DUF535 - PFAM28P - GREMLIN Contacts

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DUF535 - Protein of unknown function (DUF535)

PFAM:	PF04393	Sequences: RIWRKLRRRLKFLLRSLLHPRATRRWLRFLASSPLLRALLAAQPRLLEKLHRPYLSRGLSARQRLAALIDHYRFLEQLFPPALLRALYSGEGLVLAELSGKDGERYRLRLDAPPGFRREGELTLSLRDGDGERLYSLTFSLAPGDGERTLFIGGLQGPRGEDALELIREATKACHGLRPKNLLLEALRALARALGVERILAVSNAGHVYRALRYRLRKRRKLKADYDEFWEELGGVPRDDGFFELPLPLPRKPLEEIPSKKRAEYRRRYALLDELAAQIAQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	281 (275)
Sequences:	1576 (1162)
Seq/√Len:	70.1
META:	0.626

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
263_A	267_R	7.040	1.00
251_R	273_D	5.328	1.00
150_L	191_A	4.070	1.00
204_N	225_D	3.757	1.00
205_A	227_D	3.642	1.00
198_R	244_E	3.569	1.00
74_F	141_L	3.555	1.00
108_L	186_A	3.544	1.00
178_R	232_E	3.491	1.00
60_S	63_Q	3.427	1.00
253_P	256_E	3.266	1.00
150_L	187_L	3.173	1.00
225_D	228_E	3.006	1.00
54_Y	121_E	2.837	1.00
270_A	274_E	2.587	1.00
231_E	243_F	2.554	1.00
138_T	154_G	2.536	1.00
263_A	266_R	2.495	1.00
147_E	197_E	2.365	1.00
72_Y	121_E	2.323	1.00
260_K	263_A	2.307	1.00
261_K	265_Y	2.271	1.00
184_L	233_L	2.241	1.00
102_D	173_A	2.036	1.00
152_I	187_L	2.005	1.00
261_K	264_E	2.001	1.00
175_H	267_R	1.998	1.00
94_V	97_E	1.959	1.00
265_Y	269_Y	1.956	1.00
170_A	182_L	1.949	1.00
80_P	83_L	1.891	1.00
264_E	269_Y	1.833	1.00
206_G	241_G	1.822	1.00
123_T	136_S	1.813	1.00
274_E	278_Q	1.727	1.00
74_F	78_L	1.705	1.00
123_T	138_T	1.697	1.00
94_V	107_R	1.678	1.00
137_L	187_L	1.675	1.00
97_E	105_R	1.654	0.99
164_L	168_R	1.653	0.99
94_V	109_R	1.634	0.99
188_R	249_L	1.608	0.99
265_Y	272_L	1.607	0.99
92_G	109_R	1.595	0.99
55_L	67_A	1.590	0.99
261_K	269_Y	1.581	0.99
261_K	272_L	1.565	0.99
21_R	25_R	1.542	0.99
67_A	142_A	1.528	0.99
49_K	121_E	1.515	0.99
184_L	229_F	1.514	0.99
178_R	181_N	1.513	0.99
259_S	264_E	1.510	0.99
231_E	237_P	1.502	0.99
26_W	65_L	1.489	0.99
269_Y	272_L	1.476	0.99
238_R	244_E	1.474	0.99
71_H	122_L	1.452	0.99
139_F	187_L	1.441	0.99
265_Y	268_R	1.438	0.99
207_H	213_R	1.399	0.98
55_L	59_L	1.399	0.98
25_R	69_I	1.383	0.98
22_A	65_L	1.380	0.98
155_L	229_F	1.372	0.98
180_K	204_N	1.368	0.98
141_L	194_L	1.357	0.98
192_R	276_A	1.351	0.98
171_T	176_G	1.335	0.98
201_A	235_G	1.330	0.98
149_T	200_L	1.327	0.97
20_P	24_R	1.324	0.97
203_S	227_D	1.303	0.97
29_F	73_R	1.301	0.97
238_R	241_G	1.297	0.97
269_Y	273_D	1.271	0.97
259_S	263_A	1.262	0.97
106_Y	173_A	1.260	0.97
56_S	242_F	1.258	0.97
181_N	232_E	1.243	0.96
11_K	15_R	1.243	0.96
106_Y	128_D	1.239	0.96
271_L	275_L	1.237	0.96
23_T	27_L	1.232	0.96
181_N	233_L	1.230	0.96
168_R	172_K	1.226	0.96
109_R	127_R	1.210	0.96
