DUF2240 - PFAM28P - GREMLIN Contacts

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DUF2240 - Uncharacterized protein conserved in archaea (DUF2240)

PFAM:	PF09999	Sequences: SLRIAVAAPFKRKGKDRLSESEFVVALSLDLKWFSPDQAKRLLDVALEEGLLEREGGDLRPTFDPSEVEIPLGFKPSESILEEEDLFERLLDRIAAKTGLEKQEVVAEINRKQEELGGLVTIEAAALLVAREQGVDVSDLADEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	144 (141)
Sequences:	1060 (727)
Seq/√Len:	61.2
META:	0.876

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
93_R	139_D	3.349	1.00
43_L	59_L	3.331	1.00
85_D	88_E	3.088	1.00
64_D	67_E	3.069	1.00
109_I	126_A	2.805	1.00
112_K	132_E	2.724	1.00
108_E	132_E	2.642	1.00
20_E	54_R	2.622	1.00
101_E	104_E	2.491	1.00
93_R	140_L	2.381	1.00
53_E	62_T	2.272	1.00
17_R	58_D	2.140	1.00
120_V	125_A	2.121	1.00
106_V	110_N	2.077	1.00
6_V	46_A	2.048	1.00
110_N	113_Q	2.036	1.00
17_R	60_R	2.035	1.00
49_E	84_E	2.024	1.00
89_R	143_E	1.969	1.00
35_S	38_Q	1.922	1.00
91_L	106_V	1.892	1.00
23_F	43_L	1.854	1.00
8_A	12_R	1.810	1.00
34_F	39_A	1.765	0.99
45_V	48_E	1.703	0.99
7_A	10_F	1.666	0.99
107_A	110_N	1.625	0.99
87_F	110_N	1.583	0.99
47_L	59_L	1.576	0.99
98_T	105_V	1.570	0.99
26_A	30_D	1.569	0.99
100_L	104_E	1.568	0.99
130_A	137_V	1.535	0.98
4_I	73_G	1.514	0.98
30_D	33_W	1.506	0.98
33_W	76_P	1.502	0.98
61_P	65_P	1.446	0.98
18_L	61_P	1.400	0.97
116_L	120_V	1.382	0.97
91_L	105_V	1.311	0.96
90_L	94_I	1.310	0.96
102_K	106_V	1.260	0.95
30_D	76_P	1.253	0.95
46_A	74_F	1.227	0.94
113_Q	122_I	1.214	0.94
6_V	9_P	1.209	0.94
30_D	110_N	1.206	0.94
87_F	122_I	1.176	0.93
16_D	60_R	1.169	0.92
45_V	49_E	1.155	0.92
25_V	29_L	1.138	0.91
54_R	57_G	1.119	0.91
6_V	39_A	1.109	0.90
86_L	89_R	1.109	0.90
129_V	133_Q	1.099	0.90
47_L	52_L	1.088	0.89
5_A	27_L	1.085	0.89
15_K	61_P	1.065	0.88
27_L	42_L	1.060	0.88
95_A	105_V	1.040	0.87
5_A	13_K	1.037	0.87
23_F	79_S	1.030	0.87
52_L	109_I	1.030	0.87
105_V	130_A	1.029	0.87
42_L	45_V	1.025	0.86
108_E	111_R	1.023	0.86
5_A	42_L	1.021	0.86
53_E	95_A	1.009	0.86
86_L	131_R	1.007	0.85
14_G	40_K	0.992	0.85
103_Q	106_V	0.974	0.84
48_E	85_D	0.965	0.83
10_F	76_P	0.933	0.81
35_S	125_A	0.926	0.80
91_L	126_A	0.922	0.80
12_R	26_A	0.921	0.80
84_E	92_D	0.920	0.80
5_A	9_P	0.917	0.80
46_A	52_L	0.915	0.79
94_I	130_A	0.912	0.79
34_F	76_P	0.906	0.79
46_A	51_L	0.904	0.79
94_I	98_T	0.898	0.78
85_D	91_L	0.890	0.78
96_A	111_R	0.889	0.77
32_K	92_D	0.881	0.77
9_P	23_F	0.869	0.76
3_R	49_E	0.858	0.75
123_E	126_A	0.857	0.75
102_K	110_N	0.843	0.74
120_V	124_A	0.838	0.73
120_V	133_Q	0.832	0.73
32_K	74_F	0.825	0.72
34_F	109_I	0.811	0.71
119_L	126_A	0.792	0.69
52_L	69_E	0.792	0.69
20_E	40_K	0.790	0.69
8_A	13_K	0.790	0.69
67_E	79_S	0.784	0.68
128_L	140_L	0.778	0.68
68_V	96_A	0.775	0.67
18_L	47_L	0.775	0.67
38_Q	46_A	0.771	0.67
124_A	127_L	0.768	0.67
51_L	63_F	0.765	0.66
4_I	8_A	0.765	0.66
2_L	45_V	0.764	0.66
