TM2 - PFAM28P - GREMLIN Contacts

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TM2 - TM2 domain

PFAM:	PF05154	Sequences: RDKSKLVALLLAIFLGGLGIHRFYLGKTGTGILYLLTLWGGFGIWWLIDLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	51 (49)
Sequences:	31414 (18683)
Seq/√Len:	2669.1
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
22_R	30_T	2.699	1.00
27_K	30_T	2.410	1.00
8_A	25_L	2.232	1.00
22_R	34_Y	2.184	1.00
5_K	9_L	2.009	1.00
23_F	35_L	1.947	1.00
45_W	49_D	1.873	1.00
23_F	31_G	1.856	1.00
21_H	34_Y	1.844	1.00
12_A	21_H	1.733	1.00
15_L	20_I	1.709	1.00
22_R	27_K	1.631	1.00
11_L	24_Y	1.548	1.00
9_L	12_A	1.485	1.00
29_G	33_L	1.385	1.00
32_I	36_L	1.347	1.00
28_T	32_I	1.333	1.00
34_Y	45_W	1.246	1.00
7_V	11_L	1.189	1.00
12_A	50_L	1.173	1.00
8_A	24_Y	1.158	1.00
4_S	7_V	1.157	1.00
6_L	10_L	1.107	1.00
3_K	24_Y	1.068	1.00
41_G	45_W	1.059	1.00
9_L	50_L	1.040	1.00
18_L	46_W	0.971	1.00
46_W	50_L	0.964	1.00
30_T	34_Y	0.960	1.00
9_L	13_I	0.947	1.00
13_I	50_L	0.945	1.00
40_G	43_G	0.878	1.00
42_F	45_W	0.872	1.00
37_T	41_G	0.871	1.00
6_L	9_L	0.854	1.00
23_F	28_T	0.802	1.00
27_K	34_Y	0.801	1.00
37_T	42_F	0.790	1.00
17_G	46_W	0.785	1.00
5_K	8_A	0.733	1.00
29_G	32_I	0.726	1.00
38_L	42_F	0.720	1.00
11_L	15_L	0.716	1.00
10_L	14_F	0.693	1.00
37_T	40_G	0.687	1.00
5_K	12_A	0.683	1.00
2_D	5_K	0.678	1.00
46_W	49_D	0.677	1.00
33_L	37_T	0.676	1.00
15_L	18_L	0.666	1.00
19_G	31_G	0.661	1.00
44_I	48_I	0.637	1.00
20_I	23_F	0.632	1.00
32_I	35_L	0.631	1.00
8_A	12_A	0.629	1.00
11_L	20_I	0.583	1.00
48_I	51_I	0.581	1.00
33_L	36_L	0.575	1.00
3_K	8_A	0.574	1.00
8_A	11_L	0.565	1.00
9_L	25_L	0.561	1.00
7_V	24_Y	0.550	1.00
16_G	19_G	0.548	1.00
37_T	43_G	0.541	1.00
12_A	46_W	0.535	1.00
43_G	47_L	0.535	1.00
20_I	24_Y	0.533	1.00
43_G	49_D	0.532	1.00
10_L	13_I	0.526	1.00
14_F	20_I	0.524	1.00
30_T	33_L	0.517	1.00
28_T	31_G	0.514	1.00
7_V	10_L	0.500	1.00
41_G	44_I	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
2gsmA	1	1	3.3	0.848	Contact Map
1v54A	1	1	2.7	0.854	Contact Map
2yevA	1	1	1.9	0.866	Contact Map
3s8fA	1	1	1.8	0.868	Contact Map
2jafA	3	0.9804	1.8	0.868	Contact Map
1eysM	1	0.8235	1.7	0.869	Contact Map
4px7A	1	1	1.6	0.872	Contact Map
1h4rA	2	0.5294	1.5	0.874	Contact Map
4yl8A	1	0.5098	1.4	0.875	Contact Map
4hyjA	2	0.9804	1.4	0.875	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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