NIDO - PFAM28P - GREMLIN Contacts

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NIDO - Nidogen-like

PFAM:	PF06119	Sequences: TNTFQLVLIDRGAGDFDIFNYDQGGIQWTTGDGGSTPARAGFSAGDGGAPGTFFELPGSGTNGALLLTNSSNSGVPGRWVFRVRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (78)
Sequences:	2521 (1899)
Seq/√Len:	215.0
META:	0.704

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_R	60_G	3.712	1.00
23_Q	27_Q	3.609	1.00
20_N	78_R	3.196	1.00
46_D	52_T	3.000	1.00
39_R	55_E	2.590	1.00
32_D	35_S	2.352	1.00
12_G	15_D	2.199	1.00
37_P	62_N	2.025	1.00
40_A	56_L	1.951	1.00
3_T	22_D	1.948	1.00
46_D	51_G	1.860	1.00
11_R	17_D	1.838	1.00
26_I	68_T	1.751	1.00
71_S	74_G	1.612	1.00
55_E	60_G	1.599	1.00
67_L	71_S	1.589	1.00
30_T	37_P	1.559	1.00
21_Y	40_A	1.528	1.00
2_N	28_W	1.437	1.00
42_F	54_F	1.376	1.00
44_A	52_T	1.346	1.00
47_G	51_G	1.325	1.00
66_L	69_N	1.291	1.00
75_V	78_R	1.231	1.00
30_T	33_G	1.218	1.00
17_D	83_V	1.216	1.00
36_T	60_G	1.203	1.00
29_T	63_G	1.200	1.00
71_S	81_F	1.198	1.00
17_D	84_R	1.178	1.00
11_R	15_D	1.146	1.00
66_L	70_S	1.135	1.00
8_L	18_I	1.113	1.00
10_D	15_D	1.105	1.00
42_F	81_F	1.061	1.00
69_N	79_W	1.058	1.00
70_S	79_W	1.045	1.00
61_T	64_A	1.043	1.00
33_G	36_T	1.032	1.00
30_T	34_G	1.011	1.00
3_T	23_Q	1.004	1.00
18_I	80_V	1.004	1.00
66_L	71_S	0.953	1.00
61_T	65_L	0.929	0.99
11_R	14_G	0.884	0.99
6_L	19_F	0.866	0.99
66_L	72_N	0.861	0.99
18_I	83_V	0.858	0.99
29_T	37_P	0.858	0.99
3_T	7_V	0.854	0.99
33_G	37_P	0.844	0.99
11_R	84_R	0.832	0.99
3_T	6_L	0.817	0.99
58_G	63_G	0.815	0.99
23_Q	26_I	0.809	0.98
46_D	53_F	0.808	0.98
6_L	32_D	0.805	0.98
73_S	80_V	0.804	0.98
71_S	79_W	0.788	0.98
19_F	81_F	0.762	0.98
7_V	20_N	0.712	0.97
9_I	18_I	0.710	0.97
28_W	38_A	0.702	0.96
68_T	76_P	0.689	0.96
9_I	78_R	0.686	0.96
15_D	84_R	0.679	0.96
54_F	57_P	0.677	0.96
29_T	64_A	0.674	0.95
29_T	65_L	0.674	0.95
31_G	38_A	0.668	0.95
63_G	69_N	0.663	0.95
10_D	14_G	0.662	0.95
67_L	79_W	0.659	0.95
7_V	18_I	0.646	0.94
70_S	76_P	0.645	0.94
72_N	79_W	0.637	0.94
67_L	76_P	0.637	0.94
23_Q	68_T	0.635	0.94
2_N	38_A	0.634	0.94
69_N	74_G	0.634	0.94
20_N	80_V	0.626	0.93
30_T	38_A	0.625	0.93
16_F	83_V	0.622	0.93
39_R	83_V	0.618	0.93
78_R	81_F	0.617	0.93
43_S	46_D	0.601	0.92
14_G	82_R	0.600	0.92
22_D	26_I	0.598	0.92
14_G	17_D	0.595	0.91
14_G	84_R	0.588	0.91
73_S	79_W	0.579	0.90
47_G	52_T	0.578	0.90
54_F	81_F	0.576	0.90
37_P	64_A	0.573	0.90
47_G	82_R	0.573	0.90
40_A	67_L	0.565	0.89
6_L	18_I	0.562	0.89
43_S	53_F	0.557	0.89
68_T	71_S	0.551	0.88
44_A	53_F	0.548	0.88
55_E	59_S	0.545	0.87
9_I	20_N	0.542	0.87
42_F	84_R	0.539	0.87
15_D	19_F	0.538	0.87
73_S	78_R	0.537	0.87
19_F	31_G	0.534	0.86
68_T	72_N	0.528	0.86
37_P	61_T	0.526	0.86
56_L	79_W	0.524	0.85
16_F	41_G	0.522	0.85
70_S	73_S	0.515	0.84
13_A	23_Q	0.513	0.84
39_R	42_F	0.511	0.84
6_L	10_D	0.507	0.83
9_I	16_F	0.505	0.83
73_S	76_P	0.502	0.83
22_D	27_Q	0.500	0.83

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
3lsoA	1	0.9176	2.4	0.916	Contact Map
2bu3A	1	0.8941	2.2	0.917	Contact Map
4a1xC	1	0.1059	1.9	0.92	Contact Map
4u36A	3	0.7412	1.5	0.924	Contact Map
1lrwB	1	0.7529	1.2	0.929	Contact Map
1w6sB	1	0.7529	1.2	0.929	Contact Map
4dvyP	1	0.8588	1	0.932	Contact Map
1upiA	2	0.2118	0.9	0.933	Contact Map
1kwiA	1	0.4706	0.9	0.935	Contact Map
3vrpA	1	0.7647	0.9	0.935	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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