DUF2452 - PFAM28P - GREMLIN Contacts

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DUF2452 - Protein of unknown function (DUF2452)

PFAM:	PF10504	Sequences: VALVERNPNPQGPANVSPYPTSRLGPKFDLVDVAKQIDIADNVARAHAQQKLDVIAEQIRVLQEQAREILERAERDDALHHAECNFQKVPGQIYHLYRRRDGQTYFSMLSPDEWGTGPPHEYLGSYRLEGDMSWTEVDEIEKRDAERALVDKLLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	155 (126)
Sequences:	534 (324)
Seq/√Len:	28.9
META:	0.762

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
95_H	125_S	4.637	1.00
57_E	64_E	3.349	1.00
124_G	128_L	2.940	1.00
29_D	38_D	2.839	1.00
126_Y	129_E	2.796	1.00
57_E	65_Q	2.729	1.00
83_E	103_Q	2.628	1.00
31_V	41_D	2.509	0.99
124_G	129_E	2.331	0.99
63_Q	67_R	2.063	0.97
20_P	24_L	2.059	0.97
49_Q	53_D	2.012	0.97
97_Y	100_R	1.962	0.96
72_R	76_D	1.938	0.96
48_A	73_A	1.934	0.96
109_L	113_E	1.919	0.96
43_V	46_A	1.858	0.95
80_H	88_K	1.843	0.95
19_Y	22_S	1.746	0.93
43_V	47_H	1.745	0.93
53_D	57_E	1.682	0.92
59_I	63_Q	1.666	0.91
96_L	106_F	1.663	0.91
105_Y	109_L	1.618	0.90
32_D	35_K	1.562	0.88
47_H	50_Q	1.552	0.88
129_E	135_T	1.551	0.88
92_Q	108_M	1.546	0.88
64_E	68_E	1.538	0.87
123_L	126_Y	1.505	0.86
89_V	92_Q	1.495	0.86
51_K	72_R	1.494	0.86
98_R	121_E	1.486	0.85
65_Q	68_E	1.476	0.85
124_G	127_R	1.461	0.84
17_S	20_P	1.460	0.84
87_Q	134_W	1.418	0.83
24_L	50_Q	1.412	0.82
32_D	37_I	1.398	0.82
82_A	104_T	1.305	0.77
30_L	34_A	1.276	0.75
97_Y	107_S	1.261	0.74
19_Y	23_R	1.247	0.74
125_S	129_E	1.237	0.73
123_L	127_R	1.225	0.72
18_P	22_S	1.222	0.72
97_Y	102_G	1.209	0.71
71_E	75_R	1.205	0.71
34_A	41_D	1.183	0.70
74_E	78_A	1.179	0.69
14_A	21_T	1.172	0.69
125_S	128_L	1.137	0.66
41_D	81_H	1.102	0.64
98_R	123_L	1.061	0.61
98_R	101_D	1.059	0.61
93_I	137_V	1.054	0.60
36_Q	39_I	1.048	0.60
31_V	34_A	1.036	0.59
86_F	108_M	1.021	0.58
85_N	103_Q	1.016	0.58
46_A	69_I	1.004	0.57
71_E	74_E	1.003	0.57
105_Y	120_H	0.996	0.56
123_L	129_E	0.996	0.56
22_S	26_P	0.996	0.56
20_P	23_R	0.985	0.55
83_E	99_R	0.977	0.55
82_A	96_L	0.975	0.54
109_L	120_H	0.974	0.54
80_H	114_W	0.964	0.54
89_V	104_T	0.939	0.52
119_P	132_M	0.929	0.51
76_D	133_S	0.908	0.49
47_H	90_P	0.895	0.48
107_S	113_E	0.887	0.48
43_V	90_P	0.873	0.46
60_R	67_R	0.862	0.46
98_R	104_T	0.852	0.45
97_Y	103_Q	0.833	0.43
21_T	33_V	0.831	0.43
60_R	69_I	0.830	0.43
20_P	28_F	0.829	0.43
69_I	74_E	0.825	0.43
31_V	80_H	0.803	0.41
14_A	112_D	0.801	0.41
20_P	34_A	0.799	0.41
19_Y	24_L	0.797	0.41
59_I	77_D	0.791	0.40
108_M	134_W	0.788	0.40
88_K	134_W	0.787	0.40
64_E	67_R	0.787	0.40
23_R	26_P	0.781	0.39
29_D	48_A	0.780	0.39
90_P	128_L	0.771	0.39
19_Y	25_G	0.771	0.39
70_L	74_E	0.765	0.38
