YOSP - BACSU - GREMLIN Contacts

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YOSP - SPBc2 prophage-derived ribonucleoside-diphosphate reductase subunit beta

UniProt:	O30601	Sequences: MTKIYDAANWSKHEDDFTQMFYNQNVKQFWLPEEIALNGDLLTWKYLGKNEQDTYMKVLAGLTLLDTEQGNTGMPIVAEHVDGHQRKAVLNFMAMMENAVHAKSYSNIFLTLAPTEQINEVFEWVKNNRFLQKKARTIVSVYKTIKKNDEISLFKGMVASVFLESFLFYSGFYYPLYFYGQGKLMQSGEIINLIIRDEAIHGVYVGLLAQEIYKKQTPQKQKELYAWALNLLQELYENELEYTEDVYDQVGLAPDVKKFIRYNANKALNNLGFDHWFEEEDVNPIVINGLNTKTKSHDFFSTKGNGYKKATVEPLKDSDFIFTEKGCIQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	329 (300)
Sequences:	2184 (804)
Seq/√Len:	46.4

ECOLI - RIR4 RIR2
BACSU - YOSP RIR2
HALSA - Q9HMU4
SULSO - Q97VV7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
133_K	241_E	5.830	1.00
244_E	257_K	4.713	1.00
49_K	52_Q	4.226	1.00
265_N	278_E	4.110	1.00
240_L	261_R	4.072	1.00
35_I	104_S	3.972	1.00
132_Q	136_R	3.490	1.00
155_K	227_W	3.425	1.00
56_M	117_Q	3.380	1.00
53_D	57_K	3.248	1.00
229_L	276_W	2.992	1.00
233_Q	276_W	2.967	1.00
162_F	232_L	2.924	1.00
48_G	51_E	2.828	1.00
236_Y	277_F	2.787	1.00
229_L	268_L	2.606	1.00
240_L	257_K	2.415	1.00
157_M	208_L	2.389	1.00
229_L	273_F	2.302	1.00
229_L	274_D	2.302	1.00
164_E	198_E	2.295	1.00
236_Y	264_A	2.291	1.00
158_V	228_A	2.168	1.00
129_R	133_K	2.098	1.00
230_N	234_E	2.095	1.00
226_A	230_N	2.072	1.00
44_W	52_Q	2.071	1.00
66_D	105_Y	2.054	1.00
43_T	46_Y	2.003	0.99
228_A	273_F	1.989	0.99
233_Q	277_F	1.970	0.99
41_L	45_K	1.957	0.99
69_Q	142_Y	1.921	0.99
261_R	279_E	1.915	0.99
97_E	164_E	1.914	0.99
10_W	88_A	1.884	0.99
56_M	113_A	1.852	0.99
198_E	201_H	1.843	0.99
209_A	216_Q	1.830	0.99
237_E	241_E	1.827	0.99
26_V	31_L	1.813	0.99
222_K	226_A	1.779	0.99
229_L	233_Q	1.750	0.98
37_L	107_N	1.734	0.98
283_N	286_V	1.730	0.98
25_N	96_M	1.716	0.98
222_K	225_Y	1.707	0.98
32_P	104_S	1.707	0.98
97_E	198_E	1.686	0.98
91_N	94_A	1.682	0.98
286_V	289_G	1.673	0.98
23_N	33_E	1.653	0.98
227_W	230_N	1.648	0.98
89_V	204_Y	1.600	0.97
17_F	211_E	1.596	0.97
178_F	184_L	1.580	0.97
50_N	249_Q	1.574	0.97
104_S	190_I	1.548	0.96
287_I	290_L	1.547	0.96
151_I	227_W	1.547	0.96
193_L	196_R	1.547	0.96
15_D	83_G	1.537	0.96
91_N	99_A	1.532	0.96
255_D	258_K	1.512	0.96
286_V	290_L	1.493	0.96
140_S	234_E	1.492	0.96
269_N	275_H	1.463	0.95
209_A	273_F	1.460	0.95
