DUF2040 - PFAM28P - GREMLIN Contacts

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DUF2040 - Coiled-coil domain-containing protein 55 (DUF2040)

PFAM:	PF09745	Sequences: AKKQAEKALEEDPSVYDYDEVYDSMKAKKEEKKAAKKEDAKERKPKYIENLLKAAERRKREQERAEERKLQKEREAEGDEFADKEKFVTSAYKKKLEERRKWEEEEKRREEEEEKKDVTKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (118)
Sequences:	561 (417)
Seq/√Len:	38.4
META:	0.319

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_D	20_E	7.219	1.00
56_E	59_K	3.235	1.00
59_K	62_Q	2.748	1.00
105_E	109_R	2.640	1.00
26_K	29_K	2.593	1.00
70_L	86_K	2.507	1.00
108_R	112_E	2.468	1.00
101_K	105_E	2.145	0.99
74_R	78_G	2.115	0.99
104_E	108_R	2.111	0.99
107_K	111_E	2.093	0.99
21_V	25_M	2.027	0.99
90_S	94_K	2.022	0.99
103_E	107_K	1.951	0.98
61_E	68_R	1.870	0.98
108_R	111_E	1.861	0.98
6_E	10_E	1.810	0.98
94_K	97_E	1.718	0.97
53_K	56_E	1.647	0.96
50_N	53_K	1.574	0.94
111_E	115_K	1.562	0.94
64_R	103_E	1.557	0.94
48_I	85_E	1.464	0.92
5_A	16_Y	1.448	0.91
63_E	95_K	1.409	0.90
2_K	90_S	1.398	0.90
15_V	21_V	1.392	0.90
57_R	60_R	1.380	0.89
4_Q	16_Y	1.378	0.89
22_Y	25_M	1.337	0.88
56_E	60_R	1.324	0.87
112_E	116_K	1.313	0.87
97_E	101_K	1.301	0.86
60_R	99_R	1.300	0.86
78_G	82_A	1.271	0.85
8_A	16_Y	1.250	0.84
61_E	65_A	1.240	0.83
109_R	112_E	1.240	0.83
16_Y	48_I	1.238	0.83
100_R	103_E	1.233	0.83
81_F	84_K	1.231	0.83
9_L	16_Y	1.199	0.81
2_K	5_A	1.184	0.80
25_M	46_K	1.182	0.80
96_L	99_R	1.182	0.80
39_D	43_R	1.156	0.79
64_R	99_R	1.140	0.78
102_W	105_E	1.136	0.78
94_K	98_E	1.127	0.77
17_D	21_V	1.114	0.76
14_S	17_D	1.085	0.74
4_Q	10_E	1.065	0.73
109_R	113_E	1.062	0.73
110_E	114_E	1.045	0.71
101_K	104_E	1.041	0.71
68_R	72_K	1.036	0.71
106_E	109_R	1.032	0.70
104_E	107_K	1.005	0.68
2_K	6_E	1.001	0.68
29_K	53_K	0.985	0.67
7_K	11_E	0.979	0.66
5_A	9_L	0.940	0.63
51_L	88_V	0.939	0.63
63_E	99_R	0.921	0.62
97_E	100_R	0.913	0.61
106_E	110_E	0.906	0.60
55_A	59_K	0.904	0.60
16_Y	34_A	0.903	0.60
66_E	69_K	0.900	0.60
3_K	7_K	0.898	0.60
15_V	28_K	0.881	0.58
47_Y	58_R	0.871	0.57
100_R	104_E	0.870	0.57
46_K	67_E	0.857	0.56
9_L	15_V	0.856	0.56
13_P	88_V	0.851	0.55
57_R	110_E	0.848	0.55
95_K	99_R	0.845	0.55
46_K	59_K	0.839	0.54
115_K	118_V	0.833	0.54
64_R	102_W	0.825	0.53
67_E	85_E	0.825	0.53
95_K	101_K	0.812	0.52
74_R	77_E	0.812	0.52
21_V	27_A	0.795	0.50
115_K	119_T	0.791	0.50
3_K	6_E	0.786	0.50
88_V	91_A	0.766	0.48
9_L	96_L	0.763	0.48