51_K	54_V	0.757	0.38
46_A	91_G	0.756	0.38
14_A	17_S	0.738	0.36
55_I	65_Q	0.729	0.36
43_V	128_L	0.727	0.36
50_Q	69_I	0.721	0.35
60_R	115_G	0.720	0.35
88_K	97_Y	0.717	0.35
54_V	138_D	0.713	0.35
100_R	138_D	0.711	0.34
15_N	18_P	0.703	0.34
61_V	139_E	0.702	0.34
97_Y	101_D	0.697	0.33
39_I	42_N	0.694	0.33
25_G	28_F	0.694	0.33
34_A	37_I	0.684	0.33
46_A	115_G	0.678	0.32
51_K	133_S	0.676	0.32
82_A	119_P	0.675	0.32
99_R	103_Q	0.670	0.32
103_Q	107_S	0.669	0.31
88_K	133_S	0.661	0.31
25_G	122_Y	0.660	0.31
54_V	133_S	0.650	0.30
102_G	120_H	0.646	0.30
48_A	69_I	0.644	0.30
108_M	133_S	0.643	0.30
105_Y	110_S	0.643	0.30
65_Q	82_A	0.643	0.30
54_V	122_Y	0.642	0.30
44_A	51_K	0.641	0.30
88_K	135_T	0.640	0.30
67_R	135_T	0.640	0.30
93_I	97_Y	0.640	0.30
82_A	110_S	0.639	0.30
79_L	106_F	0.639	0.30
90_P	135_T	0.637	0.29
93_I	125_S	0.634	0.29
17_S	26_P	0.628	0.29
75_R	78_A	0.624	0.29
102_G	107_S	0.622	0.28
45_R	134_W	0.617	0.28
19_Y	26_P	0.615	0.28
82_A	134_W	0.609	0.28
39_I	43_V	0.608	0.28
78_A	99_R	0.604	0.27
41_D	48_A	0.603	0.27
63_Q	104_T	0.603	0.27
28_F	35_K	0.600	0.27
84_C	88_K	0.600	0.27
78_A	104_T	0.594	0.27
123_L	128_L	0.592	0.27
42_N	104_T	0.588	0.26
85_N	105_Y	0.587	0.26
128_L	135_T	0.586	0.26
83_E	127_R	0.581	0.26
55_I	103_Q	0.580	0.26
50_Q	54_V	0.577	0.26
27_K	30_L	0.570	0.25
33_V	85_N	0.570	0.25
120_H	123_L	0.567	0.25
64_E	139_E	0.566	0.25
42_N	134_W	0.564	0.25
79_L	84_C	0.563	0.25
93_I	113_E	0.560	0.25
44_A	49_Q	0.557	0.24
57_E	60_R	0.552	0.24
34_A	124_G	0.552	0.24
28_F	44_A	0.552	0.24
38_D	61_V	0.548	0.24
33_V	77_D	0.548	0.24
59_I	65_Q	0.548	0.24
110_S	118_P	0.543	0.24
72_R	136_E	0.541	0.24
110_S	116_T	0.540	0.24
92_Q	110_S	0.535	0.23
89_V	128_L	0.531	0.23
97_Y	105_Y	0.531	0.23
99_R	105_Y	0.530	0.23
41_D	128_L	0.529	0.23
88_K	106_F	0.526	0.23
130_G	136_E	0.524	0.23
45_R	130_G	0.523	0.23
116_T	119_P	0.517	0.22
80_H	128_L	0.516	0.22
33_V	87_Q	0.513	0.22
43_V	89_V	0.509	0.22
113_E	137_V	0.509	0.22
34_A	88_K	0.506	0.22
42_N	45_R	0.506	0.22
20_P	26_P	0.503	0.22
34_A	70_L	0.502	0.21
114_W	128_L	0.500	0.21

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
2d1zA	1	0.4452	9.3	0.96	Contact Map
2mctA	1	0.6323	8.1	0.961	Contact Map
4xx6A	2	0.4516	7.7	0.962	Contact Map
1xqoA	1	0.6194	7.7	0.962	Contact Map
1wb9A	2	0.9355	7.5	0.962	Contact Map
1t95A	1	0.7419	7.3	0.962	Contact Map
2rlwA	1	0.2129	7.1	0.962	Contact Map
4ghnA	1	0.3806	6.8	0.962	Contact Map
2wbmA	1	0.7161	6.7	0.963	Contact Map
1v0lA	1	0.4387	6.5	0.963	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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