YVCJ - BACSU - GREMLIN Contacts

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YVCJ - UPF0042 nucleotide-binding protein YvcJ

UniProt:	O06973	Sequences: MSVSESHDIQLVIITGMSGAGKTVAIQSFEDLGYFCVDNLPPSLLPKFLELMKESNSKMSKVALVMDLRGREFFDRLIEALDEMAENPWITPRILFLDAKDSILVTRYKETRRSHPLAATGLPLEGIALERELLEELKGRSQIIYDTSDMKPRDLREKIVKHFATNQGETFTVNVMSFGFKYGIPIDADLVFDVRFLPNPYYIESMRPLTGKDKEVSSYVMKWNETQKFNEKLIDLLSFMLPSYKREGKSQVVIAIGCTGGQHRSVTLAENLADYFKKDYYTHVTHRDIEKRSRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	295 (281)
Sequences:	2250 (1473)
Seq/√Len:	87.9

ECOLI - YHBJ
BACSU - YVCJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
188_A	255_A	7.295	1.00
214_K	218_S	5.977	1.00
212_K	270_E	5.123	1.00
209_L	215_E	4.702	1.00
175_V	269_A	3.840	1.00
232_K	235_D	3.635	1.00
175_V	276_F	3.256	1.00
209_L	213_D	3.242	1.00
10_Q	93_R	3.232	1.00
192_F	233_L	3.158	1.00
273_A	284_V	3.092	1.00
101_D	128_A	2.951	1.00
101_D	131_R	2.832	1.00
238_S	275_Y	2.780	1.00
103_I	148_S	2.748	1.00
184_I	191_V	2.740	1.00
234_I	275_Y	2.561	1.00
230_N	268_L	2.500	1.00
230_N	271_N	2.435	1.00
153_R	202_Y	2.433	1.00
221_M	267_T	2.364	1.00
100_K	103_I	2.356	1.00
201_Y	208_P	2.310	1.00
271_N	274_D	2.308	1.00
190_L	244_Y	2.266	1.00
225_E	246_R	2.201	1.00
256_I	272_L	2.119	1.00
237_L	272_L	2.111	1.00
220_V	267_T	2.093	1.00
232_K	239_F	2.063	1.00
271_N	275_Y	2.045	1.00
270_E	274_D	1.973	1.00
37_V	48_F	1.966	1.00
210_T	262_Q	1.956	1.00
217_S	267_T	1.951	1.00
26_I	65_V	1.928	1.00
191_V	255_A	1.888	1.00
17_M	98_D	1.881	1.00
228_K	232_K	1.880	1.00
151_K	154_D	1.863	1.00
143_I	162_H	1.779	1.00
47_K	50_E	1.761	1.00
158_K	161_K	1.727	1.00
81_L	92_P	1.725	1.00
231_E	275_Y	1.719	1.00
14_I	95_L	1.703	1.00
82_D	140_R	1.679	1.00
25_A	159_I	1.639	1.00
214_K	217_S	1.634	1.00
11_L	49_L	1.620	1.00
132_E	135_E	1.615	1.00
194_V	268_L	1.590	1.00
270_E	284_V	1.568	1.00
50_E	87_N	1.567	1.00
190_L	252_V	1.551	1.00
196_F	229_F	1.550	1.00
230_N	275_Y	1.543	1.00
269_A	284_V	1.522	1.00
173_V	241_L	1.521	1.00
129_L	132_E	1.517	1.00
229_F	233_L	1.509	1.00
154_D	157_E	1.508	1.00
100_K	149_D	1.472	0.99
10_Q	91_T	1.464	0.99
135_E	139_G	1.455	0.99
234_I	238_S	1.443	0.99
188_A	191_V	1.441	0.99
173_V	254_I	1.420	0.99
224_N	228_K	1.416	0.99
138_K	144_I	1.409	0.99
45_L	64_L	1.408	0.99
85_A	140_R	1.379	0.99
98_D	138_K	1.376	0.99
225_E	243_S	1.345	0.99
227_Q	231_E	1.333	0.99
226_T	268_L	1.328	0.99
12_V	29_F	1.322	0.99
274_D	277_K	1.312	0.99
79_E	82_D	1.296	0.99
32_L	159_I	1.274	0.98
152_P	202_Y	1.241	0.98
224_N	227_Q	1.234	0.98
180_F	194_V	1.231	0.98
219_Y	223_W	1.226	0.98
194_V	229_F	1.224	0.98
129_L	133_L	1.207	0.98
217_S	271_N	1.207	0.98
217_S	221_M	1.206	0.98
45_L	66_M	1.199	0.98