34_A	112_E	0.762	0.47
66_E	70_L	0.759	0.47
12_D	23_D	0.755	0.47
110_E	113_E	0.755	0.47
78_G	102_W	0.751	0.47
48_I	51_L	0.750	0.46
58_R	87_F	0.747	0.46
3_K	52_L	0.742	0.46
54_A	63_E	0.741	0.46
15_V	23_D	0.739	0.45
4_Q	7_K	0.728	0.44
111_E	114_E	0.727	0.44
9_L	14_S	0.725	0.44
32_K	36_K	0.718	0.44
63_E	96_L	0.716	0.43
61_E	95_K	0.713	0.43
45_P	63_E	0.711	0.43
64_R	94_K	0.707	0.43
91_A	103_E	0.704	0.42
62_Q	66_E	0.692	0.41
15_V	94_K	0.690	0.41
97_E	108_R	0.689	0.41
61_E	116_K	0.688	0.41
65_A	95_K	0.683	0.41
71_Q	78_G	0.683	0.41
11_E	76_A	0.679	0.40
33_K	40_A	0.670	0.39
99_R	102_W	0.670	0.39
24_S	29_K	0.669	0.39
32_K	94_K	0.665	0.39
86_K	113_E	0.660	0.39
72_K	89_T	0.655	0.38
33_K	39_D	0.655	0.38
70_L	113_E	0.651	0.38
41_K	97_E	0.648	0.38
113_E	117_D	0.642	0.37
63_E	66_E	0.642	0.37
29_K	93_K	0.638	0.37
74_R	84_K	0.637	0.37
54_A	57_R	0.637	0.37
48_I	117_D	0.628	0.36
86_K	114_E	0.623	0.35
54_A	64_R	0.616	0.35
3_K	110_E	0.607	0.34
28_K	42_E	0.605	0.34
7_K	15_V	0.596	0.33
97_E	102_W	0.595	0.33
8_A	91_A	0.589	0.33
64_R	86_K	0.588	0.33
114_E	119_T	0.586	0.32
52_L	56_E	0.585	0.32
75_E	78_G	0.584	0.32
7_K	41_K	0.584	0.32
31_E	37_K	0.573	0.31
77_E	81_F	0.572	0.31
51_L	55_A	0.571	0.31
51_L	118_V	0.570	0.31
12_D	18_Y	0.569	0.31
34_A	38_E	0.568	0.31
12_D	75_E	0.568	0.31
67_E	96_L	0.567	0.31
48_I	96_L	0.565	0.31
16_Y	60_R	0.562	0.31
37_K	40_A	0.561	0.31
21_V	24_S	0.559	0.30
45_P	74_R	0.559	0.30
55_A	98_E	0.557	0.30
67_E	73_E	0.550	0.30
33_K	81_F	0.541	0.29
33_K	108_R	0.540	0.29
25_M	108_R	0.540	0.29
87_F	92_Y	0.538	0.29
50_N	62_Q	0.537	0.29
91_A	94_K	0.534	0.28
50_N	54_A	0.534	0.28
93_K	97_E	0.533	0.28
87_F	91_A	0.533	0.28
8_A	22_Y	0.533	0.28
2_K	29_K	0.529	0.28
9_L	12_D	0.527	0.28
48_I	74_R	0.525	0.28
6_E	49_E	0.524	0.28
79_D	82_A	0.524	0.28
2_K	33_K	0.514	0.27
7_K	21_V	0.511	0.27
5_A	85_E	0.503	0.26
16_Y	27_A	0.501	0.26
43_R	89_T	0.500	0.26

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
1ytzI	1	0.3306	3.8	0.936	Contact Map
2fh5A	3	0.2727	2.3	0.943	Contact Map
1j1eC	1	0.3306	2.2	0.943	Contact Map
1j1dC	1	0.3306	2.1	0.944	Contact Map
1obbA	2	0.3306	1.9	0.945	Contact Map
2j7nA	2	0.0909	1.7	0.947	Contact Map
1wj2A	1	0.2231	1.3	0.951	Contact Map
3plwA	1	0	0.9	0.954	Contact Map
3beeA	1	0.4298	0.9	0.955	Contact Map
3fvcA	3	0.3306	0.9	0.956	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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