172_F	307_Y	1.454	0.95
149_D	152_S	1.450	0.95
285_I	289_G	1.445	0.95
44_W	56_M	1.435	0.95
168_F	194_I	1.434	0.95
134_K	239_E	1.420	0.94
25_N	93_M	1.412	0.94
92_F	95_M	1.402	0.94
92_F	96_M	1.400	0.94
51_E	183_K	1.394	0.94
244_E	254_P	1.383	0.93
144_T	155_K	1.375	0.93
154_F	209_A	1.360	0.93
218_P	274_D	1.360	0.93
166_F	232_L	1.359	0.93
26_V	32_P	1.348	0.92
168_F	198_E	1.345	0.92
101_H	201_H	1.327	0.92
52_Q	56_M	1.326	0.92
257_K	261_R	1.320	0.92
7_A	12_K	1.297	0.91
233_Q	237_E	1.293	0.91
47_L	184_L	1.283	0.90
133_K	234_E	1.276	0.90
136_R	140_S	1.265	0.90
189_E	305_N	1.264	0.90
225_Y	274_D	1.238	0.89
45_K	114_P	1.236	0.89
32_P	35_I	1.230	0.88
297_H	302_T	1.229	0.88
173_Y	243_T	1.226	0.88
136_R	274_D	1.223	0.88
70_G	99_A	1.209	0.88
298_D	301_S	1.202	0.87
241_E	244_E	1.186	0.87
108_I	187_S	1.184	0.87
258_K	279_E	1.167	0.86
23_N	103_K	1.161	0.85
158_V	271_L	1.161	0.85
173_Y	287_I	1.154	0.85
62_L	69_Q	1.153	0.85
61_G	242_Y	1.143	0.84
97_E	168_F	1.138	0.84
168_F	172_F	1.135	0.84
244_E	248_D	1.133	0.84
23_N	31_L	1.132	0.84
303_K	309_K	1.125	0.84
179_Y	188_G	1.121	0.83
21_F	87_K	1.118	0.83
210_Q	213_Y	1.117	0.83
152_S	155_K	1.106	0.82
41_L	111_T	1.104	0.82
117_Q	120_E	1.098	0.82
54_T	246_V	1.089	0.81
50_N	248_D	1.078	0.81
55_Y	187_S	1.060	0.80
151_I	223_E	1.058	0.80
301_S	304_G	1.056	0.79
35_I	193_L	1.056	0.79
32_P	107_N	1.054	0.79
172_F	198_E	1.052	0.79
134_K	242_Y	1.046	0.79
16_D	20_M	1.026	0.77
48_G	257_K	1.003	0.76
172_F	201_H	0.998	0.75
213_Y	220_K	0.994	0.75
236_Y	261_R	0.993	0.75
248_D	255_D	0.988	0.75
17_F	20_M	0.985	0.74
240_L	244_E	0.982	0.74
171_G	194_I	0.978	0.74
201_H	307_Y	0.976	0.74
32_P	100_V	0.975	0.74
81_V	153_L	0.974	0.74
144_T	151_I	0.973	0.74
153_L	157_M	0.971	0.73
42_L	45_K	0.971	0.73
237_E	240_L	0.966	0.73
19_Q	23_N	0.964	0.73
206_G	270_N	0.954	0.72
176_L	195_I	0.953	0.72
211_E	215_K	0.951	0.72
230_N	237_E	0.950	0.72
88_A	99_A	0.950	0.72
51_E	250_V	0.949	0.72
17_F	207_L	0.944	0.71
49_K	255_D	0.943	0.71
43_T	178_F	0.940	0.71
76_I	79_E	0.939	0.71
202_G	267_A	0.936	0.71
35_I	196_R	0.930	0.70
225_Y	273_F	0.927	0.70
261_R	277_F	0.922	0.69
66_D	187_S	0.919	0.69
88_A	91_N	0.919	0.69
213_Y	225_Y	0.916	0.69
26_V	100_V	0.913	0.69
18_T	211_E	0.911	0.69
263_N	267_A	0.911	0.69
138_I	163_L	0.909	0.68
294_T	306_G	0.903	0.68
