DUF3612 - PFAM28P - GREMLIN Contacts

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DUF3612 - Protein of unknown function (DUF3612)

PFAM:	PF12268	Sequences: TAVSPYPHWHYFDAYPPGYLRAVYRGNGIPLPWGNMRQVSDPCPHWAVFRMLNEPRGKPSSQISVLRDGDRSRLYCCHSIRTRDMAGNPHVLSVGIDLNPALEAQGVDAEEIVAEIKEACLRNGGSAPIPKAAKKALRSVAKILNIAWIEDALEKPARIICPRSSACPRTPHCYQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (174)
Sequences:	624 (304)
Seq/√Len:	23.0
META:	0.912

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
108_D	111_E	4.443	1.00
96_I	149_I	3.950	1.00
103_E	109_A	3.097	1.00
99_N	113_V	3.078	1.00
98_L	149_I	2.692	0.99
74_L	113_V	2.533	0.98
107_V	136_A	2.305	0.97
134_K	153_L	2.268	0.97
97_D	100_P	2.154	0.96
47_A	60_S	2.111	0.95
63_I	129_I	2.093	0.95
21_R	98_L	2.076	0.95
61_S	78_H	2.067	0.95
164_S	174_Y	1.993	0.93
40_S	165_S	1.967	0.93
1_T	4_S	1.966	0.93
21_R	164_S	1.923	0.92
21_R	90_H	1.811	0.90
90_H	98_L	1.767	0.88
120_C	125_G	1.760	0.88
116_I	133_A	1.694	0.86
5_P	98_L	1.690	0.86
53_N	102_L	1.655	0.85
149_I	168_P	1.644	0.84
147_A	162_P	1.631	0.84
15_Y	20_L	1.621	0.84
119_A	127_A	1.617	0.83
2_A	11_Y	1.610	0.83
9_W	12_F	1.571	0.82
47_A	77_C	1.569	0.82
51_M	59_P	1.558	0.81
23_V	41_D	1.536	0.80
134_K	137_L	1.491	0.78
66_L	81_R	1.483	0.78
150_E	158_R	1.482	0.78
104_A	126_S	1.471	0.77
35_N	39_V	1.464	0.77
90_H	145_N	1.459	0.76
52_L	105_Q	1.455	0.76
76_C	120_C	1.454	0.76
78_H	94_V	1.453	0.76
141_A	150_E	1.422	0.75
14_A	18_G	1.413	0.74
74_L	133_A	1.398	0.73
169_R	173_C	1.391	0.73
50_R	77_C	1.373	0.72
107_V	139_S	1.367	0.72
36_M	142_K	1.363	0.71
103_E	140_V	1.362	0.71
18_G	33_W	1.361	0.71
96_I	146_I	1.355	0.71
161_C	167_C	1.353	0.71
2_A	7_P	1.349	0.71
159_I	164_S	1.334	0.70
21_R	85_M	1.326	0.69
52_L	85_M	1.307	0.68
39_V	79_S	1.301	0.68
6_Y	9_W	1.288	0.67
115_E	132_A	1.286	0.67
147_A	158_R	1.253	0.65
44_P	78_H	1.234	0.63
86_A	127_A	1.231	0.63
68_D	71_R	1.226	0.63
6_Y	10_H	1.207	0.62
23_V	28_G	1.197	0.61
143_I	152_A	1.192	0.61
106_G	112_I	1.183	0.60
34_G	43_C	1.175	0.60
87_G	140_V	1.160	0.59
87_G	129_I	1.152	0.58
167_C	173_C	1.135	0.57
128_P	135_K	1.133	0.57
1_T	6_Y	1.106	0.55
65_V	122_R	1.103	0.55
142_K	152_A	1.097	0.54
66_L	73_R	1.096	0.54
78_H	93_S	1.088	0.54
80_I	149_I	1.083	0.53
31_L	77_C	1.080	0.53
20_L	35_N	1.062	0.52