54_Y	72_Y	1.204	0.96
230_W	235_G	1.198	0.95
236_V	244_E	1.191	0.95
105_R	129_G	1.189	0.95
251_R	269_Y	1.167	0.95
107_R	127_R	1.163	0.95
106_Y	170_A	1.150	0.94
150_L	196_V	1.150	0.94
204_N	227_D	1.134	0.94
257_I	265_Y	1.132	0.94
56_S	241_G	1.131	0.94
207_H	214_Y	1.129	0.94
36_L	76_E	1.123	0.93
118_R	202_V	1.123	0.93
274_E	277_A	1.120	0.93
158_P	167_I	1.119	0.93
17_L	21_R	1.113	0.93
200_L	238_R	1.110	0.93
74_F	194_L	1.106	0.93
152_I	201_A	1.096	0.93
128_D	132_E	1.093	0.93
95_L	124_L	1.092	0.93
70_D	143_P	1.090	0.92
50_L	65_L	1.078	0.92
55_L	140_S	1.073	0.92
227_D	231_E	1.072	0.92
268_R	272_L	1.070	0.92
180_K	224_A	1.069	0.92
13_L	24_R	1.063	0.91
38_A	85_R	1.059	0.91
9_R	13_L	1.056	0.91
252_K	261_K	1.052	0.91
187_L	191_A	1.048	0.91
98_L	275_L	1.042	0.91
153_G	230_W	1.031	0.90
125_S	133_R	1.028	0.90
71_H	140_S	1.020	0.90
176_G	261_K	1.020	0.90
118_R	209_Y	1.018	0.90
124_L	139_F	1.012	0.89
124_L	190_L	1.006	0.89
254_L	257_I	1.005	0.89
126_L	183_L	1.003	0.89
211_A	214_Y	1.001	0.89
66_A	70_D	0.995	0.89
264_E	272_L	0.991	0.88
55_L	242_F	0.990	0.88
260_K	265_Y	0.979	0.88
206_G	242_F	0.979	0.88
167_I	171_T	0.979	0.88
116_F	138_T	0.962	0.87
24_R	28_R	0.961	0.87
108_L	126_L	0.957	0.87
133_R	136_S	0.957	0.87
111_D	125_S	0.955	0.86
56_S	59_L	0.952	0.86
165_E	169_E	0.951	0.86
171_T	179_P	0.949	0.86
260_K	264_E	0.948	0.86
87_L	255_E	0.945	0.86
116_F	136_S	0.943	0.86
12_F	15_R	0.941	0.86
38_A	41_A	0.938	0.85
264_E	271_L	0.937	0.85
195_G	198_R	0.935	0.85
95_L	199_I	0.934	0.85
252_K	265_Y	0.930	0.85
104_E	129_G	0.930	0.85
254_L	260_K	0.928	0.85
6_L	13_L	0.920	0.84
48_E	52_R	0.919	0.84
101_K	175_H	0.916	0.84
167_I	182_L	0.915	0.84
20_P	25_R	0.908	0.83
151_F	200_L	0.900	0.83
21_R	32_S	0.894	0.83
38_A	42_A	0.887	0.82
143_P	146_G	0.870	0.81
48_E	118_R	0.865	0.80
256_E	275_L	0.862	0.80
135_Y	171_T	0.852	0.79
21_R	28_R	0.846	0.79
151_F	242_F	0.846	0.79
58_G	241_G	0.846	0.79
154_G	204_N	0.843	0.79
127_R	133_R	0.841	0.79
155_L	201_A	0.832	0.78
265_Y	273_D	0.827	0.77
253_P	269_Y	0.827	0.77
165_E	168_R	0.822	0.77
173_A	202_V	0.816	0.76
134_L	166_L	0.815	0.76
59_L	113_P	0.815	0.76
209_Y	213_R	0.813	0.76
178_R	264_E	0.812	0.76
235_G	246_P	0.803	0.75
207_H	211_A	0.799	0.75
33_S	76_E	0.793	0.74
235_G	245_L	0.793	0.74
65_L	69_I	0.790	0.74
75_L	122_L	0.789	0.74
68_L	230_W	0.786	0.74
40_L	47_L	0.780	0.73
104_E	173_A	0.779	0.73
203_S	206_G	0.778	0.73
166_L	169_E	0.776	0.73
126_L	174_C	0.776	0.73
194_L	243_F	0.772	0.72
23_T	30_L	0.770	0.72
227_D	243_F	0.770	0.72
51_H	178_R	0.767	0.72
40_L	44_P	0.766	0.72
158_P	222_L	0.764	0.72
87_L	112_A	0.763	0.71
133_R	166_L	0.757	0.71
