DUF4494 - PFAM28P - GREMLIN Contacts

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DUF4494 - Domain of unknown function (DUF4494)

PFAM:	PF14902	Sequences: WFECKVKYEKTMENGKQKKVTEPYLVDALSFTEAEARIIEEMSPYISGEFEVTDIKRANYSEIFFSEDENGDRWYKAKVSFITLDEKSGKEKKTAVYMLVQASDLKEAYKNLEEGMKGTMADYEIASITETPIMDVFPY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	139 (138)
Sequences:	1942 (1230)
Seq/√Len:	104.7
META:	0.898

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
106_K	113_E	3.868	1.00
77_A	112_L	3.603	1.00
80_S	95_A	2.632	1.00
29_L	33_E	2.494	1.00
109_Y	128_I	2.482	1.00
4_C	38_I	2.370	1.00
59_N	97_Y	2.230	1.00
3_E	56_K	2.099	1.00
114_E	117_K	2.023	1.00
106_K	109_Y	1.999	1.00
64_F	115_G	1.976	1.00
60_Y	99_L	1.962	1.00
80_S	126_A	1.936	1.00
32_T	36_A	1.915	1.00
39_I	50_F	1.900	1.00
105_L	109_Y	1.900	1.00
106_K	110_K	1.891	1.00
65_F	74_W	1.869	1.00
46_I	50_F	1.815	1.00
79_V	98_M	1.813	1.00
11_T	17_Q	1.811	1.00
77_A	128_I	1.804	1.00
7_K	21_T	1.776	1.00
76_K	97_Y	1.630	1.00
31_F	55_I	1.622	1.00
76_K	129_T	1.601	1.00
40_E	43_S	1.590	1.00
78_K	95_A	1.557	1.00
9_E	17_Q	1.553	1.00
73_R	130_E	1.551	1.00
107_E	111_N	1.530	1.00
26_V	38_I	1.521	1.00
124_E	130_E	1.521	1.00
66_S	111_N	1.497	1.00
53_T	57_R	1.496	1.00
102_A	107_E	1.461	1.00
9_E	19_K	1.443	1.00
5_K	54_D	1.425	1.00
84_L	89_G	1.420	1.00
12_M	16_K	1.420	1.00
12_M	18_K	1.416	1.00
109_Y	125_I	1.411	1.00
93_K	124_E	1.393	1.00
72_D	103_S	1.346	0.99
51_E	57_R	1.325	0.99
82_I	91_E	1.282	0.99
39_I	43_S	1.271	0.99
31_F	57_R	1.264	0.99
66_S	71_G	1.259	0.99
100_V	111_N	1.253	0.99
4_C	55_I	1.244	0.99
65_F	101_Q	1.236	0.99
28_A	34_A	1.229	0.99
103_S	107_E	1.219	0.99
41_E	137_F	1.213	0.99
65_F	138_P	1.209	0.99
36_A	40_E	1.193	0.99
68_D	71_G	1.183	0.99
10_K	22_E	1.153	0.98
71_G	107_E	1.146	0.98
1_W	4_C	1.144	0.98
79_V	116_M	1.141	0.98
7_K	19_K	1.138	0.98
3_E	23_P	1.109	0.98
115_G	118_G	1.091	0.98
1_W	136_V	1.085	0.98
100_V	112_L	1.078	0.97
67_E	70_N	1.074	0.97
118_G	122_D	1.062	0.97
78_K	97_Y	1.048	0.97
110_K	113_E	1.047	0.97
109_Y	113_E	1.025	0.97
105_L	128_I	1.014	0.96
12_M	17_Q	1.014	0.96
23_P	132_P	0.999	0.96
5_K	23_P	0.998	0.96
107_E	110_K	0.986	0.96
80_S	93_K	0.983	0.96
63_I	99_L	0.980	0.96
52_V	55_I	0.975	0.95
112_L	116_M	0.962	0.95
36_A	39_I	0.955	0.95
74_W	99_L	0.947	0.95
54_D	57_R	0.940	0.94
113_E	123_Y	0.938	0.94
75_Y	103_S	0.930	0.94
85_D	88_S	0.929	0.94
95_A	126_A	0.923	0.94
61_S	96_V	0.921	0.94
126_A	130_E	0.915	0.94
119_T	122_D	0.910	0.93
126_A	132_P	0.904	0.93
83_T	94_T	0.892	0.93
3_E	58_A	0.890	0.93
81_F	94_T	0.875	0.92
71_G	101_Q	0.874	0.92
42_M	46_I	0.865	0.92
105_L	125_I	0.859	0.91
6_V	42_M	0.816	0.89
65_F	136_V	0.814	0.89
31_F	52_V	0.801	0.88
99_L	133_I	0.797	0.88
27_D	33_E	0.793	0.88
38_I	42_M	0.792	0.87