29_F	92_F	0.902	0.68
101_H	197_D	0.900	0.68
15_D	211_E	0.900	0.68
166_F	170_S	0.896	0.67
180_G	286_V	0.894	0.67
225_Y	229_L	0.892	0.67
22_Y	103_K	0.891	0.67
151_I	221_Q	0.889	0.67
262_Y	266_K	0.889	0.67
74_M	79_E	0.884	0.66
227_W	231_L	0.879	0.66
66_D	307_Y	0.873	0.65
173_Y	255_D	0.871	0.65
189_E	193_L	0.867	0.65
45_K	230_N	0.866	0.65
164_E	172_F	0.865	0.64
39_G	43_T	0.865	0.64
204_Y	208_L	0.864	0.64
106_S	110_L	0.862	0.64
164_E	201_H	0.860	0.64
248_D	253_A	0.859	0.64
66_D	201_H	0.857	0.64
87_K	91_N	0.856	0.64
19_Q	103_K	0.849	0.63
14_E	84_H	0.848	0.63
101_H	307_Y	0.845	0.63
265_N	279_E	0.844	0.63
160_S	205_V	0.843	0.62
202_G	266_K	0.838	0.62
107_N	110_L	0.827	0.61
122_F	131_L	0.824	0.61
62_L	171_G	0.822	0.61
243_T	260_I	0.821	0.60
136_R	277_F	0.815	0.60
46_Y	183_K	0.808	0.59
36_A	39_G	0.807	0.59
295_K	306_G	0.807	0.59
49_K	244_E	0.800	0.58
49_K	228_A	0.799	0.58
175_P	191_I	0.793	0.58
165_S	267_A	0.790	0.57
268_L	276_W	0.787	0.57
49_K	233_Q	0.784	0.57
229_L	275_H	0.784	0.57
212_I	215_K	0.782	0.57
283_N	287_I	0.781	0.57
66_D	197_D	0.781	0.57
123_E	127_N	0.779	0.56
248_D	254_P	0.777	0.56
86_R	208_L	0.775	0.56
7_A	11_S	0.775	0.56
136_R	230_N	0.775	0.56
18_T	207_L	0.771	0.56
179_Y	192_N	0.768	0.55
105_Y	201_H	0.766	0.55
37_L	190_I	0.766	0.55
170_S	260_I	0.763	0.55
120_E	244_E	0.761	0.55
93_M	168_F	0.759	0.54
275_H	278_E	0.753	0.54
134_K	238_N	0.749	0.53
265_N	275_H	0.748	0.53
136_R	276_W	0.746	0.53
202_G	262_Y	0.744	0.53
134_K	298_D	0.743	0.53
120_E	127_N	0.742	0.53
21_F	203_V	0.742	0.53
9_N	12_K	0.741	0.53
25_N	204_Y	0.740	0.53
19_Q	22_Y	0.738	0.52
17_F	32_P	0.737	0.52
18_T	86_R	0.737	0.52
46_Y	120_E	0.737	0.52
198_E	307_Y	0.736	0.52
23_N	27_K	0.734	0.52
91_N	227_W	0.734	0.52
95_M	100_V	0.731	0.52
285_I	288_N	0.730	0.52
101_H	172_F	0.730	0.52
164_E	168_F	0.729	0.51
151_I	224_L	0.729	0.51
295_K	302_T	0.729	0.51
182_G	305_N	0.728	0.51
127_N	274_D	0.728	0.51
38_N	41_L	0.728	0.51
285_I	290_L	0.725	0.51
81_V	157_M	0.725	0.51
37_L	186_Q	0.725	0.51
100_V	310_A	0.723	0.51
25_N	28_Q	0.721	0.51
133_K	137_T	0.720	0.51
39_G	42_L	0.720	0.51
127_N	136_R	0.711	0.50
192_N	295_K	0.710	0.50
209_A	271_L	0.710	0.50
204_Y	207_L	0.710	0.50
42_L	241_E	0.703	0.49
42_L	255_D	0.703	0.49
97_E	201_H	0.703	0.49
237_E	244_E	0.694	0.48
128_N	162_F	0.690	0.48
197_D	201_H	0.689	0.48