52_R	118_R	0.756	0.71
162_D	166_L	0.756	0.71
15_R	201_A	0.754	0.71
17_L	20_P	0.753	0.70
253_P	258_P	0.752	0.70
137_L	155_L	0.752	0.70
137_L	154_G	0.751	0.70
27_L	30_L	0.750	0.70
20_P	23_T	0.750	0.70
12_F	26_W	0.749	0.70
72_Y	203_S	0.749	0.70
181_N	249_L	0.749	0.70
176_G	268_R	0.748	0.70
142_A	151_F	0.743	0.69
251_R	265_Y	0.743	0.69
8_R	11_K	0.743	0.69
75_L	79_F	0.741	0.69
96_A	278_Q	0.740	0.69
63_Q	67_A	0.735	0.69
29_F	229_F	0.734	0.68
257_I	269_Y	0.732	0.68
21_R	41_A	0.729	0.68
14_L	18_L	0.728	0.68
172_K	180_K	0.728	0.68
28_R	34_P	0.725	0.68
73_R	143_P	0.725	0.68
235_G	247_L	0.725	0.68
190_L	279_I	0.723	0.67
188_R	199_I	0.723	0.67
45_R	186_A	0.721	0.67
59_L	67_A	0.716	0.67
178_R	252_K	0.711	0.66
68_L	86_A	0.711	0.66
49_K	112_A	0.707	0.66
75_L	84_L	0.704	0.65
141_L	183_L	0.703	0.65
135_Y	183_L	0.703	0.65
261_K	268_R	0.703	0.65
222_L	252_K	0.701	0.65
158_P	180_K	0.700	0.65
110_L	122_L	0.692	0.64
191_A	196_V	0.691	0.64
6_L	14_L	0.690	0.64
108_L	183_L	0.690	0.64
101_K	259_S	0.686	0.63
152_I	176_G	0.683	0.63
49_K	52_R	0.681	0.63
240_D	244_E	0.681	0.63
101_K	264_E	0.679	0.62
177_L	182_L	0.676	0.62
184_L	187_L	0.676	0.62
257_I	260_K	0.673	0.62
254_L	266_R	0.672	0.62
75_L	141_L	0.672	0.62
258_P	263_A	0.667	0.61
121_E	140_S	0.667	0.61
171_T	204_N	0.665	0.61
245_L	257_I	0.661	0.60
130_D	195_G	0.655	0.60
115_G	133_R	0.654	0.60
79_F	229_F	0.653	0.59
138_T	179_P	0.652	0.59
62_R	66_A	0.651	0.59
177_L	272_L	0.649	0.59
52_R	261_K	0.648	0.59
171_T	178_R	0.645	0.59
141_L	176_G	0.643	0.58
208_V	211_A	0.642	0.58
61_A	64_R	0.641	0.58
182_L	275_L	0.639	0.58
147_E	236_V	0.639	0.58
23_T	51_H	0.638	0.58
98_L	193_A	0.636	0.57
157_G	171_T	0.636	0.57
255_E	273_D	0.634	0.57
12_F	16_S	0.632	0.57
68_L	216_L	0.631	0.57
139_F	156_Q	0.630	0.57
23_T	50_L	0.628	0.56
22_A	25_R	0.627	0.56
252_K	259_S	0.627	0.56
13_L	16_S	0.626	0.56
122_L	221_K	0.622	0.56
62_R	195_G	0.620	0.56
16_S	20_P	0.619	0.55
7_R	10_L	0.619	0.55
201_A	230_W	0.619	0.55
70_D	142_A	0.617	0.55
181_N	185_E	0.616	0.55
73_R	77_Q	0.616	0.55
140_S	151_F	0.615	0.55
15_R	55_L	0.615	0.55
49_K	72_Y	0.613	0.55
103_G	255_E	0.612	0.55
236_V	278_Q	0.611	0.54
262_R	268_R	0.610	0.54
135_Y	180_K	0.610	0.54
79_F	87_L	0.609	0.54
16_S	19_H	0.607	0.54
147_E	198_R	0.605	0.54
196_V	247_L	0.604	0.54
59_L	242_F	0.602	0.53
111_D	115_G	0.599	0.53
248_P	277_A	0.598	0.53
249_L	253_P	0.598	0.53
203_S	237_P	0.597	0.53
8_R	12_F	0.595	0.53
49_K	54_Y	0.595	0.53
46_L	83_L	0.595	0.53
59_L	125_S	0.595	0.53
115_G	208_V	0.594	0.52
153_G	180_K	0.594	0.52
167_I	170_A	0.592	0.52
189_A	276_A	0.592	0.52
276_A	279_I	0.592	0.52
127_R	130_D	0.591	0.52
