DUF4228 - PFAM28P - GREMLIN Contacts

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DUF4228 - Domain of unknown function (DUF4228)

PFAM:	PF14009	Sequences: MGNLRSCQLPAGAAAAVVKVVHPDGRVEEFYRPVTAAEVMKENPGHFVCDSDSLGFGRRIKALSPDEELQPGQIYFLLPLSRLRSVLSAEEMAALAVKASSALKKSSKRSKRSSVAKKSRSSPFEVVKGSSSSGRSRVRVVELKKQLSERVRRGSRSRSWRPSLESISE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	169 (167)
Sequences:	1669 (1421)
Seq/√Len:	109.9
META:	0.027

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_E	147_L	2.725	1.00
128_K	132_S	2.643	1.00
93_A	96_A	2.465	1.00
134_G	137_R	2.385	1.00
136_S	140_V	2.259	1.00
90_E	93_A	2.217	1.00
99_A	102_A	2.212	1.00
164_L	169_E	2.135	1.00
39_V	43_N	2.103	1.00
99_A	103_L	2.057	1.00
146_Q	149_E	1.983	1.00
114_S	117_K	1.963	1.00
147_L	150_R	1.956	1.00
22_H	28_E	1.951	1.00
134_G	139_R	1.935	1.00
30_F	63_L	1.790	1.00
122_S	126_V	1.774	1.00
123_P	126_V	1.771	1.00
154_G	157_S	1.762	1.00
137_R	140_V	1.682	1.00
136_S	139_R	1.668	1.00
121_S	124_F	1.644	1.00
124_F	129_G	1.634	1.00
125_E	129_G	1.630	1.00
152_R	155_S	1.616	1.00
135_R	138_V	1.605	1.00
126_V	129_G	1.596	1.00
116_A	119_S	1.590	1.00
114_S	118_K	1.586	1.00
120_R	123_P	1.559	1.00
142_E	149_E	1.514	1.00
132_S	136_S	1.513	1.00
121_S	129_G	1.501	1.00
47_F	50_D	1.497	1.00
86_V	89_A	1.494	1.00
151_V	156_R	1.481	1.00
117_K	124_F	1.479	1.00
145_K	149_E	1.471	1.00
35_T	73_Q	1.460	1.00
137_R	141_V	1.458	1.00
49_C	78_L	1.448	1.00
164_L	167_I	1.447	1.00
101_S	104_K	1.437	1.00
126_V	130_S	1.432	1.00
64_S	67_E	1.409	1.00
9_L	13_A	1.405	1.00
125_E	132_S	1.391	1.00
91_E	94_A	1.350	1.00
123_P	127_V	1.343	1.00
152_R	156_R	1.338	1.00
151_V	155_S	1.333	1.00
153_R	157_S	1.283	0.99
133_S	136_S	1.274	0.99
54_L	57_G	1.266	0.99
35_T	68_E	1.259	0.99
8_Q	13_A	1.256	0.99
122_S	128_K	1.241	0.99
126_V	133_S	1.239	0.99
125_E	130_S	1.237	0.99
122_S	130_S	1.235	0.99
97_V	100_S	1.215	0.99
132_S	137_R	1.177	0.99
142_E	145_K	1.167	0.99
128_K	136_S	1.161	0.99
62_A	67_E	1.142	0.99
97_V	103_L	1.133	0.98
136_S	141_V	1.130	0.98
119_S	122_S	1.129	0.98
118_K	124_F	1.129	0.98
117_K	120_R	1.129	0.98
134_G	140_V	1.121	0.98
125_E	131_S	1.113	0.98
122_S	129_G	1.111	0.98
119_S	128_K	1.107	0.98
98_K	103_L	1.106	0.98
129_G	132_S	1.104	0.98
120_R	128_K	1.103	0.98
100_S	103_L	1.090	0.98
145_K	150_R	1.086	0.98
156_R	159_S	1.084	0.98
145_K	148_S	1.084	0.98
121_S	126_V	1.066	0.98
96_A	100_S	1.059	0.98
121_S	127_V	1.048	0.97
162_P	169_E	1.044	0.97
28_E	40_M	1.034	0.97
128_K	140_V	1.033	0.97
83_L	92_M	1.032	0.97
108_K	111_K	1.028	0.97
83_L	95_L	1.022	0.97
98_K	104_K	1.021	0.97
123_P	132_S	1.015	0.97
46_H	77_L	1.013	0.97
100_S	104_K	1.009	0.97
122_S	125_E	1.007	0.97
40_M	45_G	1.007	0.97
134_G	138_V	1.003	0.97
128_K	138_V	1.002	0.97
114_S	119_S	1.000	0.97
21_V	79_P	0.995	0.96
126_V	131_S	0.992	0.96
104_K	107_S	0.982	0.96
152_R	157_S	0.982	0.96
9_L	12_G	0.974	0.96
119_S	127_V	0.971	0.96
118_K	123_P	0.970	0.96
133_S	137_R	0.969	0.96
45_G	67_E	0.959	0.96
128_K	134_G	0.959	0.96
63_L	75_Y	0.959	0.96
47_F	54_L	0.950	0.95
123_P	133_S	0.949	0.95
119_S	123_P	0.948	0.95
103_L	107_S	0.946	0.95
132_S	135_R	0.939	0.95
11_A	14_A	0.937	0.95
133_S	138_V	0.934	0.95
10_P	13_A	0.930	0.95
27_V	37_A	0.930	0.95
144_K	147_L	0.920	0.95
151_V	154_G	0.908	0.94
119_S	133_S	0.902	0.94
91_E	99_A	0.895	0.94
124_F	130_S	0.890	0.93