105_V	124_L	1.186	0.98
17_M	131_R	1.185	0.98
174_N	285_T	1.180	0.97
274_D	278_K	1.172	0.97
262_Q	290_E	1.168	0.97
82_D	86_E	1.159	0.97
216_V	262_Q	1.157	0.97
24_V	110_E	1.144	0.97
150_M	158_K	1.142	0.97
221_M	230_N	1.142	0.97
194_V	256_I	1.141	0.97
46_P	83_E	1.136	0.97
233_L	236_L	1.130	0.97
201_Y	207_R	1.130	0.97
26_I	36_C	1.129	0.97
228_K	231_E	1.127	0.97
179_G	288_D	1.127	0.97
122_L	125_E	1.120	0.97
182_Y	291_K	1.104	0.96
14_I	29_F	1.102	0.96
201_Y	216_V	1.096	0.96
14_I	65_V	1.085	0.96
218_S	222_K	1.082	0.96
179_G	182_Y	1.076	0.96
203_I	219_Y	1.069	0.95
121_G	129_L	1.066	0.95
10_Q	61_K	1.059	0.95
182_Y	262_Q	1.057	0.95
209_L	216_V	1.052	0.95
170_T	281_Y	1.049	0.95
198_P	223_W	1.047	0.95
118_A	126_G	1.045	0.95
158_K	162_H	1.036	0.95
32_L	164_A	1.032	0.94
73_F	126_G	1.030	0.94
220_V	249_K	1.022	0.94
108_Y	111_T	1.020	0.94
42_P	74_F	1.018	0.94
100_K	148_S	1.016	0.94
233_L	256_I	1.013	0.94
221_M	271_N	1.013	0.94
238_S	276_F	1.012	0.94
201_Y	226_T	1.010	0.94
204_E	207_R	1.006	0.94
244_Y	288_D	1.006	0.94
232_K	236_L	1.004	0.94
95_L	163_F	1.002	0.94
176_M	253_V	0.990	0.93
201_Y	210_T	0.985	0.93
173_V	276_F	0.981	0.93
175_V	282_T	0.972	0.93
227_Q	271_N	0.969	0.92
190_L	240_M	0.964	0.92
176_M	255_A	0.963	0.92
105_V	186_I	0.958	0.92
143_I	163_F	0.953	0.92
151_K	202_Y	0.942	0.91
155_L	159_I	0.940	0.91
175_V	272_L	0.939	0.91
42_P	73_F	0.928	0.91
50_E	54_E	0.927	0.91
256_I	268_L	0.925	0.91
85_A	142_Q	0.914	0.90
98_D	131_R	0.914	0.90
83_E	86_E	0.904	0.90
25_A	97_L	0.899	0.89
231_E	235_D	0.898	0.89
100_K	146_D	0.886	0.89
203_I	207_R	0.884	0.88
122_L	176_M	0.882	0.88
177_S	286_H	0.880	0.88
240_M	249_K	0.876	0.88
242_P	252_V	0.872	0.88
156_R	160_V	0.866	0.87
81_L	167_Q	0.865	0.87
242_P	249_K	0.864	0.87
104_L	108_Y	0.859	0.87
11_L	90_I	0.859	0.87
230_N	234_I	0.857	0.87
13_I	49_L	0.854	0.87
244_Y	252_V	0.844	0.86
77_L	137_L	0.842	0.86
234_I	272_L	0.842	0.86
109_K	253_V	0.841	0.86
52_M	62_V	0.840	0.86
79_E	83_E	0.825	0.85
104_L	127_I	0.820	0.84
159_I	163_F	0.818	0.84
240_M	244_Y	0.808	0.84
12_V	34_Y	0.805	0.83
267_T	270_E	0.803	0.83
217_S	274_D	0.801	0.83
40_L	64_L	0.797	0.83
124_L	128_A	0.794	0.82
225_E	228_K	0.790	0.82
175_V	254_I	0.790	0.82
212_K	284_V	0.780	0.81
23_T	27_Q	0.779	0.81
256_I	269_A	0.779	0.81
20_A	97_L	0.777	0.81
123_P	126_G	0.772	0.81
170_T	245_K	0.770	0.80
91_T	170_T	0.767	0.80
173_V	280_Y	0.766	0.80
243_S	246_R	0.759	0.80
35_F	47_K	0.758	0.79
268_L	272_L	0.756	0.79
122_L	126_G	0.755	0.79
118_A	123_P	0.753	0.79
215_E	218_S	0.749	0.79
241_L	280_Y	0.749	0.79
34_Y	61_K	0.746	0.78
221_M	226_T	0.738	0.78
188_A	253_V	0.737	0.78
168_G	201_Y	0.735	0.77
78_I	140_R	0.731	0.77
81_L	94_I	0.728	0.77
96_F	131_R	0.727	0.77
