YTPR - BACSU - GREMLIN Contacts

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YTPR - Putative tRNA-binding protein YtpR

UniProt:	O34943	Sequences: MNAFYNKEGVGDTLLISLQDVTREQLGYEKHGDVVKIFNNETKETTGFNIFNASSYLTIDENGPVALSETFVQDVNEILNRNGVEETLVVDLSPKFVVGYVESKEKHPNADKLSVCKVNVGEETLQIVCGAPNVDQGQKVVVAKVGAVMPSGLVIKDAELRGVPSSGMICSAKELDLPDAPAEKGILVLEGDYEAGDAFQF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	201 (196)
Sequences:	382 (284)
Seq/√Len:	20.3

BACSU - YTPR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
159_E	164_P	4.912	1.00
102_E	119_N	4.033	1.00
30_K	35_V	3.554	1.00
36_K	45_T	3.428	1.00
138_Q	188_V	3.212	1.00
99_G	142_V	2.803	0.99
91_D	95_K	2.631	0.98
103_S	117_K	2.604	0.98
131_A	186_I	2.601	0.98
12_D	54_S	2.582	0.98
79_L	82_N	2.516	0.98
129_C	186_I	2.439	0.97
33_D	52_N	2.416	0.97
38_F	45_T	2.399	0.97
50_I	75_V	2.362	0.96
106_K	114_S	2.330	0.96
101_V	134_V	2.323	0.96
173_K	182_A	2.286	0.96
157_D	166_S	2.274	0.95
129_C	172_A	2.138	0.94
120_V	125_L	2.129	0.94
132_P	180_A	2.124	0.93
172_A	187_L	2.067	0.92
135_D	138_Q	2.031	0.92
69_E	73_Q	1.982	0.91
135_D	188_V	1.961	0.90
33_D	56_Y	1.954	0.90
194_E	197_D	1.914	0.89
129_C	134_V	1.878	0.88
77_E	81_R	1.875	0.88
131_A	138_Q	1.803	0.86
132_P	181_P	1.790	0.86
10_V	15_L	1.715	0.83
142_V	169_I	1.710	0.83
19_Q	44_E	1.668	0.81
69_E	92_L	1.668	0.81
193_Y	197_D	1.624	0.79
139_K	195_A	1.597	0.78
138_Q	186_I	1.572	0.77
134_V	186_I	1.512	0.74
114_S	129_C	1.500	0.74
129_C	138_Q	1.491	0.73
16_I	50_I	1.477	0.72
104_K	114_S	1.454	0.71
96_F	147_A	1.427	0.70
30_K	51_F	1.418	0.69
5_Y	11_G	1.418	0.69
129_C	170_C	1.380	0.67
172_A	186_I	1.375	0.67
36_K	86_E	1.368	0.66
39_N	42_T	1.344	0.65
141_V	199_F	1.325	0.64
31_H	84_V	1.317	0.63
2_N	148_V	1.291	0.62
5_Y	12_D	1.286	0.61
134_V	138_Q	1.275	0.61
141_V	187_L	1.272	0.61
131_A	184_K	1.271	0.61
109_N	161_R	1.270	0.60
131_A	172_A	1.256	0.60
141_V	172_A	1.214	0.57
121_G	144_K	1.211	0.57
8_E	62_N	1.195	0.56
114_S	184_K	1.194	0.56
91_D	147_A	1.193	0.56
129_C	141_V	1.181	0.55
79_L	84_V	1.179	0.55
157_D	164_P	1.157	0.53
75_V	88_L	1.135	0.52
118_V	156_K	1.119	0.51
131_A	134_V	1.105	0.50
7_K	29_E	1.102	0.50
4_F	148_V	1.101	0.50
37_I	47_G	1.079	0.48
125_L	163_V	1.075	0.48
140_V	169_I	1.069	0.47
33_D	53_A	1.067	0.47
56_Y	78_I	1.065	0.47
125_L	144_K	1.065	0.47
99_G	140_V	1.050	0.46
116_C	156_K	1.048	0.46
134_V	169_I	1.047	0.46
100_Y	191_G	1.047	0.46
37_I	95_K	1.045	0.46
118_V	169_I	1.040	0.46
100_Y	136_Q	1.032	0.45
153_L	157_D	1.030	0.45
148_V	154_V	1.027	0.45
170_C	186_I	1.021	0.44
