YIH50 - HALSA - GREMLIN Contacts

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YIH50 - Uncharacterized protein in transposable element ISH50

UniProt:	P04137	Sequences: MMPIKTFVSERRAANLLAQIRWRNGVYCPSCRAESVIRYGSYRVFQRYLCKDCDRTFNDQTGTVFEHSAVALRKWFLAVYTYIRLNTSIRQLDAEIDVSYKTVYRRVQRFLRALDAPRPHLEGPVEIDEFYVKAGLKGRERDQPSRSRGLSTRGRGTYAEDKLPVFVLADRGTGERHVIPAKAATESRIRLLLADRQQESLTVYTDGFRAYDPLDEDDAFTREYVVHGDGEYVNGDVHVNTCESHASLARRWLSPHRGVSKDRLTPYLRAFQLRREVFRKPGKEALKTILETAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	294 (255)
Sequences:	1038 (892)
Seq/√Len:	55.8

HALSA - YIH50

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
126_E	171_R	5.166	1.00
167_V	246_A	4.429	1.00
185_T	188_R	3.652	1.00
130_F	250_R	3.517	1.00
270_A	274_R	3.123	1.00
89_I	100_Y	3.122	1.00
183_A	188_R	3.111	1.00
98_V	102_T	3.094	1.00
231_E	234_N	3.033	1.00
30_S	55_R	2.817	1.00
49_L	56_T	2.670	1.00
28_C	31_C	2.652	1.00
265_T	269_R	2.651	1.00
9_S	12_R	2.596	1.00
167_V	242_C	2.482	1.00
68_S	75_W	2.450	1.00
127_I	203_V	2.445	1.00
78_A	92_L	2.359	1.00
92_L	107_V	2.346	1.00
168_L	192_L	2.292	1.00
207_G	224_Y	2.286	1.00
253_L	259_V	2.213	1.00
105_R	109_R	2.084	1.00
33_A	52_D	2.019	1.00
28_C	53_C	2.015	1.00
71_A	74_K	2.004	1.00
31_C	53_C	1.952	1.00
238_H	241_T	1.947	1.00
193_L	197_Q	1.887	1.00
125_V	201_L	1.879	1.00
13_A	76_F	1.851	0.99
168_L	177_H	1.849	0.99
129_E	211_Y	1.844	0.99
74_K	96_I	1.835	0.99
47_R	56_T	1.817	0.99
239_V	243_E	1.803	0.99
132_V	165_V	1.799	0.99
226_V	229_D	1.753	0.99
11_R	15_N	1.736	0.99
227_H	243_E	1.702	0.99
240_N	243_E	1.667	0.99
171_R	241_T	1.641	0.99
247_S	251_R	1.603	0.98
128_D	206_D	1.590	0.98
115_D	269_R	1.572	0.98
104_Y	108_Q	1.556	0.98
151_S	157_T	1.553	0.98
157_T	161_D	1.543	0.98
176_R	245_H	1.539	0.98
227_H	239_V	1.507	0.98
189_I	208_F	1.499	0.98
117_P	273_L	1.461	0.97
166_F	205_T	1.461	0.97
181_A	189_I	1.454	0.97
242_C	246_A	1.453	0.97
98_V	103_V	1.443	0.97
132_V	249_A	1.442	0.97
205_T	222_R	1.437	0.97
60_Q	68_S	1.428	0.97
244_S	275_R	1.427	0.97
170_D	175_E	1.390	0.96
70_V	106_R	1.368	0.96
28_C	50_C	1.365	0.96
124_P	204_Y	1.360	0.96
10_E	13_A	1.354	0.96
78_A	106_R	1.349	0.95
89_I	107_V	1.340	0.95
249_A	259_V	1.337	0.95
120_H	198_Q	1.336	0.95
127_I	205_T	1.332	0.95
166_F	189_I	1.297	0.94
182_K	188_R	1.296	0.94
243_E	246_A	1.294	0.94
65_F	68_S	1.279	0.94
178_V	272_Q	1.276	0.94
239_V	246_A	1.272	0.94
70_V	102_T	1.271	0.94
248_L	275_R	1.270	0.94
240_N	244_S	1.258	0.93
163_L	261_K	1.251	0.93
