Swi3 - PFAM28P - GREMLIN Contacts

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Swi3 - Replication Fork Protection Component Swi3

PFAM:	PF07962	Sequences: KLDEERLLSPRGLPKLRKEFKKLKFKGKGHEASDLKRLLNFYQLWAHRLYPKAKFDDFLERVEKLGHKKRVQVYLKEWRDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	81 (80)
Sequences:	592 (446)
Seq/√Len:	49.8
META:	0.343

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_G	34_D	4.401	1.00
54_K	57_D	2.947	1.00
75_L	79_R	2.898	1.00
3_D	6_R	2.784	1.00
16_L	20_F	2.590	1.00
58_F	62_V	2.424	1.00
46_A	58_F	2.197	1.00
13_L	66_G	1.843	0.99
55_F	59_L	1.818	0.99
15_K	19_E	1.729	0.99
26_K	30_H	1.708	0.98
27_G	30_H	1.648	0.98
29_G	34_D	1.607	0.98
32_A	36_K	1.574	0.97
53_A	57_D	1.533	0.97
38_L	42_Y	1.454	0.96
31_E	34_D	1.387	0.95
53_A	75_L	1.363	0.94
27_G	31_E	1.325	0.93
72_Q	76_K	1.304	0.93
35_L	47_H	1.254	0.91
37_R	41_F	1.240	0.91
46_A	57_D	1.239	0.91
61_R	75_L	1.230	0.90
11_R	15_K	1.186	0.88
63_E	66_G	1.137	0.86
30_H	34_D	1.124	0.86
61_R	79_R	1.119	0.85
53_A	61_R	1.102	0.85
65_L	69_K	1.095	0.84
7_L	13_L	1.089	0.84
40_N	71_V	1.086	0.84
32_A	54_K	1.083	0.83
35_L	59_L	1.066	0.82
37_R	42_Y	1.061	0.82
35_L	58_F	1.046	0.81
4_E	70_R	1.027	0.80
34_D	45_W	1.024	0.80
74_Y	78_W	1.021	0.80
4_E	65_L	1.011	0.79
14_P	17_R	1.008	0.79
15_K	48_R	1.005	0.79
20_F	48_R	0.982	0.77
16_L	19_E	0.980	0.77
76_K	80_D	0.963	0.76
35_L	55_F	0.952	0.75
69_K	72_Q	0.945	0.74
47_H	52_K	0.945	0.74
9_S	49_L	0.928	0.73
45_W	51_P	0.921	0.72
19_E	41_F	0.899	0.70
49_L	58_F	0.897	0.70
49_L	55_F	0.892	0.70
69_K	73_V	0.873	0.68
59_L	66_G	0.871	0.68
21_K	80_D	0.866	0.67
26_K	34_D	0.858	0.67
25_F	28_K	0.823	0.63
23_L	64_K	0.822	0.63
77_E	80_D	0.819	0.63
30_H	33_S	0.819	0.63
20_F	41_F	0.814	0.63
22_K	42_Y	0.811	0.62
9_S	60_E	0.804	0.62
30_H	55_F	0.803	0.62
13_L	17_R	0.794	0.61
53_A	58_F	0.788	0.60
23_L	37_R	0.780	0.59
43_Q	55_F	0.777	0.59
51_P	55_F	0.775	0.59
10_P	33_S	0.764	0.58
44_L	57_D	0.760	0.57
1_K	10_P	0.758	0.57
43_Q	47_H	0.751	0.56
2_L	10_P	0.742	0.56
36_K	39_L	0.740	0.55
4_E	68_K	0.732	0.55
2_L	64_K	0.730	0.54
28_K	31_E	0.722	0.53
39_L	79_R	0.716	0.53
16_L	41_F	0.705	0.52
62_V	69_K	0.691	0.50
1_K	5_E	0.691	0.50
10_P	18_K	0.681	0.49
50_Y	54_K	0.673	0.48
61_R	64_K	0.670	0.48
26_K	29_G	0.667	0.48
32_A	38_L	0.657	0.47
2_L	58_F	0.656	0.47
4_E	50_Y	0.644	0.46
6_R	14_P	0.634	0.45
19_E	76_K	0.624	0.44
36_K	53_A	0.621	0.43
5_E	59_L	0.618	0.43
50_Y	57_D	0.616	0.43
47_H	58_F	0.613	0.42
56_D	62_V	0.609	0.42
7_L	12_G	0.605	0.42
66_G	75_L	0.596	0.41
9_S	18_K	0.596	0.41
25_F	65_L	0.573	0.38
21_K	24_K	0.572	0.38
60_E	64_K	0.572	0.38
20_F	39_L	0.562	0.37
76_K	79_R	0.561	0.37
21_K	40_N	0.559	0.37
50_Y	68_K	0.552	0.36
5_E	22_K	0.536	0.35
3_D	16_L	0.534	0.35
68_K	73_V	0.532	0.35
4_E	8_L	0.528	0.34
49_L	64_K	0.524	0.34
23_L	53_A	0.523	0.34
15_K	60_E	0.519	0.33
23_L	41_F	0.518	0.33
26_K	31_E	0.517	0.33
9_S	58_F	0.516	0.33
13_L	64_K	0.514	0.33
25_F	34_D	0.513	0.33
16_L	28_K	0.500	0.32

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
2v6eA	2	0.9753	40.1	0.856	Contact Map
2wscF	1	0.6914	14.6	0.883	Contact Map
5chsA	1	0.6296	13.6	0.885	Contact Map
4xk8F	1	0.6914	13.5	0.885	Contact Map
3j7aG	1	0.8025	13.4	0.885	Contact Map
4kt0F	1	0.679	9.6	0.893	Contact Map
1jb0F	1	0.679	9.4	0.893	Contact Map
3us6A	1	0.5926	8.7	0.894	Contact Map
1tohA	3	0.9012	8.2	0.896	Contact Map
4bujB	1	1	7.5	0.898	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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