109_Y	126_A	0.788	0.87
74_W	101_Q	0.783	0.87
41_E	44_P	0.782	0.87
102_A	111_N	0.781	0.87
31_F	54_D	0.764	0.86
79_V	112_L	0.758	0.85
81_F	96_V	0.753	0.85
6_V	46_I	0.748	0.84
22_E	134_M	0.747	0.84
23_P	133_I	0.747	0.84
98_M	112_L	0.740	0.84
31_F	35_E	0.731	0.83
2_F	57_R	0.726	0.83
117_K	121_A	0.721	0.82
60_Y	63_I	0.721	0.82
5_K	21_T	0.700	0.80
98_M	115_G	0.700	0.80
19_K	51_E	0.691	0.79
75_Y	133_I	0.690	0.79
27_D	37_R	0.689	0.79
102_A	108_A	0.685	0.79
63_I	104_D	0.685	0.79
8_Y	46_I	0.684	0.79
4_C	26_V	0.682	0.78
6_V	38_I	0.681	0.78
82_I	122_D	0.679	0.78
8_Y	22_E	0.679	0.78
38_I	52_V	0.667	0.77
110_K	114_E	0.666	0.77
9_E	12_M	0.665	0.77
71_G	103_S	0.662	0.76
42_M	137_F	0.655	0.76
16_K	43_S	0.653	0.75
7_K	74_W	0.652	0.75
111_N	115_G	0.649	0.75
33_E	37_R	0.648	0.75
31_F	56_K	0.648	0.75
4_C	34_A	0.644	0.74
125_I	128_I	0.643	0.74
107_E	113_E	0.642	0.74
58_A	76_K	0.641	0.74
27_D	30_S	0.639	0.74
14_N	18_K	0.639	0.74
109_Y	132_P	0.637	0.74
116_M	119_T	0.635	0.73
111_N	114_E	0.628	0.73
7_K	53_T	0.624	0.72
93_K	126_A	0.620	0.72
57_R	109_Y	0.619	0.71
51_E	54_D	0.619	0.71
73_R	103_S	0.613	0.71
41_E	75_Y	0.612	0.71
25_L	98_M	0.609	0.70
77_A	100_V	0.605	0.70
5_K	132_P	0.605	0.70
68_D	111_N	0.600	0.69
67_E	71_G	0.595	0.68
12_M	15_G	0.595	0.68
101_Q	135_D	0.591	0.68
119_T	123_Y	0.590	0.68
1_W	27_D	0.588	0.68
113_E	125_I	0.585	0.67
78_K	126_A	0.580	0.67
46_I	49_E	0.580	0.67
66_S	101_Q	0.579	0.66
72_D	101_Q	0.576	0.66
77_A	105_L	0.574	0.66
70_N	103_S	0.569	0.65
73_R	124_E	0.565	0.65
43_S	47_S	0.565	0.65
11_T	16_K	0.564	0.64
3_E	73_R	0.564	0.64
112_L	115_G	0.559	0.64
30_S	36_A	0.558	0.64
2_F	31_F	0.551	0.63
83_T	86_E	0.548	0.62
66_S	103_S	0.547	0.62
90_K	114_E	0.540	0.61
97_Y	126_A	0.540	0.61
29_L	36_A	0.537	0.61
4_C	42_M	0.536	0.60
6_V	48_G	0.536	0.60
44_P	61_S	0.533	0.60
25_L	63_I	0.533	0.60
115_G	120_M	0.531	0.60
24_Y	135_D	0.531	0.60
32_T	55_I	0.529	0.60
42_M	45_Y	0.528	0.59
116_M	122_D	0.525	0.59
29_L	37_R	0.521	0.58
2_F	54_D	0.520	0.58
98_M	116_M	0.520	0.58
89_G	94_T	0.519	0.58
2_F	6_V	0.519	0.58
48_G	52_V	0.508	0.56
80_S	129_T	0.507	0.56
10_K	20_V	0.506	0.56
34_A	55_I	0.504	0.56
62_E	84_L	0.501	0.55
27_D	91_E	0.501	0.55
38_I	50_F	0.501	0.55
29_L	120_M	0.500	0.55
58_A	61_S	0.500	0.55

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
2ieqA	3	0.2878	3.3	0.941	Contact Map
2pjpA	1	0.705	2.5	0.945	Contact Map
2mamA	1	0.2878	2.4	0.945	Contact Map
2g3rA	2	0.6906	1.9	0.948	Contact Map
1cvrA	1	0.3885	1.8	0.949	Contact Map
1wdgA	3	0.259	1.7	0.95	Contact Map
2k0mA	1	0.3669	1.6	0.951	Contact Map
4lh9A	4	0.2878	1.5	0.951	Contact Map
1yobA	1	0.3381	1.5	0.951	Contact Map
2cozA	1	0.2878	1.4	0.952	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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