143_A	149_M	1.017	0.44
137_G	188_V	1.015	0.44
13_T	20_D	1.009	0.44
107_H	115_V	0.999	0.43
118_V	134_V	0.987	0.42
28_Y	35_V	0.985	0.42
98_V	193_Y	0.985	0.42
158_A	166_S	0.984	0.42
76_N	79_L	0.981	0.42
23_R	46_T	0.980	0.42
129_C	169_I	0.976	0.41
145_V	166_S	0.969	0.41
139_K	191_G	0.959	0.40
114_S	153_L	0.947	0.40
36_K	48_F	0.946	0.40
2_N	17_S	0.945	0.40
33_D	55_S	0.936	0.39
39_N	44_E	0.926	0.38
72_V	91_D	0.923	0.38
3_A	71_F	0.917	0.38
35_V	145_V	0.913	0.38
187_L	199_F	0.912	0.37
72_V	90_V	0.899	0.37
41_E	85_E	0.895	0.36
38_F	43_K	0.893	0.36
129_C	184_K	0.886	0.36
131_A	188_V	0.877	0.35
108_P	115_V	0.872	0.35
8_E	59_I	0.869	0.35
4_F	9_G	0.867	0.35
101_V	140_V	0.864	0.35
8_E	177_L	0.863	0.35
50_I	78_I	0.862	0.34
96_F	144_K	0.860	0.34
169_I	172_A	0.859	0.34
107_H	163_V	0.857	0.34
107_H	110_A	0.834	0.33
70_T	182_A	0.822	0.32
53_A	78_I	0.822	0.32
139_K	192_D	0.819	0.32
178_P	181_P	0.818	0.32
52_N	56_Y	0.818	0.32
131_A	170_C	0.811	0.32
133_N	174_E	0.810	0.31
38_F	42_T	0.809	0.31
21_V	46_T	0.806	0.31
36_K	84_V	0.804	0.31
32_G	82_N	0.801	0.31
110_A	183_E	0.798	0.31
112_K	183_E	0.797	0.31
129_C	140_V	0.789	0.30
97_V	144_K	0.782	0.30
39_N	46_T	0.779	0.30
31_H	83_G	0.778	0.30
98_V	189_L	0.777	0.30
99_G	169_I	0.775	0.30
15_L	68_S	0.775	0.30
94_P	179_D	0.771	0.29
104_K	116_C	0.771	0.29
101_V	169_I	0.766	0.29
51_F	186_I	0.762	0.29
71_F	156_K	0.760	0.29
140_V	187_L	0.757	0.29
166_S	188_V	0.757	0.29
116_C	169_I	0.750	0.28
132_P	184_K	0.746	0.28
3_A	116_C	0.745	0.28
149_M	160_L	0.742	0.28
27_G	38_F	0.740	0.28
158_A	177_L	0.738	0.28
31_H	87_T	0.737	0.28
15_L	136_Q	0.732	0.27
76_N	112_K	0.731	0.27
102_E	124_T	0.730	0.27
76_N	84_V	0.730	0.27
34_V	67_L	0.726	0.27
95_K	144_K	0.724	0.27
109_N	131_A	0.721	0.27
5_Y	10_V	0.721	0.27
22_T	41_E	0.719	0.27
2_N	108_P	0.716	0.26
104_K	134_V	0.714	0.26
99_G	127_I	0.710	0.26
57_L	74_D	0.710	0.26
71_F	116_C	0.709	0.26
18_L	60_D	0.708	0.26
118_V	184_K	0.704	0.26
58_T	124_T	0.704	0.26
104_K	136_Q	0.703	0.26
130_G	133_N	0.703	0.26
15_L	47_G	0.700	0.26
132_P	179_D	0.699	0.26
117_K	125_L	0.697	0.25
191_G	195_A	0.696	0.25
134_V	170_C	0.694	0.25
3_A	15_L	0.694	0.25
78_I	81_R	0.693	0.25
117_K	147_A	0.693	0.25
138_Q	172_A	0.691	0.25
38_F	41_E	0.689	0.25
51_F	131_A	0.685	0.25
62_N	87_T	0.679	0.25
138_Q	184_K	0.679	0.25
13_T	32_G	0.679	0.25
70_T	80_N	0.676	0.24
62_N	192_D	0.665	0.24
130_G	174_E	0.665	0.24
172_A	184_K	0.663	0.24
65_V	173_K	0.658	0.24
114_S	172_A	0.654	0.23
101_V	144_K	0.653	0.23
71_F	112_K	0.647	0.23
105_E	163_V	0.644	0.23
93_S	135_D	0.644	0.23