217_S	220_V	0.727	0.77
108_Y	251_Q	0.727	0.77
44_L	48_F	0.726	0.76
114_S	172_T	0.726	0.76
22_K	26_I	0.723	0.76
34_Y	202_Y	0.722	0.76
230_N	272_L	0.722	0.76
235_D	239_F	0.720	0.76
267_T	271_N	0.719	0.76
20_A	32_L	0.716	0.75
32_L	108_Y	0.712	0.75
262_Q	288_D	0.712	0.75
77_L	81_L	0.711	0.75
201_Y	262_Q	0.711	0.75
137_L	161_K	0.710	0.75
233_L	272_L	0.710	0.75
236_L	248_G	0.708	0.75
109_K	247_E	0.705	0.74
42_P	70_G	0.704	0.74
229_F	268_L	0.702	0.74
225_E	237_L	0.702	0.74
26_I	192_F	0.701	0.74
35_F	99_A	0.701	0.74
125_E	128_A	0.698	0.74
14_I	48_F	0.693	0.73
201_Y	253_V	0.693	0.73
93_R	142_Q	0.692	0.73
228_K	239_F	0.690	0.73
209_L	262_Q	0.690	0.73
213_D	256_I	0.685	0.72
105_V	180_F	0.684	0.72
185_P	255_A	0.683	0.72
48_F	62_V	0.682	0.72
85_A	92_P	0.679	0.72
14_I	285_T	0.677	0.71
40_L	67_D	0.676	0.71
45_L	80_A	0.676	0.71
202_Y	207_R	0.675	0.71
187_D	202_Y	0.674	0.71
83_E	87_N	0.674	0.71
22_K	48_F	0.672	0.71
71_R	74_F	0.672	0.71
243_S	276_F	0.667	0.70
14_I	26_I	0.663	0.70
133_L	136_E	0.662	0.70
259_T	288_D	0.661	0.70
55_S	168_G	0.659	0.69
220_V	226_T	0.659	0.69
218_S	221_M	0.658	0.69
140_R	144_I	0.657	0.69
102_S	106_T	0.656	0.69
110_E	202_Y	0.656	0.69
288_D	291_K	0.656	0.69
93_R	162_H	0.655	0.69
89_W	92_P	0.653	0.69
17_M	247_E	0.653	0.69
44_L	108_Y	0.652	0.68
192_F	242_P	0.651	0.68
236_L	249_K	0.651	0.68
239_F	243_S	0.649	0.68
165_T	227_Q	0.649	0.68
70_G	74_F	0.647	0.68
273_A	277_K	0.641	0.67
196_F	244_Y	0.637	0.67
212_K	215_E	0.635	0.66
124_L	237_L	0.634	0.66
94_I	137_L	0.633	0.66
76_R	79_E	0.632	0.66
37_V	208_P	0.632	0.66
80_A	83_E	0.631	0.66
85_A	91_T	0.631	0.66
156_R	242_P	0.628	0.66
181_K	201_Y	0.628	0.66
35_F	40_L	0.627	0.65
43_S	76_R	0.620	0.65
95_L	159_I	0.614	0.64
171_F	245_K	0.614	0.64
145_Y	158_K	0.610	0.63
94_I	140_R	0.608	0.63
103_I	262_Q	0.607	0.63
77_L	80_A	0.600	0.62
101_D	126_G	0.599	0.62
11_L	92_P	0.599	0.62
48_F	52_M	0.599	0.62
27_Q	108_Y	0.598	0.62
221_M	227_Q	0.594	0.61
114_S	196_F	0.590	0.61
171_F	252_V	0.590	0.61
156_R	248_G	0.590	0.61
109_K	187_D	0.589	0.61
228_K	243_S	0.588	0.61
11_L	62_V	0.587	0.60
229_F	240_M	0.587	0.60
65_V	288_D	0.586	0.60
127_I	241_L	0.586	0.60
15_T	67_D	0.584	0.60
98_D	101_D	0.584	0.60
143_I	254_I	0.584	0.60
106_T	256_I	0.582	0.60
109_K	251_Q	0.581	0.60
108_Y	188_A	0.581	0.60
160_V	249_K	0.580	0.59
150_M	154_D	0.580	0.59
202_Y	251_Q	0.579	0.59
63_A	117_L	0.578	0.59
46_P	80_A	0.578	0.59
32_L	160_V	0.578	0.59
18_S	48_F	0.575	0.59
190_L	233_L	0.574	0.59
35_F	198_P	0.574	0.59
227_Q	230_N	0.574	0.59
176_M	187_D	0.573	0.59
205_S	208_P	0.572	0.58
49_L	90_I	0.572	0.58
65_V	141_S	0.572	0.58
108_Y	197_L	0.572	0.58
106_T	190_L	0.571	0.58
203_I	208_P	0.570	0.58
38_D	189_D	0.570	0.58