178_V	245_H	1.247	0.93
78_A	89_I	1.244	0.93
202_T	223_E	1.234	0.93
17_L	76_F	1.234	0.93
189_I	210_A	1.225	0.92
169_A	241_T	1.204	0.92
37_I	51_K	1.195	0.91
177_H	196_R	1.184	0.91
74_K	97_D	1.182	0.91
211_Y	222_R	1.180	0.91
108_Q	266_P	1.180	0.91
129_E	250_R	1.178	0.91
176_R	276_E	1.151	0.90
81_T	96_I	1.128	0.89
204_Y	237_V	1.122	0.89
241_T	244_S	1.119	0.89
151_S	226_V	1.114	0.88
90_R	93_D	1.114	0.88
194_A	218_D	1.113	0.88
244_S	248_L	1.099	0.88
121_L	168_L	1.096	0.87
90_R	100_Y	1.086	0.87
197_Q	201_L	1.084	0.87
251_R	254_S	1.079	0.87
78_A	103_V	1.075	0.86
85_L	255_P	1.072	0.86
180_P	265_T	1.071	0.86
107_V	111_L	1.070	0.86
207_G	226_V	1.068	0.86
252_W	271_F	1.052	0.85
179_I	195_D	1.049	0.85
150_L	153_R	1.049	0.85
75_W	106_R	1.048	0.85
132_V	268_L	1.044	0.85
184_A	208_F	1.042	0.85
191_L	195_D	1.040	0.85
15_N	19_Q	1.040	0.85
125_V	197_Q	1.033	0.84
61_T	66_E	1.032	0.84
181_A	188_R	1.030	0.84
36_V	57_F	1.017	0.83
152_T	156_G	1.008	0.83
187_S	216_E	1.004	0.82
179_I	192_L	1.000	0.82
166_F	191_L	0.989	0.81
169_A	244_S	0.989	0.81
15_N	18_A	0.987	0.81
281_P	284_E	0.986	0.81
130_F	239_V	0.983	0.81
151_S	154_G	0.982	0.81
9_S	73_R	0.980	0.81
81_T	95_E	0.980	0.81
88_S	97_D	0.974	0.80
10_E	60_Q	0.964	0.80
251_R	257_R	0.961	0.80
126_E	241_T	0.960	0.79
85_L	257_R	0.958	0.79
129_E	184_A	0.949	0.79
9_S	13_A	0.948	0.79
79_V	110_F	0.946	0.78
39_Y	56_T	0.943	0.78
39_Y	49_L	0.941	0.78
225_V	236_D	0.931	0.77
82_Y	107_V	0.931	0.77
132_V	253_L	0.930	0.77
200_S	220_F	0.927	0.77
116_A	197_Q	0.925	0.77
70_V	98_V	0.921	0.77
174_G	256_H	0.917	0.76
38_R	46_Q	0.912	0.76
164_P	184_A	0.911	0.76
169_A	242_C	0.911	0.76
31_C	50_C	0.907	0.75
36_V	39_Y	0.903	0.75
12_R	15_N	0.897	0.75
254_S	278_F	0.896	0.75
68_S	106_R	0.893	0.74
130_F	253_L	0.890	0.74
82_Y	114_L	0.889	0.74
171_R	204_Y	0.885	0.74
202_T	221_T	0.885	0.74
256_H	267_Y	0.875	0.73
11_R	14_A	0.872	0.73
244_S	247_S	0.870	0.72
225_V	239_V	0.868	0.72
32_R	52_D	0.865	0.72
130_F	246_A	0.865	0.72
205_T	211_Y	0.864	0.72
167_V	178_V	0.857	0.71
78_A	96_I	0.854	0.71
164_P	181_A	0.852	0.71
165_V	268_L	0.851	0.71
245_H	277_V	0.849	0.71
190_R	214_L	0.848	0.70
190_R	203_V	0.847	0.70
149_G	161_D	0.838	0.70
47_R	57_F	0.838	0.70
63_T	66_E	0.838	0.70
40_G	79_V	0.835	0.69
211_Y	225_V	0.832	0.69
206_D	250_R	0.825	0.68
227_H	240_N	0.821	0.68
164_P	246_A	0.820	0.68
100_Y	104_Y	0.820	0.68
171_R	174_G	0.816	0.67
14_A	48_Y	0.816	0.67
193_L	196_R	0.811	0.67
27_Y	32_R	0.810	0.67
