RNA_bind_2 - PFAM28P - GREMLIN Contacts

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RNA_bind_2 - Predicted RNA-binding protein

PFAM:	PF10133	Sequences: MCEANVYLLKDGKEGELIMEDVDRIEPEGDGVRLVDIFGEQKEVKGRIKEIDLVDHKIILE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (59)
Sequences:	4862 (3079)
Seq/√Len:	400.9
META:	0.949

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_D	40_E	2.644	1.00
17_L	20_E	2.386	1.00
31_G	43_E	2.255	1.00
32_V	60_L	2.083	1.00
26_E	33_R	1.879	1.00
31_G	45_K	1.851	1.00
5_N	17_L	1.796	1.00
52_D	55_D	1.699	1.00
28_E	33_R	1.694	1.00
7_Y	17_L	1.663	1.00
5_N	20_E	1.637	1.00
6_V	34_L	1.619	1.00
10_K	16_E	1.616	1.00
26_E	50_E	1.572	1.00
24_R	35_V	1.502	1.00
33_R	41_Q	1.466	1.00
3_E	23_D	1.432	1.00
4_A	56_H	1.429	1.00
24_R	50_E	1.405	1.00
46_G	60_L	1.401	1.00
33_R	43_E	1.366	1.00
4_A	53_L	1.360	1.00
30_D	45_K	1.316	1.00
25_I	58_I	1.263	1.00
14_E	57_K	1.243	1.00
28_E	31_G	1.211	1.00
3_E	56_H	1.198	1.00
19_M	42_K	1.164	1.00
25_I	53_L	1.158	1.00
27_P	32_V	1.105	1.00
48_I	51_I	1.064	1.00
25_I	48_I	1.045	1.00
35_V	41_Q	1.034	1.00
18_I	44_V	1.018	1.00
4_A	58_I	1.009	1.00
10_K	13_K	0.970	1.00
23_D	54_V	0.931	1.00
19_M	22_V	0.912	1.00
8_L	18_I	0.901	1.00
9_L	59_I	0.884	1.00
53_L	58_I	0.881	1.00
53_L	56_H	0.870	1.00
22_V	34_L	0.864	1.00
36_D	39_G	0.857	1.00
13_K	16_E	0.832	1.00
23_D	37_I	0.795	1.00
50_E	59_I	0.780	1.00
28_E	43_E	0.778	1.00
51_I	56_H	0.760	1.00
8_L	60_L	0.757	1.00
6_V	22_V	0.750	1.00
32_V	46_G	0.748	1.00
9_L	14_E	0.736	1.00
9_L	12_G	0.717	1.00
21_D	56_H	0.709	1.00
48_I	60_L	0.700	1.00
34_L	44_V	0.681	0.99
3_E	57_K	0.627	0.99
21_D	37_I	0.626	0.99
9_L	49_K	0.620	0.99
3_E	21_D	0.614	0.99
48_I	58_I	0.610	0.99
21_D	52_D	0.608	0.99
8_L	16_E	0.605	0.99
24_R	52_D	0.595	0.99
4_A	46_G	0.594	0.99
25_I	32_V	0.594	0.99
48_I	52_D	0.590	0.99
27_P	48_I	0.583	0.98
4_A	7_Y	0.579	0.98
20_E	38_F	0.577	0.98
19_M	34_L	0.575	0.98
49_K	59_I	0.574	0.98
23_D	52_D	0.573	0.98
37_I	41_Q	0.571	0.98
14_E	17_L	0.564	0.98
27_P	31_G	0.557	0.98
19_M	36_D	0.555	0.98
3_E	36_D	0.553	0.98
50_E	57_K	0.544	0.98
26_E	35_V	0.528	0.97
3_E	39_G	0.526	0.97
6_V	60_L	0.521	0.97
21_D	38_F	0.519	0.97
1_M	52_D	0.510	0.96
3_E	37_I	0.510	0.96
32_V	48_I	0.501	0.96
4_A	21_D	0.500	0.96

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
2l55A	1	0.3443	9.8	0.848	Contact Map
1b25A	3	0.3443	5.7	0.863	Contact Map
1aorA	2	0.3443	5.4	0.865	Contact Map
2pc6A	2	0.918	4.1	0.872	Contact Map
2f1fA	4	0.918	3.9	0.874	Contact Map
4z3xA	2	0.3607	3.3	0.879	Contact Map
2qcpX	1	0.4426	3.1	0.879	Contact Map
3j3wU	1	0.5902	2.9	0.882	Contact Map
3be6A	2	0.541	2.7	0.883	Contact Map
2ra2A	3	0.9016	2.5	0.885	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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