RBM39linker - PFAM28P - GREMLIN Contacts

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RBM39linker - linker between RRM2 and RRM3 domains in RBM39 protein

PFAM:	PF15519	Sequences: LDDDDGGGLNLNAQSRAALMAKLARTGTGLSIPGAAGAALQNTAAAPPPAPPVPAGAATKPLPVAVGIASRCLLLKNMFDPAEETEPDW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	89 (81)
Sequences:	524 (378)
Seq/√Len:	42.0
META:	0.315

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_N	15_S	3.030	1.00
30_L	33_P	2.755	1.00
45_A	48_P	2.635	1.00
15_S	22_K	2.254	1.00
64_V	67_G	2.220	1.00
43_T	48_P	2.146	0.99
77_N	80_D	2.110	0.99
43_T	47_P	2.044	0.99
4_D	7_G	2.015	0.99
33_P	36_A	1.871	0.99
42_N	45_A	1.868	0.99
4_D	9_L	1.856	0.98
52_P	57_A	1.795	0.98
21_A	25_R	1.751	0.98
51_P	62_L	1.719	0.97
3_D	6_G	1.719	0.97
33_P	40_L	1.558	0.95
24_A	27_G	1.481	0.94
1_L	16_R	1.423	0.93
42_N	49_P	1.403	0.92
12_N	17_A	1.345	0.90
34_G	37_G	1.289	0.88
34_G	38_A	1.269	0.87
37_G	41_Q	1.254	0.87
31_S	34_G	1.245	0.86
11_L	17_A	1.192	0.84
42_N	46_A	1.190	0.84
2_D	8_G	1.176	0.83
46_A	52_P	1.152	0.82
22_K	27_G	1.143	0.81
75_L	78_M	1.126	0.80
52_P	58_A	1.104	0.79
4_D	24_A	1.093	0.78
34_G	51_P	1.081	0.77
4_D	13_A	1.072	0.77
75_L	79_F	1.063	0.76
18_A	21_A	1.052	0.75
81_P	84_E	1.038	0.74
64_V	68_I	1.023	0.73
38_A	49_P	1.020	0.73
48_P	51_P	1.019	0.73
69_A	75_L	1.013	0.73
46_A	51_P	0.984	0.70
39_A	42_N	0.983	0.70
46_A	50_A	0.972	0.69
3_D	10_N	0.970	0.69
35_A	40_L	0.969	0.69
68_I	82_A	0.957	0.68
70_S	80_D	0.941	0.67
83_E	87_P	0.925	0.66
32_I	36_A	0.920	0.65
25_R	68_I	0.914	0.65
36_A	39_A	0.901	0.64
8_G	19_L	0.894	0.63
22_K	85_T	0.887	0.62
43_T	52_P	0.866	0.60
49_P	58_A	0.865	0.60
41_Q	44_A	0.861	0.60
77_N	84_E	0.861	0.60
63_P	70_S	0.852	0.59
19_L	23_L	0.844	0.58
7_G	79_F	0.835	0.58
10_N	70_S	0.826	0.57
80_D	84_E	0.823	0.57
6_G	73_L	0.812	0.55
37_G	49_P	0.810	0.55
40_L	58_A	0.794	0.54
44_A	50_A	0.791	0.54
7_G	76_K	0.787	0.53
6_G	17_A	0.769	0.51
14_Q	18_A	0.766	0.51
10_N	72_C	0.762	0.51
44_A	58_A	0.760	0.51
47_P	50_A	0.759	0.51
63_P	66_V	0.759	0.51
5_D	10_N	0.751	0.50
17_A	21_A	0.748	0.49
12_N	64_V	0.746	0.49
82_A	85_T	0.735	0.48
11_L	27_G	0.727	0.48
24_A	75_L	0.725	0.47
27_G	75_L	0.723	0.47
38_A	47_P	0.708	0.46
42_N	51_P	0.707	0.46
47_P	52_P	0.692	0.44
44_A	49_P	0.689	0.44
19_L	79_F	0.677	0.43
10_N	14_Q	0.676	0.43
78_M	81_P	0.671	0.42
45_A	58_A	0.668	0.42
15_S	71_R	0.642	0.40
37_G	42_N	0.637	0.39
6_G	11_L	0.625	0.38
66_V	69_A	0.618	0.38
34_G	39_A	0.612	0.37
73_L	78_M	0.611	0.37
11_L	25_R	0.611	0.37
38_A	46_A	0.603	0.36
10_N	22_K	0.597	0.36
22_K	66_V	0.593	0.35
21_A	73_L	0.592	0.35
74_L	86_E	0.591	0.35
37_G	40_L	0.590	0.35
47_P	51_P	0.588	0.35
1_L	6_G	0.586	0.35
14_Q	27_G	0.583	0.35
51_P	58_A	0.580	0.34
38_A	41_Q	0.575	0.34
11_L	81_P	0.573	0.34
67_G	75_L	0.571	0.34
5_D	13_A	0.568	0.33
29_G	32_I	0.560	0.33
32_I	37_G	0.558	0.32
39_A	48_P	0.549	0.32
4_D	11_L	0.533	0.30
82_A	86_E	0.530	0.30
46_A	57_A	0.514	0.29
67_G	70_S	0.514	0.29
21_A	75_L	0.509	0.29
24_A	71_R	0.507	0.28
74_L	82_A	0.507	0.28
29_G	36_A	0.500	0.28

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
3ue2A	1	0.4382	26.7	0.886	Contact Map
2ditA	1	0.382	24.2	0.888	Contact Map
2gqbA	1	0.4045	11.6	0.903	Contact Map
2pv0B	1	0.7865	8	0.91	Contact Map
3dxbA	5	0.8876	2.4	0.93	Contact Map
2adcA	1	0.3596	2	0.933	Contact Map
2khcA	1	0.6404	2	0.934	Contact Map
2ebfX	1	0.6966	1.9	0.934	Contact Map
4f02A	1	0.2022	1.9	0.934	Contact Map
3a6pA	1	0.1124	1.8	0.935	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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