117_P	277_V	0.810	0.67
62_G	66_E	0.809	0.67
259_V	264_L	0.806	0.67
149_G	154_G	0.804	0.66
169_A	176_R	0.803	0.66
93_D	100_Y	0.802	0.66
51_K	54_D	0.796	0.66
10_E	73_R	0.794	0.65
109_R	127_I	0.791	0.65
66_E	70_V	0.791	0.65
225_V	231_E	0.788	0.65
27_Y	34_E	0.784	0.64
197_Q	203_V	0.776	0.64
64_V	177_H	0.775	0.63
206_D	225_V	0.772	0.63
166_F	181_A	0.771	0.63
129_E	206_D	0.768	0.63
50_C	53_C	0.768	0.63
169_A	275_R	0.761	0.62
26_V	36_V	0.754	0.61
11_R	46_Q	0.753	0.61
152_T	157_T	0.752	0.61
18_A	22_W	0.751	0.61
34_E	52_D	0.751	0.61
252_W	258_G	0.748	0.61
154_G	157_T	0.745	0.60
40_G	47_R	0.738	0.60
153_R	156_G	0.737	0.60
129_E	205_T	0.736	0.59
17_L	21_R	0.734	0.59
247_S	254_S	0.733	0.59
67_H	70_V	0.732	0.59
53_C	63_T	0.730	0.59
12_R	23_R	0.729	0.59
114_L	278_F	0.726	0.58
184_A	210_A	0.724	0.58
168_L	197_Q	0.724	0.58
275_R	278_F	0.721	0.58
208_F	211_Y	0.721	0.58
104_Y	263_R	0.719	0.58
165_V	223_E	0.714	0.57
126_E	239_V	0.714	0.57
104_Y	109_R	0.713	0.57
65_F	93_D	0.712	0.57
252_W	256_H	0.708	0.57
37_I	40_G	0.707	0.56
209_R	212_D	0.705	0.56
57_F	61_T	0.699	0.56
90_R	94_A	0.696	0.55
123_G	201_L	0.693	0.55
203_V	228_G	0.692	0.55
111_L	270_A	0.690	0.55
168_L	245_H	0.690	0.55
193_L	220_F	0.685	0.54
206_D	227_H	0.683	0.54
18_A	36_V	0.682	0.54
186_E	191_L	0.678	0.53
127_I	193_L	0.678	0.53
122_E	170_D	0.675	0.53
166_F	192_L	0.673	0.53
224_Y	235_G	0.669	0.52
29_P	57_F	0.668	0.52
166_F	198_Q	0.668	0.52
189_I	211_Y	0.668	0.52
77_L	81_T	0.662	0.52
165_V	253_L	0.660	0.51
39_Y	47_R	0.652	0.50
131_Y	157_T	0.652	0.50
198_Q	201_L	0.651	0.50
32_R	190_R	0.649	0.50
156_G	161_D	0.649	0.50
211_Y	227_H	0.649	0.50
45_F	60_Q	0.647	0.50
184_A	188_R	0.643	0.50
18_A	59_D	0.643	0.50
68_S	72_L	0.642	0.49
34_E	284_E	0.640	0.49
228_G	231_E	0.639	0.49
263_R	266_P	0.638	0.49
93_D	99_S	0.637	0.49
14_A	45_F	0.635	0.49
254_S	257_R	0.634	0.49
48_Y	230_G	0.633	0.48
133_K	162_K	0.633	0.48
81_T	189_I	0.630	0.48
231_E	235_G	0.629	0.48
118_R	221_T	0.628	0.48
89_I	93_D	0.626	0.48
17_L	72_L	0.623	0.47
131_Y	164_P	0.622	0.47
189_I	193_L	0.620	0.47
27_Y	199_E	0.616	0.47
233_V	238_H	0.616	0.47
131_Y	162_K	0.613	0.46
182_K	185_T	0.612	0.46
11_R	38_R	0.610	0.46
127_I	180_P	0.609	0.46
115_D	185_T	0.605	0.45
247_S	257_R	0.601	0.45
155_R	162_K	0.600	0.45
47_R	87_T	0.599	0.45
149_G	152_T	0.598	0.45
65_F	75_W	0.598	0.45
86_N	113_A	0.597	0.45
181_A	208_F	0.597	0.45
178_V	268_L	0.597	0.45
151_S	156_G	0.597	0.45
189_I	220_F	0.596	0.44
88_S	278_F	0.594	0.44
