TypeIII_RM_meth - PFAM28P - GREMLIN Contacts

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TypeIII_RM_meth - Type III restriction/modification enzyme methylation subunit

PFAM:	PF12564	Sequences: DEELIKLLLSNEEIKEHFFTEVDGVLVFDKNKFIKFISNKNFLPDSYTAFKNKIGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (56)
Sequences:	1812 (917)
Seq/√Len:	122.5
META:	0.901

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_E	24_G	4.297	1.00
6_K	23_D	3.706	1.00
31_N	34_I	3.449	1.00
28_F	33_F	3.439	1.00
29_D	32_K	3.416	1.00
15_K	26_L	2.197	1.00
2_E	20_T	1.872	1.00
12_E	16_E	1.785	1.00
13_E	16_E	1.694	1.00
13_E	17_H	1.669	1.00
20_T	29_D	1.635	1.00
17_H	32_K	1.626	1.00
8_L	14_I	1.585	1.00
18_F	36_F	1.527	1.00
39_N	44_P	1.364	1.00
21_E	26_L	1.309	1.00
38_S	41_N	1.250	0.99
35_K	49_A	1.228	0.99
39_N	42_F	1.179	0.99
3_E	6_K	1.164	0.99
10_S	23_D	1.119	0.99
19_F	43_L	1.038	0.98
6_K	10_S	1.025	0.98
41_N	44_P	0.986	0.97
35_K	38_S	0.921	0.96
35_K	39_N	0.901	0.95
42_F	45_D	0.898	0.95
11_N	14_I	0.845	0.94
33_F	36_F	0.816	0.92
2_E	6_K	0.811	0.92
19_F	28_F	0.777	0.90
16_E	32_K	0.775	0.90
39_N	43_L	0.766	0.90
8_L	19_F	0.759	0.89
3_E	14_I	0.742	0.88
9_L	25_V	0.736	0.88
6_K	11_N	0.736	0.88
5_I	29_D	0.736	0.88
6_K	22_V	0.731	0.88
3_E	10_S	0.719	0.87
34_I	38_S	0.700	0.85
9_L	15_K	0.694	0.85
34_I	41_N	0.690	0.84
40_K	45_D	0.685	0.84
7_L	11_N	0.684	0.84
32_K	35_K	0.682	0.84
21_E	25_V	0.682	0.84
34_I	40_K	0.669	0.83
34_I	49_A	0.660	0.82
30_K	44_P	0.638	0.79
3_E	7_L	0.626	0.78
16_E	21_E	0.625	0.78
15_K	27_V	0.622	0.78
36_F	49_A	0.610	0.76
2_E	23_D	0.608	0.76
38_S	51_K	0.607	0.76
22_V	25_V	0.602	0.75
4_L	43_L	0.598	0.75
15_K	21_E	0.598	0.75
18_F	53_K	0.587	0.74
14_I	34_I	0.585	0.73
10_S	18_F	0.582	0.73
34_I	37_I	0.577	0.72
5_I	25_V	0.570	0.71
29_D	35_K	0.569	0.71
12_E	20_T	0.565	0.71
37_I	51_K	0.560	0.70
20_T	32_K	0.554	0.69
6_K	16_E	0.547	0.68
38_S	49_A	0.538	0.67
25_V	30_K	0.537	0.67
2_E	16_E	0.536	0.67
7_L	19_F	0.534	0.67
13_E	24_G	0.528	0.66
36_F	40_K	0.524	0.65
29_D	34_I	0.523	0.65
17_H	41_N	0.515	0.64
37_I	43_L	0.513	0.63
6_K	21_E	0.513	0.63
3_E	20_T	0.512	0.63
26_L	45_D	0.512	0.63
28_F	40_K	0.507	0.63
18_F	43_L	0.504	0.62
43_L	51_K	0.500	0.62

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
2kjgA	1	1	6.6	0.878	Contact Map
3c5yA	5	0.6429	5.5	0.882	Contact Map
3onoA	4	0.625	5.3	0.884	Contact Map
4u8fA	4	0.6607	4.4	0.887	Contact Map
2mu0A	1	0.6607	4	0.89	Contact Map
4dcuA	1	0.9286	3.5	0.893	Contact Map
2m46A	1	0.6964	3	0.897	Contact Map
2qdjA	1	0.8214	3	0.897	Contact Map
4kegA	2	0.3929	2.8	0.898	Contact Map
3fz4A	1	0.6607	2.7	0.899	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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