RPAP3_C - PFAM28P - GREMLIN Contacts

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RPAP3_C - Potential Monad-binding region of RPAP3

PFAM:	PF13877	Sequences: PPKTAYEFERDWRRLKKSDPDRYAYLLQIPPETLPKLFKNSLEPDLLGEILQALADHLIEKDPDLEILEALSKVPRFDLALMFLSKSEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	89 (87)
Sequences:	863 (680)
Seq/√Len:	72.9
META:	0.333

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_L	67_I	3.857	1.00
8_F	12_W	3.664	1.00
7_E	10_R	3.534	1.00
12_W	49_E	3.520	1.00
79_L	82_M	3.179	1.00
35_P	76_R	2.639	1.00
7_E	11_D	2.329	1.00
3_K	7_E	2.291	1.00
20_P	24_A	2.254	1.00
71_L	76_R	1.971	1.00
35_P	73_K	1.903	1.00
48_G	84_L	1.693	1.00
38_F	41_S	1.691	1.00
30_P	33_T	1.537	0.99
85_S	89_K	1.486	0.99
54_L	67_I	1.422	0.99
78_D	81_L	1.417	0.99
38_F	44_P	1.401	0.98
9_E	43_E	1.355	0.98
26_L	34_L	1.331	0.98
33_T	89_K	1.286	0.97
41_S	79_L	1.222	0.96
33_T	36_K	1.215	0.96
6_Y	41_S	1.167	0.95
5_A	80_A	1.127	0.94
29_I	78_D	1.115	0.94
72_S	77_F	1.091	0.93
64_D	86_K	1.075	0.93
28_Q	61_K	1.060	0.92
9_E	71_L	1.059	0.92
47_L	57_H	1.029	0.91
55_A	64_D	1.029	0.91
6_Y	79_L	1.025	0.91
18_S	85_S	1.006	0.90
31_P	70_A	1.003	0.90
30_P	35_P	0.984	0.89
46_L	60_E	0.983	0.89
69_E	86_K	0.979	0.89
41_S	74_V	0.975	0.89
4_T	20_P	0.951	0.87
5_A	8_F	0.951	0.87
48_G	71_L	0.942	0.87
52_Q	73_K	0.942	0.87
10_R	83_F	0.941	0.87
31_P	40_N	0.935	0.86
18_S	23_Y	0.930	0.86
8_F	74_V	0.923	0.86
86_K	89_K	0.921	0.86
48_G	88_E	0.919	0.85
5_A	41_S	0.915	0.85
31_P	76_R	0.914	0.85
25_Y	28_Q	0.913	0.85
44_P	82_M	0.913	0.85
41_S	84_L	0.887	0.83
9_E	78_D	0.886	0.83
31_P	35_P	0.882	0.83
29_I	51_L	0.874	0.82
42_L	80_A	0.856	0.81
29_I	89_K	0.852	0.81
66_E	87_S	0.848	0.80
21_D	24_A	0.819	0.78
83_F	88_E	0.812	0.78
50_I	54_L	0.810	0.77
69_E	72_S	0.806	0.77
38_F	74_V	0.805	0.77
14_R	83_F	0.804	0.77
36_K	73_K	0.802	0.77
32_E	87_S	0.800	0.76
13_R	49_E	0.800	0.76
31_P	42_L	0.789	0.75
46_L	59_I	0.787	0.75
14_R	46_L	0.781	0.75
5_A	10_R	0.781	0.75
15_L	84_L	0.778	0.74
65_L	69_E	0.778	0.74
8_F	13_R	0.767	0.73
23_Y	32_E	0.760	0.73
52_Q	87_S	0.759	0.73
43_E	74_V	0.757	0.72
3_K	56_D	0.741	0.71
20_P	25_Y	0.739	0.71
66_E	69_E	0.726	0.69
61_K	64_D	0.724	0.69
58_L	65_L	0.714	0.68
36_K	52_Q	0.704	0.67
22_R	25_Y	0.696	0.66
38_F	42_L	0.688	0.65
3_K	59_I	0.687	0.65
81_L	84_L	0.680	0.64
35_P	70_A	0.672	0.63
19_D	25_Y	0.667	0.63
12_W	22_R	0.660	0.62
9_E	79_L	0.659	0.62
18_S	22_R	0.657	0.62
5_A	9_E	0.652	0.61
74_V	80_A	0.649	0.61
31_P	74_V	0.646	0.60
61_K	65_L	0.645	0.60
42_L	76_R	0.644	0.60
15_L	22_R	0.641	0.60
20_P	32_E	0.635	0.59
32_E	66_E	0.629	0.58
28_Q	56_D	0.619	0.57
56_D	72_S	0.616	0.57
6_Y	11_D	0.612	0.56
47_L	80_A	0.610	0.56
24_A	65_L	0.610	0.56
26_L	70_A	0.594	0.54
71_L	77_F	0.587	0.53
74_V	82_M	0.576	0.52
2_P	38_F	0.569	0.51
36_K	62_D	0.568	0.51
29_I	37_L	0.566	0.50
32_E	69_E	0.562	0.50
22_R	79_L	0.561	0.50
6_Y	9_E	0.548	0.48
51_L	60_E	0.544	0.48
43_E	72_S	0.533	0.46
37_L	52_Q	0.530	0.46
42_L	74_V	0.529	0.46
17_K	65_L	0.521	0.45
2_P	71_L	0.520	0.45
4_T	14_R	0.520	0.45
19_D	23_Y	0.517	0.44
31_P	34_L	0.515	0.44
29_I	33_T	0.514	0.44
24_A	64_D	0.508	0.43
6_Y	44_P	0.500	0.42
14_R	38_F	0.500	0.42
29_I	39_K	0.500	0.42

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
1ylmA	2	0.7416	11	0.873	Contact Map
2m9vA	1	0.8539	10.4	0.874	Contact Map
2inbA	2	0.764	8.5	0.879	Contact Map
2zndA	2	0.8876	7.2	0.883	Contact Map
4uslA	2	0.9213	5.8	0.888	Contact Map
4qoxA	1	0.7978	5.4	0.889	Contact Map
3d3qA	1	0.9213	5	0.891	Contact Map
1xi4A	8	1	5	0.891	Contact Map
3hjlA	1	0.9101	5	0.891	Contact Map
3qq6A	2	0.7528	4.9	0.892	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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