CAF1A - PFAM28P - GREMLIN Contacts

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CAF1A - Chromatin assembly factor 1 subunit A

PFAM:	PF12253	Sequences: KLLQFHEDVRPPYYGTWTKKSSVVGPRNPFAKDLPDLDYDYDSEAEWEEEEEGEDLDDDDDEEEEEDEDDDEDM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (71)
Sequences:	736 (547)
Seq/√Len:	64.9
META:	0.402

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_D	44_E	3.968	1.00
41_Y	46_E	3.752	1.00
21_S	33_D	2.696	1.00
13_Y	16_T	2.588	1.00
4_Q	12_P	2.463	1.00
17_W	37_L	2.443	1.00
2_L	14_Y	2.187	1.00
58_D	61_D	2.092	1.00
9_V	44_E	2.076	1.00
21_S	24_V	2.018	1.00
3_L	6_H	1.825	1.00
55_D	58_D	1.765	1.00
24_V	33_D	1.731	1.00
10_R	47_W	1.664	0.99
16_T	42_D	1.360	0.97
41_Y	44_E	1.315	0.97
2_L	12_P	1.230	0.95
30_F	33_D	1.212	0.95
11_P	47_W	1.202	0.94
13_Y	18_T	1.136	0.93
16_T	41_Y	1.126	0.92
1_K	16_T	1.113	0.92
9_V	45_A	1.111	0.92
59_D	62_E	1.109	0.92
20_K	67_D	1.072	0.90
8_D	42_D	1.059	0.90
29_P	33_D	1.049	0.89
22_S	65_E	1.045	0.89
39_Y	42_D	1.034	0.88
52_E	56_L	0.999	0.87
11_P	43_S	0.994	0.86
17_W	24_V	0.993	0.86
8_D	45_A	0.990	0.86
68_E	71_D	0.979	0.86
39_Y	43_S	0.979	0.86
22_S	25_G	0.962	0.85
18_T	41_Y	0.946	0.84
10_R	49_E	0.928	0.82
21_S	30_F	0.928	0.82
17_W	36_D	0.924	0.82
17_W	48_E	0.923	0.82
64_E	67_D	0.888	0.80
32_K	35_P	0.868	0.78
28_N	60_D	0.867	0.78
34_L	37_L	0.855	0.77
40_D	54_E	0.837	0.75
16_T	51_E	0.835	0.75
65_E	68_E	0.834	0.75
28_N	31_A	0.831	0.75
21_S	26_P	0.826	0.74
25_G	28_N	0.815	0.73
60_D	63_E	0.810	0.73
45_A	55_D	0.802	0.72
64_E	69_D	0.789	0.71
13_Y	17_W	0.783	0.70
18_T	59_D	0.772	0.69
65_E	70_D	0.762	0.68
8_D	32_K	0.756	0.68
10_R	48_E	0.756	0.68
26_P	30_F	0.744	0.66
45_A	57_D	0.742	0.66
42_D	47_W	0.741	0.66
17_W	50_E	0.737	0.66
41_Y	69_D	0.727	0.65
10_R	43_S	0.726	0.65
1_K	18_T	0.723	0.64
40_D	50_E	0.720	0.64
40_D	44_E	0.704	0.62
49_E	52_E	0.703	0.62
43_S	46_E	0.702	0.62
31_A	55_D	0.688	0.60
41_Y	52_E	0.683	0.60
23_V	31_A	0.660	0.57
39_Y	47_W	0.659	0.57
18_T	55_D	0.643	0.55
22_S	67_D	0.640	0.55
59_D	66_E	0.639	0.55
23_V	66_E	0.634	0.54
37_L	53_G	0.633	0.54
38_D	52_E	0.633	0.54
18_T	25_G	0.632	0.54
21_S	27_R	0.629	0.54
30_F	38_D	0.619	0.52
24_V	31_A	0.617	0.52
23_V	63_E	0.611	0.52
34_L	40_D	0.605	0.51
5_F	8_D	0.602	0.50
3_L	12_P	0.598	0.50
4_Q	9_V	0.597	0.50
33_D	36_D	0.593	0.49
41_Y	48_E	0.592	0.49
21_S	25_G	0.592	0.49
43_S	47_W	0.590	0.49
37_L	50_E	0.590	0.49
36_D	50_E	0.580	0.48
20_K	68_E	0.558	0.45
11_P	41_Y	0.554	0.45
51_E	56_L	0.544	0.44
4_Q	54_E	0.531	0.42
19_K	46_E	0.530	0.42
27_R	38_D	0.527	0.42
60_D	64_E	0.521	0.41
6_H	22_S	0.520	0.41
10_R	19_K	0.513	0.40
23_V	67_D	0.506	0.39
12_P	56_L	0.500	0.39

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
4kblA	2	0	54	0.85	Contact Map
4u7aA	1	0	41.7	0.86	Contact Map
2ca6A	1	0.6486	28.7	0.872	Contact Map
4fp9B	2	0.5541	25.5	0.875	Contact Map
4gyiA	1	0.5946	18.7	0.883	Contact Map
2ayuA	2	0.5405	16.8	0.885	Contact Map
4ui9I	1	0.6351	6.5	0.904	Contact Map
2a1xA	1	0.2703	3.8	0.914	Contact Map
1tljA	2	0.1351	3.8	0.915	Contact Map
1vluA	2	0.1757	3.6	0.915	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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