DNA_pol_alpha_N - PFAM28P - GREMLIN Contacts

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DNA_pol_alpha_N - DNA polymerase alpha subunit p180 N terminal

PFAM:	PF12254	Sequences: LEELKAARAGGKKRLDQYEVEEEEDIYDEVDEEEYKKIVRKRLDDDDFVVDDDGEGYVDDGREDWD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (65)
Sequences:	613 (435)
Seq/√Len:	54.0
META:	0.409

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_K	41_K	3.658	1.00
38_I	42_R	3.584	1.00
30_V	38_I	3.121	1.00
2_E	6_A	2.191	1.00
39_V	42_R	2.012	1.00
51_D	54_G	1.979	1.00
14_R	17_Q	1.826	0.99
31_D	34_E	1.823	0.99
41_K	45_D	1.628	0.98
17_Q	29_E	1.582	0.98
5_K	9_A	1.560	0.98
25_D	28_D	1.502	0.97
59_D	62_R	1.363	0.95
35_Y	42_R	1.357	0.95
34_E	38_I	1.349	0.95
40_R	43_L	1.283	0.93
32_E	55_E	1.282	0.93
38_I	63_E	1.181	0.90
2_E	42_R	1.172	0.90
48_F	65_W	1.166	0.90
13_K	18_Y	1.159	0.89
43_L	62_R	1.157	0.89
50_V	54_G	1.150	0.89
34_E	37_K	1.132	0.88
21_E	25_D	1.123	0.88
57_Y	61_G	1.121	0.88
12_K	15_L	1.109	0.87
7_A	10_G	1.098	0.87
19_E	22_E	1.095	0.86
2_E	5_K	1.084	0.86
48_F	60_D	1.073	0.85
7_A	14_R	1.050	0.84
60_D	63_E	1.044	0.84
25_D	29_E	1.044	0.84
30_V	42_R	1.039	0.83
4_L	36_K	1.037	0.83
27_Y	64_D	1.033	0.83
4_L	58_V	1.031	0.83
49_V	58_V	1.029	0.83
11_G	35_Y	0.991	0.80
33_E	49_V	0.987	0.80
13_K	49_V	0.955	0.78
45_D	50_V	0.951	0.78
40_R	46_D	0.940	0.77
3_E	7_A	0.923	0.75
48_F	59_D	0.921	0.75
43_L	47_D	0.916	0.75
35_Y	59_D	0.912	0.75
27_Y	40_R	0.889	0.73
36_K	48_F	0.881	0.72
9_A	12_K	0.804	0.65
39_V	44_D	0.802	0.65
32_E	39_V	0.799	0.64
22_E	25_D	0.780	0.63
14_R	23_E	0.780	0.63
7_A	11_G	0.770	0.62
44_D	47_D	0.765	0.61
13_K	16_D	0.761	0.61
6_A	9_A	0.761	0.61
49_V	59_D	0.760	0.61
48_F	64_D	0.745	0.59
58_V	64_D	0.729	0.57
3_E	19_E	0.728	0.57
39_V	49_V	0.722	0.57
3_E	12_K	0.705	0.55
4_L	26_I	0.692	0.53
34_E	41_K	0.674	0.52
7_A	37_K	0.674	0.52
26_I	29_E	0.666	0.51
10_G	13_K	0.663	0.50
26_I	39_V	0.638	0.48
40_R	50_V	0.634	0.47
17_Q	24_E	0.630	0.47
47_D	51_D	0.629	0.47
40_R	58_V	0.615	0.45
12_K	31_D	0.605	0.44
6_A	10_G	0.598	0.43
3_E	6_A	0.594	0.43
38_I	41_K	0.589	0.43
29_E	37_K	0.572	0.41
17_Q	22_E	0.568	0.40
31_D	56_G	0.568	0.40
32_E	65_W	0.564	0.40
4_L	47_D	0.561	0.40
6_A	12_K	0.551	0.39
7_A	13_K	0.543	0.38
5_K	20_V	0.540	0.38
49_V	55_E	0.539	0.37
32_E	40_R	0.537	0.37
10_G	47_D	0.535	0.37
3_E	17_Q	0.529	0.36
27_Y	39_V	0.528	0.36
52_D	56_G	0.516	0.35
58_V	65_W	0.515	0.35
8_R	59_D	0.511	0.35
24_E	37_K	0.511	0.35
15_L	31_D	0.508	0.34
28_D	55_E	0.500	0.34

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
2pi2A	1	0	6	0.889	Contact Map
3bo6A	1	0.4394	4.4	0.895	Contact Map
3i0uA	1	0.303	4.4	0.895	Contact Map
2p1wA	1	0.3182	4.4	0.896	Contact Map
1b5eA	4	0.5758	3.5	0.901	Contact Map
4d10B	1	0	3.2	0.903	Contact Map
4kqtA	1	0.9545	2.5	0.908	Contact Map
4az1A	2	0.5303	2.4	0.908	Contact Map
1xg4A	4	0.6364	2.3	0.91	Contact Map
1l1lA	1	0.803	2.2	0.911	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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