73_Q	93_S	0.641	0.23
119_N	195_A	0.641	0.23
114_S	131_A	0.638	0.23
4_F	151_S	0.635	0.23
55_S	124_T	0.634	0.22
88_L	91_D	0.633	0.22
151_S	173_K	0.632	0.22
101_V	156_K	0.627	0.22
141_V	169_I	0.625	0.22
44_E	65_V	0.624	0.22
2_N	158_A	0.624	0.22
52_N	77_E	0.623	0.22
3_A	86_E	0.622	0.22
171_S	176_D	0.621	0.22
109_N	184_K	0.620	0.22
163_V	166_S	0.616	0.22
97_V	137_G	0.615	0.22
103_S	136_Q	0.614	0.22
112_K	184_K	0.613	0.22
27_G	42_T	0.610	0.21
67_L	71_F	0.608	0.21
60_D	73_Q	0.608	0.21
79_L	195_A	0.606	0.21
128_V	185_G	0.604	0.21
55_S	81_R	0.603	0.21
57_L	80_N	0.602	0.21
143_A	150_P	0.602	0.21
76_N	89_V	0.598	0.21
91_D	94_P	0.598	0.21
76_N	86_E	0.596	0.21
4_F	47_G	0.594	0.21
125_L	140_V	0.593	0.21
106_K	112_K	0.592	0.21
43_K	61_E	0.589	0.21
17_S	37_I	0.582	0.20
171_S	186_I	0.577	0.20
4_F	50_I	0.576	0.20
43_K	122_E	0.576	0.20
114_S	134_V	0.575	0.20
32_G	164_P	0.572	0.20
95_K	147_A	0.571	0.20
77_E	85_E	0.570	0.20
73_Q	85_E	0.569	0.20
37_I	125_L	0.568	0.20
112_K	156_K	0.568	0.20
41_E	197_D	0.566	0.20
56_Y	82_N	0.565	0.20
140_V	153_L	0.564	0.19
32_G	137_G	0.561	0.19
144_K	147_A	0.560	0.19
45_T	93_S	0.558	0.19
9_G	159_E	0.557	0.19
121_G	124_T	0.556	0.19
24_E	125_L	0.554	0.19
42_T	45_T	0.549	0.19
52_N	81_R	0.549	0.19
27_G	80_N	0.548	0.19
109_N	177_L	0.547	0.19
19_Q	116_C	0.546	0.19
138_Q	187_L	0.545	0.19
33_D	50_I	0.544	0.19
48_F	86_E	0.543	0.19
3_A	53_A	0.543	0.19
52_N	74_D	0.542	0.19
116_C	134_V	0.539	0.18
96_F	159_E	0.539	0.18
22_T	191_G	0.539	0.18
12_D	149_M	0.537	0.18
58_T	69_E	0.536	0.18
79_L	108_P	0.536	0.18
118_V	186_I	0.533	0.18
41_E	137_G	0.533	0.18
159_E	171_S	0.529	0.18
91_D	144_K	0.528	0.18
104_K	132_P	0.525	0.18
150_P	162_G	0.523	0.18
153_L	184_K	0.522	0.18
35_V	51_F	0.522	0.18
76_N	83_G	0.521	0.18
145_V	173_K	0.520	0.18
45_T	70_T	0.520	0.18
32_G	78_I	0.519	0.18
153_L	159_E	0.518	0.18
133_N	150_P	0.517	0.18
114_S	186_I	0.517	0.18
107_H	181_P	0.513	0.17
116_C	172_A	0.513	0.17
57_L	93_S	0.509	0.17
131_A	161_R	0.508	0.17
13_T	120_V	0.500	0.17
179_D	182_A	0.500	0.17

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
3bu2A	3	0.9701	100	0.294	Contact Map
4p72A	2	0.7214	100	0.497	Contact Map
3pcoB	2	0.7214	100	0.501	Contact Map
1b7yB	2	0.7114	100	0.51	Contact Map
2rhqB	2	0.7114	100	0.515	Contact Map
4up7A	2	0.2139	100	0.651	Contact Map
1pybA	2	0.5323	100	0.675	Contact Map
1mkhA	2	0.5274	100	0.679	Contact Map
2e8gA	1	0.8756	99.9	0.682	Contact Map
2cwpA	2	0.5274	99.9	0.684	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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