80_Y	95_E	0.590	0.44
64_V	79_V	0.587	0.43
68_S	102_T	0.585	0.43
194_A	219_A	0.584	0.43
273_L	277_V	0.582	0.43
115_D	265_T	0.582	0.43
163_L	180_P	0.581	0.43
203_V	220_F	0.581	0.43
21_R	26_V	0.580	0.43
232_Y	238_H	0.579	0.43
149_G	157_T	0.577	0.42
108_Q	263_R	0.576	0.42
165_V	264_L	0.571	0.42
232_Y	240_N	0.571	0.42
171_R	238_H	0.570	0.42
88_S	114_L	0.569	0.42
207_G	243_E	0.568	0.41
18_A	46_Q	0.564	0.41
152_T	226_V	0.563	0.41
122_E	198_Q	0.562	0.41
101_K	105_R	0.562	0.41
190_R	213_P	0.561	0.41
230_G	234_N	0.558	0.40
205_T	244_S	0.557	0.40
85_L	91_Q	0.557	0.40
190_R	219_A	0.557	0.40
186_E	213_P	0.555	0.40
18_A	24_N	0.554	0.40
282_G	285_A	0.554	0.40
148_R	151_S	0.550	0.40
28_C	32_R	0.547	0.39
81_T	92_L	0.546	0.39
20_I	23_R	0.546	0.39
112_R	176_R	0.546	0.39
22_W	254_S	0.545	0.39
179_I	265_T	0.544	0.39
51_K	121_L	0.543	0.39
23_R	63_T	0.542	0.39
134_A	208_F	0.542	0.39
263_R	267_Y	0.541	0.39
187_S	194_A	0.538	0.38
237_V	243_E	0.537	0.38
134_A	163_L	0.537	0.38
184_A	246_A	0.537	0.38
238_H	242_C	0.537	0.38
148_R	152_T	0.535	0.38
105_R	285_A	0.534	0.38
103_V	254_S	0.534	0.38
207_G	245_H	0.533	0.38
148_R	153_R	0.533	0.38
23_R	56_T	0.532	0.38
10_E	33_A	0.532	0.38
271_F	275_R	0.530	0.38
184_A	239_V	0.530	0.38
85_L	95_E	0.529	0.37
185_T	208_F	0.528	0.37
121_L	177_H	0.528	0.37
29_P	99_S	0.527	0.37
200_S	219_A	0.527	0.37
63_T	114_L	0.525	0.37
167_V	188_R	0.522	0.37
249_A	268_L	0.521	0.37
69_A	109_R	0.520	0.37
225_V	240_N	0.520	0.37
164_P	167_V	0.520	0.37
166_F	210_A	0.520	0.37
36_V	41_S	0.519	0.36
122_E	195_D	0.518	0.36
16_L	20_I	0.516	0.36
105_R	108_Q	0.513	0.36
29_P	267_Y	0.513	0.36
35_S	51_K	0.512	0.36
124_P	256_H	0.511	0.36
41_S	45_F	0.511	0.36
153_R	157_T	0.510	0.36
85_L	242_C	0.509	0.35
152_T	223_E	0.508	0.35
207_G	230_G	0.507	0.35
18_A	48_Y	0.507	0.35
241_T	275_R	0.506	0.35
36_V	51_K	0.504	0.35
14_A	18_A	0.502	0.35
170_D	174_G	0.501	0.35
194_A	198_Q	0.501	0.35
77_L	80_Y	0.500	0.35

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
4u7bA	2	0.949	98.2	0.881	Contact Map
3l3uA	2	0.4864	96.7	0.911	Contact Map
4mq3A	1	0.4286	96.6	0.912	Contact Map
4fcyA	4	0.8673	96.4	0.914	Contact Map
3f2kA	1	0.5918	96.2	0.915	Contact Map
1c6vA	4	0.4592	95.9	0.918	Contact Map
4mdaA	1	0.585	95.7	0.919	Contact Map
4fw1A	2	0.5238	95.4	0.921	Contact Map
1bcoA	1	0.5442	95.1	0.922	Contact Map
3o9xA	2	0.3707	94.5	0.925	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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