
59_A	65_L	0.930	1.00
32_Q	42_A	0.928	1.00
14_R	17_S	0.923	1.00
3_C	6_C	0.921	1.00
44_G	64_F	0.919	1.00
18_Y	41_G	0.917	1.00
31_Q	40_G	0.911	1.00
10_T	23_V	0.909	1.00
2_P	7_G	0.908	1.00
17_S	33_L	0.891	1.00
11_L	28_D	0.879	1.00
29_D	42_A	0.864	1.00
49_E	52_E	0.863	1.00
8_Y	23_V	0.856	1.00
32_Q	38_V	0.832	1.00
20_I	25_F	0.823	1.00
29_D	43_N	0.815	1.00
31_Q	36_P	0.806	1.00
9_L	51_R	0.805	1.00
2_P	51_R	0.791	1.00
30_G	34_D	0.773	1.00
23_V	58_G	0.738	0.99
32_Q	41_G	0.737	0.99
21_C	24_C	0.736	0.99
40_G	46_S	0.732	0.99
4_P	33_L	0.709	0.99
45_V	53_N	0.709	0.99
26_W	50_A	0.701	0.99
67_H	72_L	0.701	0.99
9_L	12_D	0.695	0.99
31_Q	35_D	0.687	0.99
23_V	54_F	0.687	0.99
29_D	32_Q	0.677	0.99
35_D	48_R	0.670	0.99
32_Q	40_G	0.670	0.99
33_L	39_R	0.659	0.99
11_L	16_G	0.649	0.99
13_E	16_G	0.637	0.98
25_F	60_C	0.634	0.98
53_N	58_G	0.629	0.98
43_N	46_S	0.627	0.98
12_D	73_P	0.627	0.98
14_R	28_D	0.621	0.98
70_P	74_E	0.616	0.98
18_Y	42_A	0.615	0.98
16_G	30_G	0.613	0.98
44_G	61_E	0.602	0.98
38_V	45_V	0.601	0.98
11_L	17_S	0.598	0.98
40_G	45_V	0.597	0.98
9_L	23_V	0.596	0.98
23_V	69_R	0.595	0.98
39_R	46_S	0.590	0.97
65_L	68_V	0.589	0.97
9_L	55_A	0.575	0.97
4_P	28_D	0.575	0.97
31_Q	42_A	0.572	0.97
70_P	73_P	0.569	0.97
31_Q	34_D	0.558	0.97
11_L	19_E	0.556	0.96
50_A	53_N	0.551	0.96
34_D	37_D	0.548	0.96
2_P	55_A	0.545	0.96
23_V	51_R	0.537	0.96
5_C	54_F	0.536	0.96
14_R	32_Q	0.535	0.96
50_A	60_C	0.514	0.95
52_E	62_E	0.511	0.94
11_L	33_L	0.501	0.94
54_F	58_G	0.500	0.94

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
3pwfA	4	0.4267	81.7	0.826	Contact Map
1lkoA	3	0.48	79.4	0.83	Contact Map
1yuzA	2	0.4133	77.4	0.833	Contact Map
1s24A	1	0.48	70.2	0.842	Contact Map
2kn9A	1	0.5067	69.1	0.843	Contact Map
1dx8A	1	0.6267	69	0.843	Contact Map
1vq8Z	1	0.6133	66.1	0.847	Contact Map
4tpuA	3	0.4533	62.6	0.85	Contact Map
1yk4A	1	0.4533	54.9	0.857	Contact Map
2v3bB	1	0.4533	54.9	0.857	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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