37_R	93_S	1.057	0.51
132_A	135_K	1.042	0.50
70_D	88_N	1.041	0.50
59_P	124_G	1.040	0.50
10_H	13_D	1.039	0.50
66_L	88_N	1.034	0.50
162_P	174_Y	1.028	0.49
105_Q	142_K	1.025	0.49
149_I	153_L	1.012	0.48
44_P	93_S	1.001	0.48
45_H	60_S	0.995	0.47
54_E	116_I	0.991	0.47
6_Y	12_F	0.991	0.47
61_S	152_A	0.988	0.47
52_L	90_H	0.986	0.47
1_T	9_W	0.980	0.46
145_N	148_W	0.975	0.46
38_Q	141_A	0.975	0.46
9_W	13_D	0.972	0.46
142_K	156_P	0.957	0.45
80_I	105_Q	0.954	0.44
112_I	136_A	0.943	0.44
102_L	107_V	0.943	0.44
98_L	174_Y	0.943	0.44
44_P	94_V	0.942	0.44
16_P	21_R	0.941	0.43
50_R	158_R	0.940	0.43
110_E	114_A	0.938	0.43
103_E	131_K	0.937	0.43
106_G	117_K	0.935	0.43
44_P	66_L	0.931	0.43
22_A	36_M	0.929	0.43
67_R	159_I	0.928	0.43
59_P	105_Q	0.927	0.43
3_V	6_Y	0.917	0.42
4_S	9_W	0.912	0.41
65_V	72_S	0.911	0.41
152_A	156_P	0.901	0.41
33_W	39_V	0.893	0.40
4_S	10_H	0.889	0.40
21_R	174_Y	0.872	0.39
124_G	154_E	0.870	0.39
43_C	62_Q	0.869	0.39
106_G	111_E	0.868	0.39
38_Q	164_S	0.863	0.38
5_P	21_R	0.861	0.38
81_R	96_I	0.860	0.38
113_V	149_I	0.858	0.38
83_R	110_E	0.855	0.38
19_Y	152_A	0.840	0.37
91_V	100_P	0.835	0.36
96_I	127_A	0.835	0.36
111_E	118_E	0.834	0.36
113_V	117_K	0.832	0.36
142_K	150_E	0.816	0.35
47_A	102_L	0.812	0.35
107_V	112_I	0.811	0.35
54_E	122_R	0.808	0.35
166_A	174_Y	0.807	0.35
80_I	83_R	0.804	0.34
43_C	161_C	0.802	0.34
104_A	141_A	0.797	0.34
54_E	135_K	0.792	0.34
135_K	138_R	0.790	0.34
116_I	129_I	0.790	0.34
36_M	108_D	0.783	0.33
101_A	140_V	0.781	0.33
166_A	171_P	0.780	0.33
34_G	62_Q	0.775	0.33
21_R	162_P	0.774	0.33
114_A	118_E	0.760	0.32
1_T	12_F	0.756	0.31
54_E	156_P	0.753	0.31
159_I	165_S	0.746	0.31
123_N	131_K	0.746	0.31
47_A	50_R	0.745	0.31
40_S	66_L	0.743	0.31
4_S	12_F	0.735	0.30
33_W	48_V	0.731	0.30
69_G	72_S	0.729	0.30
61_S	69_G	0.726	0.30
57_G	132_A	0.723	0.30
159_I	174_Y	0.720	0.29
141_A	153_L	0.716	0.29
87_G	116_I	0.716	0.29
131_K	137_L	0.707	0.29
74_L	85_M	0.706	0.29
30_P	76_C	0.703	0.28
142_K	145_N	0.700	0.28
91_V	101_A	0.699	0.28
119_A	130_P	0.695	0.28
129_I	133_A	0.695	0.28
76_C	80_I	0.694	0.28
37_R	78_H	0.693	0.28
141_A	158_R	0.690	0.28
138_R	141_A	0.689	0.28
24_Y	29_I	0.685	0.27
71_R	102_L	0.674	0.27
108_D	132_A	0.673	0.27
43_C	75_Y	0.670	0.27
48_V	51_M	0.668	0.26
111_E	115_E	0.665	0.26
126_S	156_P	0.665	0.26