124_F	128_K	0.887	0.93
76_F	79_P	0.887	0.93
133_S	140_V	0.881	0.93
127_V	130_S	0.876	0.93
46_H	63_L	0.863	0.92
100_S	107_S	0.861	0.92
92_M	95_L	0.859	0.92
125_E	140_V	0.856	0.92
11_A	15_A	0.850	0.92
131_S	139_R	0.844	0.92
99_A	107_S	0.844	0.92
89_A	92_M	0.843	0.92
129_G	135_R	0.841	0.91
122_S	131_S	0.838	0.91
139_R	150_R	0.832	0.91
98_K	102_A	0.829	0.91
112_R	115_V	0.826	0.91
48_V	77_L	0.825	0.91
98_K	105_K	0.820	0.90
7_C	11_A	0.819	0.90
129_G	136_S	0.818	0.90
40_M	48_V	0.808	0.90
11_A	16_A	0.804	0.89
33_P	54_L	0.801	0.89
50_D	73_Q	0.799	0.89
99_A	104_K	0.799	0.89
3_N	7_C	0.798	0.89
60_I	71_P	0.796	0.89
21_V	42_E	0.794	0.89
100_S	105_K	0.790	0.89
8_Q	11_A	0.789	0.89
39_V	48_V	0.789	0.89
97_V	102_A	0.784	0.88
24_D	40_M	0.780	0.88
34_V	37_A	0.760	0.87
119_S	124_F	0.744	0.85
38_E	59_R	0.737	0.85
95_L	98_K	0.735	0.85
6_S	19_K	0.733	0.85
155_S	161_R	0.723	0.84
100_S	106_S	0.719	0.84
124_F	132_S	0.716	0.83
70_Q	73_Q	0.716	0.83
36_A	48_V	0.712	0.83
20_V	104_K	0.710	0.83
19_K	53_S	0.707	0.82
49_C	62_A	0.703	0.82
25_G	69_L	0.701	0.82
71_P	76_F	0.699	0.82
121_S	125_E	0.698	0.82
130_S	137_R	0.692	0.81
87_L	94_A	0.690	0.81
82_R	90_E	0.689	0.81
91_E	96_A	0.687	0.81
119_S	126_V	0.685	0.80
109_R	126_V	0.684	0.80
97_V	101_S	0.683	0.80
117_K	122_S	0.674	0.79
18_V	22_H	0.669	0.79
49_C	76_F	0.664	0.78
130_S	133_S	0.662	0.78
30_F	73_Q	0.661	0.78
146_Q	150_R	0.660	0.78
35_T	80_L	0.656	0.78
54_L	60_I	0.654	0.77
82_R	86_V	0.652	0.77
128_K	135_R	0.649	0.77
135_R	141_V	0.647	0.77
87_L	92_M	0.644	0.76
27_V	161_R	0.643	0.76
94_A	98_K	0.642	0.76
123_P	128_K	0.641	0.76
87_L	95_L	0.636	0.75
123_P	129_G	0.632	0.75
134_G	147_L	0.624	0.74
131_S	138_V	0.621	0.74
93_A	97_V	0.617	0.73
124_F	133_S	0.617	0.73
130_S	136_S	0.614	0.73
142_E	146_Q	0.612	0.73
20_V	52_D	0.612	0.73
120_R	125_E	0.611	0.72
17_V	29_E	0.611	0.72
102_A	105_K	0.611	0.72
103_L	106_S	0.611	0.72
136_S	150_R	0.609	0.72
47_F	76_F	0.604	0.72
52_D	76_F	0.601	0.71
23_P	40_M	0.599	0.71
102_A	106_S	0.597	0.71
89_A	93_A	0.596	0.71
93_A	98_K	0.592	0.70
113_S	117_K	0.588	0.70
14_A	71_P	0.584	0.69
64_S	78_L	0.583	0.69
132_S	138_V	0.581	0.69
152_R	158_R	0.578	0.68
82_R	91_E	0.576	0.68
4_L	10_P	0.574	0.68
122_S	135_R	0.563	0.66
123_P	137_R	0.562	0.66
29_E	79_P	0.562	0.66
130_S	134_G	0.554	0.65
3_N	42_E	0.553	0.65
125_E	128_K	0.546	0.64
126_V	135_R	0.541	0.63
21_V	50_D	0.538	0.63
113_S	116_A	0.537	0.63
3_N	44_P	0.537	0.63
16_A	67_E	0.534	0.62
123_P	150_R	0.530	0.62
121_S	132_S	0.529	0.61
131_S	145_K	0.529	0.61
98_K	106_S	0.528	0.61
32_R	38_E	0.528	0.61
20_V	85_S	0.523	0.61
45_G	64_S	0.520	0.60
114_S	131_S	0.519	0.60
56_F	73_Q	0.517	0.60
47_F	80_L	0.514	0.59
101_S	105_K	0.509	0.59
104_K	109_R	0.509	0.59
151_V	158_R	0.506	0.58
51_S	76_F	0.504	0.58
30_F	78_L	0.503	0.58
101_S	106_S	0.500	0.57

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
2kmmA	1	0.4083	14.8	0.929	Contact Map
1wwtA	1	0.4852	13	0.931	Contact Map
3hvzA	2	0.355	12.2	0.931	Contact Map
2auvA	1	0.1893	8.8	0.936	Contact Map
2cu3A	2	0.355	6.8	0.939	Contact Map
1m2dA	2	0.284	4.6	0.944	Contact Map
1i27A	1	0.4142	4.3	0.945	Contact Map
1f0zA	1	0.3669	4.1	0.945	Contact Map
4gaiA	1	0.432	3.3	0.947	Contact Map
1l2hA	1	0.4142	3	0.948	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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