PMR5N - PFAM28P - GREMLIN Contacts

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PMR5N - PMR5 N terminal Domain

PFAM:	PF14416	Sequences: EGCDLFDGKWVYDEYPLYTNSSCPFIDEQFNCQKNGRPDSDYLKWRWQPDGCD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	53 (52)
Sequences:	1978 (872)
Seq/√Len:	121.0
META:	0.086

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_K	50_D	2.926	1.00
7_D	50_D	2.906	1.00
27_D	30_F	2.716	1.00
48_Q	53_D	2.621	1.00
31_N	34_K	2.194	1.00
33_Q	43_L	2.126	1.00
19_T	22_S	1.988	1.00
39_D	42_Y	1.815	1.00
13_D	46_R	1.505	1.00
4_D	7_D	1.439	1.00
31_N	43_L	1.364	1.00
28_E	35_N	1.340	1.00
12_Y	41_D	1.339	1.00
14_E	44_K	1.322	1.00
28_E	34_K	1.305	1.00
33_Q	42_Y	1.242	0.99
41_D	44_K	1.216	0.99
18_Y	23_C	1.200	0.99
29_Q	35_N	1.185	0.99
13_D	16_P	1.172	0.99
27_D	35_N	1.110	0.99
26_I	29_Q	1.089	0.99
15_Y	44_K	1.081	0.98
37_R	40_S	1.064	0.98
37_R	42_Y	1.062	0.98
9_K	24_P	1.053	0.98
21_S	28_E	1.022	0.98
11_V	48_Q	1.000	0.97
16_P	38_P	0.987	0.97
26_I	31_N	0.980	0.97
12_Y	34_K	0.967	0.97
46_R	49_P	0.955	0.97
25_F	35_N	0.952	0.97
29_Q	45_W	0.951	0.97
26_I	30_F	0.872	0.94
24_P	33_Q	0.865	0.94
2_G	50_D	0.860	0.94
10_W	23_C	0.843	0.93
36_G	42_Y	0.842	0.93
15_Y	30_F	0.799	0.91
13_D	17_L	0.792	0.91
5_L	27_D	0.790	0.91
49_P	52_C	0.778	0.90
7_D	51_G	0.744	0.88
25_F	29_Q	0.741	0.88
20_N	43_L	0.730	0.87
9_K	33_Q	0.718	0.86
47_W	52_C	0.714	0.86
17_L	42_Y	0.711	0.86
23_C	32_C	0.708	0.85
2_G	13_D	0.689	0.84
34_K	45_W	0.681	0.83
12_Y	48_Q	0.676	0.83
2_G	51_G	0.672	0.82
36_G	39_D	0.672	0.82
9_K	48_Q	0.652	0.80
2_G	14_E	0.633	0.79
10_W	18_Y	0.624	0.78
25_F	30_F	0.621	0.77
5_L	20_N	0.615	0.77
41_D	45_W	0.610	0.76
30_F	45_W	0.606	0.75
26_I	34_K	0.593	0.74
46_R	53_D	0.585	0.73
36_G	45_W	0.568	0.71
2_G	6_F	0.558	0.69
20_N	31_N	0.557	0.69
6_F	27_D	0.555	0.69
17_L	37_R	0.545	0.68
20_N	30_F	0.527	0.65
17_L	44_K	0.522	0.64
20_N	34_K	0.513	0.63
15_Y	46_R	0.511	0.63
45_W	50_D	0.507	0.62
5_L	17_L	0.505	0.62
2_G	12_Y	0.502	0.61
24_P	28_E	0.501	0.61
19_T	33_Q	0.500	0.61

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
2dadA	1	0.7358	4.4	0.903	Contact Map
3cw3A	1	0.7736	3.2	0.909	Contact Map
2mi5A	1	0.6415	2.5	0.915	Contact Map
1zwmA	1	0.7736	1.8	0.92	Contact Map
3pjxA	1	0.3396	1.8	0.92	Contact Map
1u5mA	1	0.5472	1.8	0.92	Contact Map
1fjrA	1	1	1.7	0.922	Contact Map
1h4aX	1	0.7925	1.5	0.924	Contact Map
4pfbA	1	0	1.5	0.924	Contact Map
1ytqA	4	0.8679	1.4	0.925	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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