52_L	159_I	0.663	0.26
164_S	172_H	0.662	0.26
68_D	152_A	0.657	0.26
85_M	126_S	0.651	0.26
166_A	170_T	0.650	0.25
44_P	68_D	0.649	0.25
112_I	133_A	0.647	0.25
67_R	70_D	0.645	0.25
2_A	105_Q	0.644	0.25
71_R	105_Q	0.643	0.25
35_N	79_S	0.638	0.25
68_D	93_S	0.635	0.25
137_L	154_E	0.632	0.25
54_E	147_A	0.631	0.24
22_A	28_G	0.630	0.24
27_N	106_G	0.624	0.24
131_K	135_K	0.619	0.24
129_I	134_K	0.610	0.23
85_M	102_L	0.608	0.23
143_I	153_L	0.608	0.23
55_P	118_E	0.603	0.23
57_G	137_L	0.599	0.23
74_L	162_P	0.599	0.23
52_L	82_T	0.597	0.23
68_D	143_I	0.597	0.23
45_H	152_A	0.596	0.23
83_R	88_N	0.594	0.23
90_H	126_S	0.594	0.23
105_Q	108_D	0.590	0.22
93_S	99_N	0.587	0.22
54_E	57_G	0.585	0.22
137_L	155_K	0.585	0.22
82_T	117_K	0.585	0.22
73_R	123_N	0.584	0.22
52_L	99_N	0.584	0.22
112_I	150_E	0.582	0.22
50_R	141_A	0.581	0.22
81_R	88_N	0.579	0.22
16_P	162_P	0.578	0.22
159_I	171_P	0.578	0.22
40_S	74_L	0.577	0.22
117_K	159_I	0.574	0.22
98_L	164_S	0.571	0.22
131_K	166_A	0.570	0.21
38_Q	59_P	0.570	0.21
5_P	149_I	0.568	0.21
76_C	127_A	0.567	0.21
164_S	169_R	0.566	0.21
45_H	91_V	0.564	0.21
115_E	154_E	0.563	0.21
31_L	41_D	0.557	0.21
24_Y	27_N	0.552	0.21
105_Q	150_E	0.549	0.21
157_A	160_I	0.546	0.20
18_G	35_N	0.543	0.20
36_M	117_K	0.543	0.20
21_R	113_V	0.542	0.20
108_D	131_K	0.542	0.20
59_P	92_L	0.540	0.20
35_N	52_L	0.540	0.20
23_V	34_G	0.538	0.20
13_D	91_V	0.533	0.20
53_N	111_E	0.532	0.20
45_H	126_S	0.528	0.20
89_P	146_I	0.525	0.19
113_V	116_I	0.524	0.19
141_A	170_T	0.522	0.19
13_D	90_H	0.522	0.19
78_H	152_A	0.521	0.19
155_K	166_A	0.521	0.19
138_R	154_E	0.520	0.19
126_S	153_L	0.516	0.19
70_D	111_E	0.516	0.19
28_G	41_D	0.515	0.19
80_I	118_E	0.511	0.19
111_E	139_S	0.509	0.19
63_I	119_A	0.508	0.19
58_K	111_E	0.500	0.18

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
3n5nX	1	0.8636	8.8	0.974	Contact Map
4v0qA	2	0.5909	7.5	0.974	Contact Map
1r69A	1	0.3239	6.6	0.975	Contact Map
4k6mA	2	0.5909	5.2	0.976	Contact Map
2ckwA	1	0.8523	5.2	0.976	Contact Map
2k53A	1	0.3977	4.4	0.977	Contact Map
1oigA	1	0.108	4.2	0.977	Contact Map
3kz3A	2	0.4205	4.2	0.977	Contact Map
2nteA	1	0.5057	4.2	0.977	Contact Map
3vh7B	1	0.1193	4.1	0.977	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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