Big_4 - PFAM28P - GREMLIN Contacts

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Big_4 - Bacterial Ig-like domain (group 4)

PFAM:	PF07532	Sequences: IEDVSVTTTVGTAPVLPATVTVTYSDGSTGEVPVTWDPIDASDYAKPGTYTVTGTVAGY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (54)
Sequences:	6087 (5007)
Seq/√Len:	681.3
META:	0.77

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_T	31_E	3.609	1.00
24_Y	30_G	3.207	1.00
22_V	32_V	2.931	1.00
19_T	31_E	2.811	1.00
21_T	29_T	2.324	1.00
20_V	34_V	2.080	1.00
23_T	29_T	1.943	1.00
10_V	47_P	1.853	1.00
19_T	33_P	1.840	1.00
13_A	44_Y	1.653	1.00
40_D	43_D	1.647	1.00
9_T	12_T	1.477	1.00
8_T	12_T	1.437	1.00
24_Y	32_V	1.341	1.00
16_L	52_V	1.271	1.00
8_T	14_P	1.265	1.00
35_T	57_A	1.211	1.00
22_V	56_V	1.197	1.00
34_V	54_G	1.155	1.00
37_D	55_T	1.146	1.00
39_I	50_Y	1.145	1.00
37_D	53_T	1.138	1.00
43_D	46_K	1.123	1.00
24_Y	28_S	1.076	1.00
32_V	56_V	1.072	1.00
39_I	44_Y	1.046	1.00
14_P	52_V	1.040	1.00
44_Y	50_Y	1.015	1.00
38_P	52_V	0.982	1.00
20_V	54_G	0.961	1.00
14_P	44_Y	0.890	1.00
33_P	57_A	0.888	1.00
32_V	57_A	0.870	1.00
42_S	45_A	0.859	1.00
40_D	44_Y	0.827	1.00
43_D	50_Y	0.826	1.00
26_D	29_T	0.788	1.00
39_I	52_V	0.786	1.00
25_S	28_S	0.784	1.00
25_S	30_G	0.774	1.00
44_Y	52_V	0.754	1.00
16_L	38_P	0.743	1.00
40_D	52_V	0.728	1.00
6_V	14_P	0.706	1.00
49_T	53_T	0.695	1.00
42_S	50_Y	0.693	1.00
47_P	50_Y	0.687	1.00
10_V	44_Y	0.675	1.00
4_V	7_T	0.663	1.00
15_V	18_A	0.661	1.00
24_Y	52_V	0.650	1.00
46_K	50_Y	0.646	1.00
27_G	30_G	0.641	1.00
24_Y	27_G	0.621	1.00
42_S	46_K	0.617	1.00
11_G	14_P	0.616	1.00
35_T	55_T	0.616	1.00
41_A	45_A	0.611	1.00
39_I	43_D	0.601	1.00
27_G	35_T	0.593	1.00
11_G	45_A	0.589	1.00
14_P	42_S	0.587	1.00
25_S	55_T	0.583	1.00
23_T	27_G	0.582	1.00
4_V	47_P	0.577	1.00
37_D	52_V	0.575	1.00
42_S	52_V	0.574	1.00
38_P	41_A	0.567	1.00
18_A	33_P	0.564	1.00
38_P	42_S	0.556	1.00
23_T	26_D	0.549	1.00
10_V	45_A	0.544	1.00
15_V	41_A	0.534	1.00
10_V	46_K	0.534	1.00
18_A	57_A	0.532	1.00
23_T	47_P	0.531	1.00
19_T	22_V	0.512	0.99
39_I	42_S	0.504	0.99
12_T	15_V	0.502	0.99
16_L	36_W	0.501	0.99
26_D	30_G	0.500	0.99

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
2mh4A	1	0.9661	46.3	0.754	Contact Map
2mogA	1	0.9661	33.2	0.772	Contact Map
4f8lA	1	0.9831	18.3	0.799	Contact Map
2kpnA	1	0.9492	16.3	0.804	Contact Map
4l3aA	1	0.9322	14.8	0.807	Contact Map
4mb4A	1	0.9661	14.6	0.808	Contact Map
2l7yA	1	1	14.3	0.809	Contact Map
4urtB	1	0.8305	12.9	0.813	Contact Map
4n68A	1	0.6102	12.8	0.813	Contact Map
3p4lA	1	0.8305	12.1	0.814	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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