DUF2073 - PFAM28P - GREMLIN Contacts

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DUF2073 - Uncharacterized protein conserved in archaea (DUF2073)

PFAM:	PF09846	Sequences: LEGLSSMERIRKILDIVKENKIVILEGRLKPEEEARLIEDTMEEIDPKKFKGIELAVIPPDKKKKGFFGKLLGKLLDRGGLTIIGPASIVKEIKKDPDKIEALVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	105 (100)
Sequences:	1536 (1018)
Seq/√Len:	101.8
META:	0.955

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_L	76_L	5.533	1.00
36_R	39_E	4.772	1.00
73_G	76_L	4.108	1.00
72_L	75_L	3.021	1.00
64_K	70_K	2.741	1.00
96_D	101_E	2.583	1.00
11_R	15_D	2.317	1.00
36_R	40_D	2.269	1.00
14_L	41_T	2.060	1.00
26_E	79_G	2.000	1.00
7_M	40_D	1.956	1.00
18_K	44_E	1.940	1.00
40_D	44_E	1.848	1.00
64_K	68_F	1.814	1.00
56_A	95_K	1.799	1.00
8_E	11_R	1.777	1.00
30_K	77_D	1.690	1.00
90_V	97_P	1.672	1.00
68_F	74_K	1.543	1.00
5_S	8_E	1.533	1.00
65_K	69_G	1.426	1.00
40_D	43_E	1.421	1.00
18_K	80_G	1.417	1.00
51_K	88_S	1.407	1.00
31_P	56_A	1.376	1.00
25_L	56_A	1.371	0.99
7_M	39_E	1.371	0.99
11_R	40_D	1.310	0.99
69_G	74_K	1.308	0.99
36_R	44_E	1.234	0.99
34_E	57_V	1.200	0.99
65_K	72_L	1.199	0.99
64_K	67_F	1.169	0.98
63_K	78_R	1.148	0.98
94_K	97_P	1.147	0.98
6_S	9_R	1.136	0.98
38_I	87_A	1.134	0.98
69_G	72_L	1.132	0.98
12_K	16_I	1.129	0.98
43_E	46_D	1.125	0.98
66_G	83_I	1.078	0.97
22_I	38_I	1.035	0.96
31_P	35_A	1.027	0.96
22_I	100_I	1.021	0.96
7_M	15_D	0.958	0.95
54_E	85_G	0.954	0.94
5_S	15_D	0.951	0.94
43_E	80_G	0.922	0.93
69_G	73_G	0.921	0.93
70_K	73_G	0.920	0.93
67_F	72_L	0.905	0.93
66_G	70_K	0.902	0.93
64_K	74_K	0.899	0.92
8_E	15_D	0.894	0.92
58_I	91_K	0.894	0.92
22_I	53_I	0.879	0.92
65_K	74_K	0.874	0.91
64_K	72_L	0.869	0.91
2_E	30_K	0.858	0.91
23_V	59_P	0.857	0.91
27_G	91_K	0.856	0.90
28_R	59_P	0.825	0.89
78_R	96_D	0.822	0.89
68_F	73_G	0.812	0.88
92_E	99_K	0.811	0.88
33_E	37_L	0.808	0.88
51_K	89_I	0.804	0.88
22_I	93_I	0.792	0.87
32_E	36_R	0.788	0.86
83_I	89_I	0.766	0.85
60_P	63_K	0.764	0.85
38_I	41_T	0.754	0.84
18_K	43_E	0.751	0.84
68_F	72_L	0.749	0.84
4_L	12_K	0.747	0.83
3_G	69_G	0.740	0.83
63_K	71_L	0.731	0.82
35_A	38_I	0.727	0.82
13_I	84_I	0.721	0.81
20_N	30_K	0.721	0.81
9_R	95_K	0.711	0.80
57_V	77_D	0.703	0.80
22_I	54_E	0.701	0.79
13_I	23_V	0.697	0.79
9_R	33_E	0.697	0.79
36_R	53_I	0.687	0.78
39_E	81_L	0.676	0.77
16_I	96_D	0.674	0.77
31_P	57_V	0.671	0.76
13_I	16_I	0.671	0.76
26_E	80_G	0.668	0.76
66_G	75_L	0.666	0.76
10_I	20_N	0.663	0.75
64_K	71_L	0.659	0.75
36_R	49_K	0.645	0.73
16_I	24_I	0.643	0.73
45_I	51_K	0.642	0.73
34_E	80_G	0.642	0.73
51_K	90_V	0.640	0.73
12_K	27_G	0.638	0.73
69_G	75_L	0.638	0.73
10_I	36_R	0.637	0.73
25_L	84_I	0.635	0.72
62_K	76_L	0.633	0.72
9_R	26_E	0.627	0.71
55_L	87_A	0.623	0.71
10_I	69_G	0.620	0.70
7_M	36_R	0.619	0.70
58_I	81_L	0.614	0.70
11_R	44_E	0.613	0.70
55_L	69_G	0.612	0.70
66_G	74_K	0.610	0.69
16_I	27_G	0.609	0.69
59_P	81_L	0.607	0.69
83_I	90_V	0.603	0.68
17_V	49_K	0.603	0.68
11_R	39_E	0.601	0.68
61_D	65_K	0.599	0.68
72_L	77_D	0.598	0.68
15_D	19_E	0.598	0.68
88_S	96_D	0.582	0.66
38_I	42_M	0.577	0.65
55_L	58_I	0.574	0.65
12_K	23_V	0.572	0.64
29_L	33_E	0.571	0.64
41_T	95_K	0.566	0.64
68_F	71_L	0.564	0.63
23_V	78_R	0.561	0.63
19_E	46_D	0.555	0.62
40_D	57_V	0.554	0.62
7_M	11_R	0.552	0.62
86_P	97_P	0.552	0.62
20_N	42_M	0.543	0.60
63_K	74_K	0.543	0.60
61_D	64_K	0.532	0.59
25_L	59_P	0.523	0.58
57_V	60_P	0.523	0.58
27_G	94_K	0.519	0.57
2_E	81_L	0.519	0.57
6_S	10_I	0.515	0.56
35_A	42_M	0.513	0.56
16_I	77_D	0.512	0.56
64_K	73_G	0.510	0.56
8_E	36_R	0.510	0.56
16_I	19_E	0.510	0.56
42_M	45_I	0.505	0.55
27_G	97_P	0.502	0.55
13_I	29_L	0.502	0.55
18_K	47_P	0.501	0.54
66_G	69_G	0.500	0.54

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
2r79A	5	0.6	7.5	0.931	Contact Map
1t7sA	3	0.781	7.2	0.931	Contact Map
3pshA	1	0.6952	6.7	0.932	Contact Map
1s99A	2	0.5333	6.5	0.932	Contact Map
4hn9A	1	0.6762	6.5	0.932	Contact Map
4mo9A	1	0.7619	6.4	0.933	Contact Map
4bjqA	2	0.4762	6.1	0.933	Contact Map
1i6zA	1	0.7714	5.7	0.934	Contact Map
4ljsA	1	0.5429	5.6	0.935	Contact Map
2l3uA	1	0.4857	4.9	0.936	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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