79_E	87_N	0.569	0.58
22_K	111_T	0.568	0.58
172_T	283_H	0.568	0.58
233_L	239_F	0.568	0.58
68_L	117_L	0.567	0.58
241_L	248_G	0.567	0.58
121_G	126_G	0.566	0.58
40_L	48_F	0.566	0.58
142_Q	162_H	0.565	0.58
28_S	160_V	0.565	0.58
46_P	64_L	0.565	0.58
12_V	95_L	0.564	0.57
11_L	93_R	0.562	0.57
215_E	219_Y	0.561	0.57
40_L	69_R	0.560	0.57
95_L	254_I	0.559	0.57
138_K	248_G	0.558	0.57
111_T	126_G	0.557	0.56
36_C	110_E	0.557	0.56
45_L	117_L	0.556	0.56
9_I	23_T	0.554	0.56
269_A	272_L	0.554	0.56
83_E	90_I	0.552	0.56
110_E	242_P	0.552	0.56
66_M	70_G	0.552	0.56
196_F	247_E	0.551	0.56
123_P	249_K	0.549	0.55
217_S	270_E	0.549	0.55
125_E	285_T	0.548	0.55
11_L	64_L	0.548	0.55
61_K	236_L	0.548	0.55
106_T	137_L	0.546	0.55
99_A	205_S	0.545	0.55
12_V	50_E	0.545	0.55
20_A	174_N	0.544	0.55
238_S	278_K	0.544	0.55
235_D	278_K	0.543	0.55
54_E	191_V	0.540	0.54
17_M	126_G	0.539	0.54
39_N	288_D	0.538	0.54
115_H	266_V	0.538	0.54
226_T	267_T	0.536	0.54
176_M	188_A	0.536	0.54
70_G	77_L	0.535	0.53
148_S	207_R	0.535	0.53
23_T	157_E	0.534	0.53
237_L	254_I	0.534	0.53
94_I	154_D	0.532	0.53
42_P	201_Y	0.532	0.53
53_K	90_I	0.532	0.53
11_L	106_T	0.531	0.53
29_F	237_L	0.531	0.53
100_K	186_I	0.530	0.53
12_V	25_A	0.530	0.53
104_L	152_P	0.530	0.53
44_L	47_K	0.530	0.53
119_A	125_E	0.530	0.53
93_R	163_F	0.529	0.53
68_L	133_L	0.528	0.53
75_D	133_L	0.528	0.53
192_F	252_V	0.526	0.52
70_G	202_Y	0.526	0.52
64_L	185_P	0.525	0.52
226_T	229_F	0.524	0.52
94_I	282_T	0.524	0.52
14_I	72_E	0.523	0.52
235_D	238_S	0.522	0.52
106_T	141_S	0.520	0.51
147_T	269_A	0.517	0.51
37_V	40_L	0.517	0.51
49_L	92_P	0.517	0.51
15_T	249_K	0.517	0.51
14_I	198_P	0.516	0.51
129_L	234_I	0.515	0.51
22_K	202_Y	0.515	0.51
114_S	156_R	0.514	0.51
14_I	25_A	0.513	0.50
14_I	289_I	0.513	0.50
109_K	184_I	0.513	0.50
229_F	232_K	0.512	0.50
15_T	59_M	0.511	0.50
42_P	187_D	0.511	0.50
108_Y	122_L	0.511	0.50
85_A	149_D	0.511	0.50
29_F	163_F	0.509	0.50
44_L	171_F	0.508	0.50
86_E	89_W	0.507	0.50
12_V	163_F	0.506	0.50
28_S	163_F	0.505	0.49
64_L	152_P	0.505	0.49
234_I	237_L	0.505	0.49
60_S	141_S	0.504	0.49
24_V	152_P	0.502	0.49
85_A	90_I	0.502	0.49
15_T	94_I	0.500	0.49
231_E	234_I	0.500	0.49

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
3nwjA	2	0.5051	99.7	0.854	Contact Map
2if2A	1	0.5186	99.6	0.864	Contact Map
3lw7A	2	0.4881	99.6	0.865	Contact Map
2grjA	2	0.4814	99.5	0.874	Contact Map
1knqA	2	0.5186	99.5	0.875	Contact Map
1ckeA	1	0.5119	99.5	0.875	Contact Map
1ak2A	1	0.5254	99.5	0.875	Contact Map
2pezA	2	0.5153	99.5	0.876	Contact Map
3trfA	2	0.5051	99.5	0.877	Contact Map
3kb2A	2	0.5288	99.5	0.877	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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