Cadherin-like - PFAM28P - GREMLIN Contacts

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Cadherin-like - Cadherin-like beta sandwich domain

PFAM:	PF12733	Sequences: LSSLTLSPAGFSPDTTSYTATVPNSVTSITVTATAADANATVTVNGTAVASGGSASGAIPLNVGSNTITIVVTAEDGTTTKTYTITVTRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	90 (85)
Sequences:	27347 (24251)
Seq/√Len:	2630.3
META:	0.933

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_T	81_K	3.670	1.00
69_T	82_T	2.526	1.00
71_V	82_T	2.324	1.00
71_V	80_T	2.195	1.00
65_S	86_T	2.166	1.00
21_T	88_T	2.146	1.00
28_S	58_A	2.030	1.00
19_T	86_T	2.010	1.00
24_N	63_V	1.996	1.00
65_S	88_T	1.903	1.00
39_N	75_E	1.892	1.00
13_P	36_A	1.786	1.00
12_S	15_T	1.758	1.00
17_S	86_T	1.751	1.00
69_T	84_T	1.733	1.00
67_T	86_T	1.724	1.00
43_T	71_V	1.672	1.00
35_A	42_V	1.609	1.00
17_S	84_T	1.585	1.00
74_A	78_T	1.574	1.00
67_T	84_T	1.529	1.00
62_N	66_N	1.507	1.00
6_L	20_A	1.504	1.00
76_D	79_T	1.435	1.00
30_T	58_A	1.362	1.00
43_T	48_A	1.353	1.00
68_I	87_V	1.286	1.00
23_P	26_V	1.271	1.00
73_T	80_T	1.255	1.00
59_I	68_I	1.255	1.00
74_A	80_T	1.229	1.00
37_D	40_A	1.208	1.00
74_A	77_G	1.202	1.00
63_V	89_R	1.198	1.00
44_V	48_A	1.195	1.00
29_I	87_V	1.157	1.00
28_S	60_P	1.156	1.00
49_V	52_G	1.151	1.00
74_A	79_T	1.147	1.00
19_T	88_T	1.146	1.00
20_A	87_V	1.097	1.00
43_T	73_T	1.085	1.00
40_A	72_V	1.080	1.00
5_T	32_T	1.040	1.00
35_A	40_A	1.028	1.00
32_T	55_A	1.022	1.00
44_V	47_T	1.011	1.00
31_V	85_I	1.001	1.00
33_A	42_V	0.977	1.00
22_V	26_V	0.960	1.00
37_D	75_E	0.960	1.00
22_V	87_V	0.958	1.00
31_V	68_I	0.955	1.00
56_S	59_I	0.887	1.00
45_N	49_V	0.875	1.00
7_S	30_T	0.846	1.00
29_I	33_A	0.834	1.00
40_A	44_V	0.822	1.00
13_P	83_Y	0.811	1.00
6_L	31_V	0.796	1.00
45_N	69_T	0.796	1.00
63_V	66_N	0.789	1.00
35_A	72_V	0.780	1.00
4_L	7_S	0.778	1.00
60_P	63_V	0.774	1.00
8_P	15_T	0.763	1.00
47_T	50_A	0.758	1.00
30_T	56_S	0.758	1.00
8_P	20_A	0.758	1.00
47_T	57_G	0.757	1.00
41_T	73_T	0.748	1.00
41_T	48_A	0.746	1.00
20_A	31_V	0.738	1.00
11_F	83_Y	0.738	1.00
46_G	49_V	0.736	1.00
72_V	81_K	0.732	1.00
22_V	61_L	0.698	1.00
3_S	34_T	0.690	1.00
47_T	51_S	0.678	1.00
20_A	29_I	0.676	1.00
43_T	49_V	0.673	1.00
54_S	57_G	0.665	1.00
15_T	18_Y	0.664	1.00
41_T	71_V	0.658	1.00
6_L	29_I	0.651	1.00
44_V	68_I	0.650	1.00
31_V	70_I	0.649	1.00
27_T	60_P	0.643	1.00
33_A	44_V	0.642	1.00
7_S	32_T	0.638	1.00
47_T	52_G	0.638	1.00
36_A	40_A	0.636	1.00
79_T	82_T	0.636	1.00
24_N	89_R	0.635	1.00
70_I	85_I	0.634	1.00
55_A	58_A	0.628	1.00
46_G	51_S	0.620	1.00
4_L	85_I	0.615	1.00
61_L	66_N	0.614	1.00
40_A	52_G	0.613	1.00
33_A	70_I	0.610	1.00
45_N	71_V	0.608	1.00
72_V	83_Y	0.605	1.00
30_T	55_A	0.598	1.00
14_D	36_A	0.597	1.00
20_A	88_T	0.596	1.00
7_S	26_V	0.595	1.00
73_T	77_G	0.593	1.00
11_F	15_T	0.585	1.00
42_V	72_V	0.583	1.00
16_T	83_Y	0.579	1.00
61_L	68_I	0.578	1.00
57_G	60_P	0.572	1.00
19_T	65_S	0.569	1.00
67_T	70_I	0.565	1.00
29_I	68_I	0.545	1.00
33_A	45_N	0.544	1.00
44_V	70_I	0.539	1.00
32_T	56_S	0.537	1.00
30_T	33_A	0.537	1.00
40_A	74_A	0.530	1.00
48_A	51_S	0.528	1.00
3_S	6_L	0.526	1.00
4_L	8_P	0.523	1.00
26_V	29_I	0.519	1.00
73_T	79_T	0.508	1.00
45_N	51_S	0.502	1.00
15_T	19_T	0.500	1.00

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
3s30A	1	0.0111	62.2	0.76	Contact Map
4hetA	1	0.9444	59.6	0.764	Contact Map
3hbzA	1	0.8333	51.9	0.774	Contact Map
3owrA	1	0.8778	45.8	0.782	Contact Map
3rrsA	2	0.7333	16.4	0.827	Contact Map
3ncxA	1	0.8667	15	0.83	Contact Map
2l7yA	1	0.8667	13.1	0.834	Contact Map
3fipA	1	0.8667	13	0.834	Contact Map
3zmrA	1	0.7778	9.6	0.844	Contact Map
1nqjA	1	0.9222	9.3	0.845	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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