27_L	115_E	0.756	0.65
13_K	23_F	0.756	0.65
29_L	76_P	0.755	0.65
13_K	19_S	0.753	0.65
52_L	99_G	0.749	0.65
92_D	95_A	0.745	0.64
28_S	36_P	0.743	0.64
4_I	15_K	0.740	0.64
140_L	143_E	0.739	0.64
75_K	114_E	0.739	0.64
138_S	142_D	0.738	0.63
112_K	129_V	0.737	0.63
52_L	108_E	0.734	0.63
25_V	30_D	0.724	0.62
108_E	112_K	0.724	0.62
8_A	34_F	0.722	0.62
24_V	35_S	0.717	0.61
99_G	115_E	0.715	0.61
29_L	35_S	0.712	0.61
19_S	58_D	0.710	0.60
36_P	103_Q	0.703	0.60
97_K	120_V	0.701	0.59
94_I	100_L	0.697	0.59
87_F	92_D	0.694	0.59
116_L	122_I	0.691	0.58
90_L	127_L	0.688	0.58
94_I	105_V	0.686	0.58
77_S	80_I	0.680	0.57
43_L	75_K	0.679	0.57
31_L	59_L	0.677	0.57
21_S	49_E	0.676	0.57
44_D	91_L	0.675	0.57
37_D	65_P	0.674	0.56
108_E	129_V	0.671	0.56
52_L	59_L	0.670	0.56
24_V	39_A	0.668	0.56
54_R	89_R	0.667	0.56
28_S	136_D	0.666	0.56
109_I	129_V	0.663	0.55
9_P	27_L	0.658	0.55
67_E	73_G	0.653	0.54
53_E	60_R	0.653	0.54
55_E	60_R	0.649	0.54
67_E	142_D	0.647	0.53
82_E	86_L	0.647	0.53
112_K	115_E	0.647	0.53
64_D	89_R	0.647	0.53
135_V	139_D	0.645	0.53
64_D	110_N	0.643	0.53
18_L	23_F	0.640	0.53
79_S	128_L	0.638	0.52
26_A	137_V	0.638	0.52
49_E	105_V	0.632	0.52
19_S	79_S	0.631	0.52
29_L	36_P	0.629	0.51
19_S	97_K	0.629	0.51
13_K	30_D	0.627	0.51
67_E	96_A	0.625	0.51
5_A	11_K	0.625	0.51
90_L	126_A	0.625	0.51
35_S	94_I	0.621	0.50
52_L	62_T	0.620	0.50
113_Q	116_L	0.611	0.49
33_W	131_R	0.607	0.49
50_G	99_G	0.605	0.49
10_F	33_W	0.599	0.48
74_F	77_S	0.597	0.48
34_F	40_K	0.595	0.48
101_E	138_S	0.592	0.47
15_K	18_L	0.592	0.47
32_K	75_K	0.589	0.47
70_I	105_V	0.585	0.46
43_L	52_L	0.585	0.46
4_I	16_D	0.585	0.46
7_A	11_K	0.580	0.46
8_A	21_S	0.580	0.46
107_A	111_R	0.580	0.46
6_V	51_L	0.571	0.45
6_V	23_F	0.565	0.44
56_G	97_K	0.564	0.44
20_E	57_G	0.564	0.44
43_L	103_Q	0.559	0.43
9_P	18_L	0.559	0.43
98_T	129_V	0.555	0.43
26_A	29_L	0.555	0.43
20_E	24_V	0.553	0.43
103_Q	122_I	0.547	0.42
108_E	133_Q	0.546	0.42
63_F	68_V	0.546	0.42
39_A	45_V	0.544	0.42
55_E	58_D	0.540	0.41
131_R	136_D	0.540	0.41
50_G	120_V	0.540	0.41
17_R	55_E	0.539	0.41
111_R	114_E	0.539	0.41
112_K	125_A	0.536	0.41
91_L	102_K	0.532	0.41
19_S	66_S	0.531	0.40
34_F	43_L	0.525	0.40
98_T	135_V	0.512	0.38
13_K	61_P	0.511	0.38
87_F	95_A	0.507	0.38
3_R	8_A	0.504	0.37
51_L	74_F	0.500	0.37
58_D	142_D	0.500	0.37

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
1lvaA	1	0.9444	75.5	0.901	Contact Map
1okrA	2	0.7361	34	0.924	Contact Map
3lmmA	1	0.4167	29.6	0.926	Contact Map
3sy8A	6	0.9444	24.8	0.929	Contact Map
2k4bA	1	0.4097	24.2	0.929	Contact Map
2adlA	2	0.2153	22.3	0.931	Contact Map
4gtnA	2	0.4306	22.2	0.931	Contact Map
4wd9A	2	0.9167	21.8	0.931	Contact Map
3ulqB	1	0.4028	18.7	0.933	Contact Map
1sd4A	2	0.7222	17.3	0.934	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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