DUF1077 - PFAM28P - GREMLIN Contacts

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DUF1077 - Protein of unknown function (DUF1077)

PFAM:	PF06417	Sequences: KKEEMDALKLKKAWEIALAPAKQLPMNAFMMYMSGNSLQIFSIMMVFMLLKNPIKALLSVNQAFARFEGEGNRSDLLLQKLVYVLCNLLALALGLYKCNSMGLLPTTASDWLAFETP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	117 (113)
Sequences:	515 (359)
Seq/√Len:	33.8
META:	0.369

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_K	15_E	4.212	1.00
29_F	33_M	3.324	1.00
81_L	85_L	3.211	1.00
27_N	49_L	2.791	1.00
96_Y	99_N	2.721	1.00
106_T	109_S	2.441	1.00
24_L	90_A	2.414	0.99
82_V	85_L	2.314	0.99
61_N	80_K	2.199	0.99
34_S	48_M	2.119	0.99
16_I	67_F	2.065	0.98
49_L	90_A	2.018	0.98
108_A	115_E	1.998	0.98
14_W	79_Q	1.991	0.98
59_S	83_Y	1.898	0.97
63_A	83_Y	1.831	0.97
14_W	82_V	1.795	0.96
88_L	92_A	1.717	0.95
36_N	100_S	1.612	0.93
32_Y	38_L	1.602	0.93
36_N	45_M	1.540	0.91
32_Y	40_I	1.538	0.91
93_L	97_K	1.501	0.90
64_F	80_K	1.489	0.90
104_L	109_S	1.455	0.89
96_Y	100_S	1.453	0.89
27_N	90_A	1.453	0.89
57_L	84_V	1.428	0.88
4_E	7_A	1.425	0.88
85_L	92_A	1.410	0.87
105_P	110_D	1.391	0.86
52_N	55_K	1.387	0.86
31_M	41_F	1.384	0.86
39_Q	87_N	1.364	0.85
30_M	87_N	1.318	0.83
41_F	104_L	1.312	0.83
69_G	72_N	1.295	0.82
56_A	87_N	1.288	0.82
25_P	86_C	1.226	0.78
76_L	80_K	1.218	0.78
86_C	89_L	1.208	0.77
44_M	48_M	1.207	0.77
95_L	98_C	1.196	0.77
94_G	97_K	1.187	0.76
18_L	22_K	1.156	0.74
15_E	77_L	1.155	0.74
57_L	62_Q	1.128	0.72
42_S	48_M	1.125	0.72
8_L	102_G	1.119	0.72
106_T	113_A	1.114	0.71
48_M	53_P	1.102	0.70
87_N	90_A	1.100	0.70
8_L	11_K	1.072	0.68
48_M	52_N	1.061	0.67
57_L	60_V	1.044	0.66
107_T	115_E	1.040	0.66
25_P	49_L	1.014	0.64
38_L	98_C	1.012	0.64
59_S	62_Q	0.999	0.63
16_I	19_A	0.995	0.62
3_E	81_L	0.988	0.62
60_V	84_V	0.983	0.61
39_Q	45_M	0.982	0.61
72_N	76_L	0.970	0.60
46_V	55_K	0.955	0.59
17_A	26_M	0.947	0.59
48_M	94_G	0.946	0.58
62_Q	71_G	0.939	0.58
66_R	82_V	0.937	0.58
31_M	57_L	0.926	0.57
38_L	94_G	0.885	0.53
40_I	62_Q	0.876	0.53
44_M	94_G	0.871	0.52
32_Y	63_A	0.863	0.52
47_F	104_L	0.860	0.51
49_L	53_P	0.857	0.51
43_I	47_F	0.847	0.50
42_S	65_A	0.845	0.50
54_I	58_L	0.845	0.50
46_V	91_L	0.821	0.48
10_L	16_I	0.818	0.48
13_A	79_Q	0.817	0.48
11_K	15_E	0.816	0.48
17_A	109_S	0.773	0.44
55_K	62_Q	0.770	0.44
62_Q	65_A	0.767	0.43
