zf-C4pol - PFAM28P - GREMLIN Contacts

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zf-C4pol - C4-type zinc-finger of DNA polymerase delta

PFAM:	PF14260	Sequences: CLGCKAPLKKSEALCKHCRDPAESYLKLLSRLRELERRFSRLWTQCQRCSQGSLHEEVLCTSRDCPIFYMR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	71 (70)
Sequences:	1339 (1011)
Seq/√Len:	120.8
META:	0.385

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_P	24_S	4.981	1.00
20_D	23_E	3.775	1.00
38_R	70_M	3.228	1.00
20_D	24_S	3.056	1.00
37_R	41_R	2.307	1.00
62_S	66_P	2.164	1.00
46_C	49_C	2.049	1.00
39_F	47_Q	1.865	1.00
42_L	67_I	1.818	1.00
28_L	31_R	1.759	1.00
1_C	4_C	1.684	1.00
60_C	65_C	1.683	1.00
43_W	47_Q	1.676	1.00
39_F	43_W	1.516	1.00
34_E	37_R	1.428	1.00
63_R	69_Y	1.409	1.00
28_L	32_L	1.327	1.00
49_C	65_C	1.245	0.99
2_L	5_K	1.210	0.99
68_F	71_R	1.206	0.99
6_A	17_H	1.190	0.99
26_L	30_S	1.166	0.99
53_S	56_E	1.152	0.99
58_V	71_R	1.089	0.99
51_Q	59_L	1.086	0.98
9_K	16_K	1.068	0.98
8_L	69_Y	1.062	0.98
19_R	22_A	1.045	0.98
49_C	60_C	1.000	0.97
35_L	38_R	0.983	0.97
30_S	33_R	0.977	0.97
44_T	47_Q	0.968	0.97
52_G	58_V	0.962	0.97
26_L	29_L	0.958	0.97
4_C	15_C	0.932	0.96
56_E	61_T	0.927	0.96
65_C	69_Y	0.924	0.96
33_R	36_E	0.924	0.96
5_K	8_L	0.906	0.95
63_R	70_M	0.905	0.95
27_K	31_R	0.901	0.95
36_E	63_R	0.901	0.95
12_E	27_K	0.893	0.95
8_L	14_L	0.881	0.95
1_C	18_C	0.879	0.95
14_L	28_L	0.876	0.94
45_Q	67_I	0.839	0.93
45_Q	62_S	0.827	0.93
28_L	37_R	0.809	0.92
12_E	19_R	0.790	0.91
1_C	15_C	0.764	0.89
6_A	26_L	0.747	0.88
39_F	58_V	0.747	0.88
20_D	37_R	0.741	0.88
26_L	31_R	0.738	0.88
9_K	32_L	0.736	0.88
48_R	56_E	0.731	0.87
43_W	67_I	0.731	0.87
7_P	34_E	0.730	0.87
47_Q	58_V	0.721	0.86
45_Q	48_R	0.720	0.86
33_R	37_R	0.706	0.85
19_R	26_L	0.698	0.85
52_G	56_E	0.697	0.85
13_A	66_P	0.696	0.84
34_E	38_R	0.695	0.84
65_C	71_R	0.689	0.84
25_Y	29_L	0.685	0.84
7_P	41_R	0.685	0.84
3_G	12_E	0.684	0.83
35_L	39_F	0.670	0.82
19_R	38_R	0.665	0.82
6_A	31_R	0.655	0.81
46_C	60_C	0.652	0.80
11_S	34_E	0.652	0.80
43_W	52_G	0.648	0.80
26_L	38_R	0.644	0.80
46_C	62_S	0.643	0.80
16_K	30_S	0.632	0.78
27_K	41_R	0.632	0.78
51_Q	54_L	0.627	0.78
3_G	20_D	0.626	0.78
12_E	30_S	0.623	0.77
43_W	68_F	0.622	0.77
29_L	33_R	0.599	0.75
10_K	22_A	0.596	0.74
49_C	62_S	0.581	0.72
15_C	18_C	0.575	0.72
4_C	46_C	0.572	0.71
58_V	68_F	0.567	0.71
46_C	64_D	0.564	0.70
63_R	68_F	0.563	0.70
19_R	23_E	0.562	0.70
17_H	44_T	0.552	0.68
11_S	30_S	0.550	0.68
4_C	18_C	0.547	0.68
10_K	31_R	0.541	0.67
28_L	56_E	0.531	0.66
16_K	19_R	0.527	0.65
18_C	46_C	0.518	0.64
47_Q	59_L	0.506	0.62
40_S	43_W	0.505	0.62
36_E	55_H	0.504	0.62
15_C	46_C	0.500	0.61
14_L	55_H	0.500	0.61

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
4u7tA	2	0.8592	51.3	0.784	Contact Map
3a1bA	1	0.8451	48.3	0.788	Contact Map
2pv0B	1	0.8592	47.6	0.79	Contact Map
4qbsA	1	0.8592	45	0.793	Contact Map
1a6yA	2	0.4085	10.7	0.846	Contact Map
1yuzA	2	0.3944	10.6	0.847	Contact Map
3vrhA	2	0.5352	10.6	0.847	Contact Map
3mpxA	1	0	9.4	0.85	Contact Map
1dvpA	2	0.5775	8.5	0.853	Contact Map
3dzyD	1	0.6338	7.9	0.855	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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