41_A	190_L	0.590	0.52
108_L	115_G	0.590	0.52
6_L	9_R	0.589	0.52
32_S	36_L	0.585	0.51
205_A	237_P	0.584	0.51
186_A	201_A	0.584	0.51
82_A	94_V	0.582	0.51
189_A	269_Y	0.581	0.51
271_L	279_I	0.580	0.51
257_I	261_K	0.579	0.51
67_A	204_N	0.578	0.50
66_A	192_R	0.578	0.50
74_F	196_V	0.577	0.50
28_R	38_A	0.577	0.50
108_L	276_A	0.577	0.50
141_L	148_R	0.576	0.50
261_K	267_R	0.575	0.50
109_R	243_F	0.572	0.50
120_G	156_Q	0.572	0.50
202_V	208_V	0.572	0.50
158_P	188_R	0.570	0.49
172_K	176_G	0.569	0.49
56_S	121_E	0.569	0.49
188_R	248_P	0.568	0.49
119_E	156_Q	0.568	0.49
203_S	241_G	0.565	0.49
29_F	69_I	0.563	0.49
254_L	263_A	0.563	0.49
10_L	14_L	0.562	0.49
185_E	188_R	0.561	0.48
19_H	37_R	0.561	0.48
115_G	209_Y	0.560	0.48
71_H	243_F	0.559	0.48
170_A	173_A	0.558	0.48
81_P	279_I	0.558	0.48
127_R	132_E	0.556	0.48
129_G	222_L	0.556	0.48
178_R	261_K	0.556	0.48
164_L	167_I	0.555	0.48
56_S	201_A	0.554	0.48
99_S	105_R	0.553	0.47
43_Q	46_L	0.553	0.47
92_G	127_R	0.553	0.47
165_E	271_L	0.552	0.47
213_R	216_L	0.550	0.47
66_A	77_Q	0.547	0.47
115_G	138_T	0.547	0.47
40_L	223_K	0.546	0.47
28_R	97_E	0.546	0.47
257_I	263_A	0.546	0.47
207_H	212_L	0.545	0.46
134_L	160_G	0.544	0.46
181_N	229_F	0.543	0.46
98_L	108_L	0.542	0.46
68_L	71_H	0.542	0.46
102_D	169_E	0.541	0.46
77_Q	277_A	0.541	0.46
153_G	196_V	0.539	0.46
135_Y	181_N	0.537	0.45
177_L	249_L	0.536	0.45
17_L	236_V	0.533	0.45
176_G	180_K	0.532	0.45
193_A	248_P	0.531	0.45
73_R	145_D	0.528	0.44
118_R	226_Y	0.527	0.44
68_L	134_L	0.522	0.44
152_I	199_I	0.522	0.44
155_L	167_I	0.520	0.43
7_R	255_E	0.520	0.43
191_A	247_L	0.519	0.43
171_T	261_K	0.519	0.43
35_L	38_A	0.519	0.43
80_P	224_A	0.519	0.43
119_E	139_F	0.519	0.43
153_G	202_V	0.519	0.43
235_G	268_R	0.518	0.43
140_S	210_R	0.515	0.43
7_R	107_R	0.513	0.43
191_A	199_I	0.513	0.43
178_R	214_Y	0.513	0.43
124_L	226_Y	0.512	0.43
153_G	203_S	0.512	0.43
270_A	275_L	0.510	0.42
80_P	84_L	0.510	0.42
23_T	26_W	0.510	0.42
13_L	201_A	0.510	0.42
266_R	270_A	0.510	0.42
56_S	206_G	0.507	0.42
107_R	152_I	0.505	0.42
167_I	180_K	0.504	0.42
139_F	202_V	0.504	0.42
38_A	235_G	0.504	0.42
172_K	211_A	0.500	0.41

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
4mh8A	1	0.1957	14.4	0.962	Contact Map
4xpcA	1	0.2028	12.6	0.963	Contact Map
1gyxA	2	0.2456	9.8	0.965	Contact Map
3bz1X	1	0.121	7.9	0.966	Contact Map
4b2uA	1	0.1281	6.2	0.968	Contact Map
1gd2E	2	0.1032	5.5	0.969	Contact Map
4q9vA	2	0.363	5.3	0.969	Contact Map
2m8vA	1	0.1068	4.6	0.97	Contact Map
3i9v4	1	0.5231	4.5	0.97	Contact Map
3tpfA	3	0.6548	4.3	0.97	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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