DUF3868 - PFAM28P - GREMLIN Contacts

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DUF3868 - Domain of unknown function, B. Theta Gene description (DUF3868)

PFAM:	PF12984	Sequences: RKIYFILLLLLLLCLSIGAAQAQTSYKGQISVENVSVERQGDSLYVDMDIDLSGLKVKSNRSLTLTPVLVSGDGSLELPPVVINGRNRYKAYERNLALNGKKEKASYEKP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	110 (95)
Sequences:	874 (760)
Seq/√Len:	77.9
META:	0.833

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_V	78_L	4.608	1.00
84_N	89_Y	4.485	1.00
84_N	92_Y	3.473	1.00
50_I	81_V	3.206	1.00
60_N	87_N	2.964	1.00
62_S	84_N	2.925	1.00
20_A	23_Q	2.400	1.00
34_N	49_D	2.382	1.00
32_V	48_M	1.909	1.00
32_V	50_I	1.853	1.00
62_S	92_Y	1.841	1.00
86_R	90_K	1.775	1.00
13_L	16_S	1.768	1.00
64_T	82_V	1.765	1.00
90_K	93_E	1.708	1.00
6_I	9_L	1.685	1.00
62_S	66_T	1.531	0.99
45_Y	57_V	1.475	0.99
69_L	78_L	1.389	0.99
62_S	82_V	1.386	0.99
89_Y	93_E	1.385	0.99
8_L	12_L	1.258	0.97
59_S	86_R	1.256	0.97
82_V	92_Y	1.205	0.97
7_L	16_S	1.201	0.97
58_K	61_R	1.193	0.97
87_N	90_K	1.190	0.96
52_L	83_I	1.185	0.96
88_R	91_A	1.164	0.96
48_M	92_Y	1.163	0.96
10_L	16_S	1.148	0.96
65_L	81_V	1.140	0.96
46_V	69_L	1.120	0.95
50_I	65_L	1.099	0.95
90_K	98_L	1.093	0.94
91_A	95_N	1.090	0.94
71_S	75_S	1.079	0.94
92_Y	95_N	1.048	0.93
52_L	81_V	1.042	0.93
73_D	76_L	1.041	0.93
19_A	23_Q	1.027	0.92
16_S	21_Q	1.006	0.91
14_C	54_G	0.993	0.91
36_S	68_V	0.988	0.91
44_L	62_S	0.979	0.90
30_I	51_D	0.978	0.90
37_V	40_Q	0.965	0.90
26_Y	29_Q	0.965	0.90
68_V	75_S	0.952	0.89
51_D	55_L	0.941	0.88
9_L	81_V	0.941	0.88
44_L	48_M	0.931	0.88
44_L	69_L	0.924	0.88
8_L	15_L	0.909	0.87
62_S	88_R	0.906	0.87
89_Y	92_Y	0.900	0.86
90_K	95_N	0.899	0.86
6_I	14_C	0.890	0.86
53_S	83_I	0.868	0.84
32_V	99_N	0.852	0.83
9_L	27_K	0.845	0.82
41_G	82_V	0.842	0.82
25_S	30_I	0.842	0.82
7_L	13_L	0.841	0.82
35_V	62_S	0.839	0.82
51_D	93_E	0.828	0.81
52_L	55_L	0.826	0.81
5_F	8_L	0.825	0.81
33_E	51_D	0.815	0.80
93_E	97_A	0.790	0.78
59_S	72_G	0.781	0.77
70_V	77_E	0.769	0.76
7_L	63_L	0.765	0.76
8_L	16_S	0.756	0.75
59_S	87_N	0.747	0.74
44_L	79_P	0.745	0.74
44_L	70_V	0.740	0.73
52_L	91_A	0.739	0.73
40_Q	45_Y	0.737	0.73
12_L	19_A	0.736	0.73
14_C	29_Q	0.733	0.73
53_S	88_R	0.729	0.72
26_Y	58_K	0.724	0.72
28_G	54_G	0.721	0.71
84_N	88_R	0.713	0.71
44_L	65_L	0.713	0.71
19_A	69_L	0.710	0.70
61_R	93_E	0.709	0.70
39_R	60_N	0.700	0.69
36_S	83_I	0.687	0.68
12_L	21_Q	0.686	0.68
28_G	64_T	0.680	0.67
49_D	77_E	0.680	0.67
15_L	20_A	0.675	0.66
52_L	62_S	0.672	0.66
33_E	40_Q	0.671	0.66
40_Q	43_S	0.667	0.65
82_V	90_K	0.666	0.65
14_C	19_A	0.663	0.65
73_D	90_K	0.643	0.63
7_L	15_L	0.643	0.63
9_L	14_C	0.637	0.62
32_V	65_L	0.636	0.62
5_F	15_L	0.635	0.62
19_A	22_A	0.629	0.61
6_I	16_S	0.628	0.61
87_N	91_A	0.623	0.60
66_T	80_P	0.615	0.59
60_N	91_A	0.614	0.59
67_P	78_L	0.612	0.59
34_N	98_L	0.605	0.58
18_G	22_A	0.602	0.58
92_Y	96_L	0.598	0.57
80_P	93_E	0.597	0.57
13_L	72_G	0.592	0.56
31_S	39_R	0.589	0.56
6_I	12_L	0.576	0.54
63_L	84_N	0.575	0.54
70_V	74_G	0.575	0.54
20_A	71_S	0.572	0.54
72_G	76_L	0.572	0.54
11_L	21_Q	0.566	0.53
35_V	90_K	0.561	0.52
51_D	97_A	0.557	0.52
43_S	73_D	0.557	0.52
73_D	83_I	0.556	0.52
39_R	89_Y	0.554	0.51
15_L	18_G	0.551	0.51
70_V	75_S	0.534	0.49
35_V	48_M	0.532	0.49
9_L	21_Q	0.531	0.49
86_R	89_Y	0.530	0.48
18_G	58_K	0.528	0.48
66_T	99_N	0.527	0.48
24_T	81_V	0.523	0.47
11_L	54_G	0.521	0.47
51_D	86_R	0.519	0.47
37_V	60_N	0.516	0.47
32_V	38_E	0.512	0.46
35_V	57_V	0.505	0.45
71_S	93_E	0.504	0.45
47_D	91_A	0.500	0.45

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
2w9xA	2	0.7091	19.6	0.89	Contact Map
4uu4A	1	0.7182	19.3	0.891	Contact Map
3zbiC	1	0.2545	9.7	0.904	Contact Map
4ncdA	2	0.6818	7.8	0.908	Contact Map
1y0gA	2	0.6545	7.7	0.908	Contact Map
1dbgA	1	0.6636	7.2	0.909	Contact Map
2qn4A	1	0.5818	7	0.91	Contact Map
2c0nA	2	0.4273	6.8	0.911	Contact Map
3j46n	1	0.7818	5.4	0.915	Contact Map
1kmoA	1	0.2818	5.3	0.915	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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