GH-E - PFAM28P - GREMLIN Contacts

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GH-E - HNH/ENDO VII superfamily nuclease with conserved GHE residues

PFAM:	PF14410	Sequences: DPDGKVIDPNTGKPIDGQWDMGHKPGVEYWNLRGRAEEGGITRKEFLDWYNDPDNYRLEDPSSNRSHGAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	70 (68)
Sequences:	1359 (1117)
Seq/√Len:	135.5
META:	0.861

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_D	65_R	4.945	1.00
43_R	47_L	2.543	1.00
29_Y	46_F	2.258	1.00
5_K	14_P	2.103	1.00
63_S	69_A	2.093	1.00
67_H	70_E	2.086	1.00
28_E	31_N	1.998	1.00
22_G	59_E	1.820	1.00
61_P	65_R	1.820	1.00
42_T	45_E	1.802	1.00
19_W	58_L	1.745	1.00
34_G	38_E	1.588	1.00
32_L	50_Y	1.578	1.00
33_R	37_E	1.552	1.00
29_Y	33_R	1.494	1.00
48_D	51_N	1.488	1.00
59_E	67_H	1.468	1.00
44_K	48_D	1.466	1.00
20_D	61_P	1.396	1.00
35_R	40_G	1.316	1.00
22_G	57_R	1.279	1.00
24_K	27_V	1.265	1.00
60_D	63_S	1.252	1.00
8_D	11_T	1.231	1.00
3_D	7_I	1.219	1.00
22_G	67_H	1.196	1.00
62_S	65_R	1.193	1.00
10_N	69_A	1.187	0.99
21_M	56_Y	1.184	0.99
49_W	55_N	1.105	0.99
32_L	49_W	1.070	0.99
52_D	55_N	1.069	0.99
34_G	37_E	1.054	0.99
11_T	63_S	1.036	0.99
20_D	62_S	1.009	0.98
41_I	49_W	0.975	0.98
6_V	19_W	0.973	0.98
63_S	67_H	0.965	0.98
50_Y	56_Y	0.961	0.98
24_K	57_R	0.955	0.98
57_R	67_H	0.942	0.97
7_I	14_P	0.925	0.97
13_K	60_D	0.923	0.97
32_L	35_R	0.917	0.97
21_M	58_L	0.903	0.97
10_N	59_E	0.871	0.96
8_D	63_S	0.859	0.96
6_V	58_L	0.851	0.95
9_P	13_K	0.841	0.95
29_Y	36_A	0.823	0.94
27_V	49_W	0.818	0.94
20_D	64_N	0.783	0.93
31_N	35_R	0.773	0.92
26_G	31_N	0.767	0.92
3_D	14_P	0.765	0.92
47_L	51_N	0.764	0.92
52_D	56_Y	0.760	0.92
43_R	51_N	0.739	0.91
35_R	49_W	0.734	0.90
41_I	46_F	0.730	0.90
59_E	63_S	0.719	0.89
27_V	55_N	0.708	0.89
32_L	46_F	0.702	0.88
30_W	34_G	0.687	0.87
19_W	61_P	0.685	0.87
5_K	16_D	0.678	0.86
35_R	39_G	0.676	0.86
41_I	45_E	0.673	0.86
43_R	46_F	0.661	0.85
22_G	56_Y	0.645	0.83
33_R	36_A	0.640	0.83
39_G	49_W	0.627	0.82
50_Y	55_N	0.626	0.82
27_V	30_W	0.623	0.81
27_V	32_L	0.616	0.81
63_S	68_G	0.612	0.80
25_P	57_R	0.601	0.79
7_I	15_I	0.596	0.78
45_E	48_D	0.588	0.77
10_N	57_R	0.581	0.77
42_T	51_N	0.565	0.75
19_W	60_D	0.564	0.75
6_V	9_P	0.564	0.75
31_N	34_G	0.561	0.74
6_V	21_M	0.558	0.74
14_P	17_G	0.558	0.74
24_K	54_D	0.556	0.73
10_N	63_S	0.553	0.73
39_G	45_E	0.545	0.72
10_N	13_K	0.543	0.72
56_Y	59_E	0.536	0.71
23_H	64_N	0.534	0.71
32_L	41_I	0.533	0.70
46_F	50_Y	0.531	0.70
47_L	50_Y	0.529	0.70
18_Q	21_M	0.523	0.69
3_D	16_D	0.523	0.69
27_V	35_R	0.521	0.69
40_G	43_R	0.515	0.68
49_W	52_D	0.515	0.68
27_V	36_A	0.501	0.66
28_E	67_H	0.500	0.66

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
4un4B	1	0.7286	88.1	0.774	Contact Map
4ogeA	1	0.7429	62.8	0.821	Contact Map
4h9dA	3	0.7286	56.6	0.827	Contact Map
3m7kA	2	0.9429	11.6	0.879	Contact Map
5aj3Q	1	0.3571	8.1	0.887	Contact Map
4iloA	3	0.2571	6.9	0.891	Contact Map
2pu3A	1	1	6.6	0.892	Contact Map
3mhsE	1	0.3571	6.1	0.894	Contact Map
2v0cA	1	0.9286	6	0.894	Contact Map
3ephA	2	0.6571	6	0.894	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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