53_P	94_G	0.763	0.43
17_A	20_P	0.756	0.43
28_A	93_L	0.751	0.42
12_K	69_G	0.747	0.42
91_L	104_L	0.745	0.42
54_I	68_E	0.745	0.42
20_P	48_M	0.728	0.40
10_L	58_L	0.719	0.40
66_R	86_C	0.716	0.39
72_N	83_Y	0.716	0.39
23_Q	102_G	0.714	0.39
77_L	88_L	0.706	0.38
32_Y	96_Y	0.703	0.38
14_W	25_P	0.702	0.38
25_P	48_M	0.702	0.38
102_G	105_P	0.699	0.38
51_K	54_I	0.696	0.38
5_M	9_K	0.696	0.38
52_N	56_A	0.693	0.37
8_L	12_K	0.689	0.37
97_K	111_W	0.686	0.37
51_K	55_K	0.682	0.37
76_L	79_Q	0.669	0.36
49_L	56_A	0.668	0.35
16_I	63_A	0.663	0.35
34_S	39_Q	0.663	0.35
37_S	95_L	0.656	0.35
14_W	20_P	0.647	0.34
27_N	52_N	0.644	0.34
36_N	98_C	0.641	0.33
41_F	106_T	0.634	0.33
24_L	27_N	0.629	0.33
77_L	85_L	0.618	0.32
19_A	24_L	0.615	0.32
23_Q	89_L	0.612	0.31
30_M	42_S	0.604	0.31
27_N	55_K	0.602	0.31
47_F	65_A	0.600	0.30
9_K	70_E	0.599	0.30
68_E	73_R	0.594	0.30
39_Q	46_V	0.593	0.30
38_L	43_I	0.591	0.30
54_I	73_R	0.591	0.30
24_L	93_L	0.583	0.29
59_S	113_A	0.576	0.29
59_S	63_A	0.575	0.29
19_A	22_K	0.573	0.29
3_E	95_L	0.571	0.28
73_R	88_L	0.565	0.28
67_F	72_N	0.565	0.28
24_L	89_L	0.563	0.28
33_M	85_L	0.562	0.28
93_L	98_C	0.559	0.28
13_A	34_S	0.558	0.28
41_F	98_C	0.556	0.27
101_M	111_W	0.555	0.27
67_F	84_V	0.554	0.27
101_M	105_P	0.554	0.27
15_E	22_K	0.552	0.27
25_P	28_A	0.551	0.27
13_A	84_V	0.548	0.27
20_P	32_Y	0.538	0.26
39_Q	49_L	0.533	0.26
41_F	76_L	0.533	0.26
60_V	80_K	0.532	0.26
23_Q	76_L	0.531	0.26
55_K	59_S	0.530	0.26
62_Q	83_Y	0.527	0.25
27_N	40_I	0.526	0.25
49_L	93_L	0.522	0.25
45_M	56_A	0.521	0.25
61_N	84_V	0.518	0.25
18_L	82_V	0.518	0.25
57_L	80_K	0.515	0.25
40_I	112_L	0.510	0.24
56_A	63_A	0.510	0.24
28_A	100_S	0.510	0.24
59_S	96_Y	0.508	0.24
3_E	24_L	0.507	0.24
22_K	25_P	0.504	0.24
21_A	36_N	0.502	0.24
54_I	83_Y	0.501	0.24
25_P	39_Q	0.501	0.24
81_L	84_V	0.500	0.24

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
3j27B	2	0.4188	8.1	0.94	Contact Map
4b03D	5	0.4615	7.8	0.941	Contact Map
3w9iA	3	1	5.8	0.944	Contact Map
1ll2A	2	0	5.3	0.945	Contact Map
4cbfB	2	0.4359	5	0.946	Contact Map
4cctD	2	0.4359	5	0.946	Contact Map
3b8cA	1	0.9402	3.3	0.95	Contact Map
4mt1A	3	0.9573	3	0.952	Contact Map
4dx5A	3	1	3	0.952	Contact Map
2ixsA	1	0.7094	2.8	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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