45_K	50_N	0.688	0.47
49_K	218_P	0.686	0.47
45_K	120_E	0.685	0.47
25_N	89_V	0.684	0.47
232_L	264_A	0.684	0.47
258_K	313_E	0.683	0.47
74_M	78_A	0.683	0.47
283_N	289_G	0.680	0.47
259_F	299_F	0.679	0.47
55_Y	62_L	0.679	0.47
236_Y	240_L	0.679	0.47
130_F	245_D	0.678	0.46
54_T	250_V	0.677	0.46
243_T	257_K	0.677	0.46
168_F	201_H	0.676	0.46
286_V	292_T	0.676	0.46
105_Y	172_F	0.675	0.46
122_F	125_V	0.675	0.46
285_I	293_K	0.672	0.46
34_E	303_K	0.670	0.46
66_D	168_F	0.668	0.45
80_H	156_G	0.668	0.45
128_N	245_D	0.667	0.45
101_H	198_E	0.664	0.45
25_N	200_I	0.664	0.45
207_L	211_E	0.664	0.45
297_H	304_G	0.662	0.45
106_S	309_K	0.661	0.45
244_E	261_R	0.655	0.44
162_F	235_L	0.652	0.44
31_L	100_V	0.647	0.43
216_Q	220_K	0.646	0.43
289_G	292_T	0.646	0.43
105_Y	198_E	0.645	0.43
46_Y	274_D	0.645	0.43
20_M	234_E	0.643	0.43
214_K	273_F	0.639	0.43
299_F	304_G	0.637	0.42
298_D	304_G	0.636	0.42
70_G	94_A	0.635	0.42
14_E	100_V	0.633	0.42
140_S	144_T	0.631	0.42
261_R	265_N	0.631	0.42
129_R	274_D	0.631	0.42
69_Q	163_L	0.627	0.41
171_G	175_P	0.626	0.41
211_E	218_P	0.623	0.41
75_P	78_A	0.622	0.41
194_I	198_E	0.622	0.41
68_E	134_K	0.620	0.41
54_T	174_Y	0.616	0.40
26_V	92_F	0.616	0.40
257_K	260_I	0.613	0.40
66_D	106_S	0.613	0.40
151_I	217_T	0.611	0.40
57_K	260_I	0.611	0.40
101_H	168_F	0.608	0.40
162_F	228_A	0.608	0.40
123_E	226_A	0.607	0.40
97_E	105_Y	0.605	0.39
36_A	186_Q	0.604	0.39
95_M	99_A	0.602	0.39
100_V	246_V	0.601	0.39
199_A	203_V	0.599	0.39
254_P	257_K	0.597	0.39
289_G	293_K	0.596	0.39
29_F	65_L	0.596	0.39
214_K	255_D	0.594	0.38
52_Q	254_P	0.594	0.38
30_W	40_D	0.594	0.38
274_D	278_E	0.592	0.38
64_L	193_L	0.592	0.38
47_L	52_Q	0.591	0.38
205_V	260_I	0.591	0.38
66_D	205_V	0.591	0.38
137_T	141_V	0.588	0.38
144_T	150_E	0.586	0.38
226_A	229_L	0.585	0.38
14_E	17_F	0.584	0.37
66_D	101_H	0.582	0.37
55_Y	184_L	0.581	0.37
143_K	255_D	0.580	0.37
65_L	69_Q	0.579	0.37
135_A	259_F	0.577	0.37
105_Y	202_G	0.575	0.37
206_G	271_L	0.573	0.36
117_Q	122_F	0.573	0.36
269_N	278_E	0.572	0.36
108_I	169_Y	0.572	0.36
173_Y	260_I	0.570	0.36
259_F	267_A	0.569	0.36
117_Q	230_N	0.569	0.36
226_A	278_E	0.568	0.36
125_V	135_A	0.568	0.36
86_R	204_Y	0.568	0.36
6_D	14_E	0.567	0.36
162_F	259_F	0.566	0.36
180_G	189_E	0.563	0.36
179_Y	184_L	0.563	0.36
152_S	240_L	0.563	0.36
63_T	194_I	0.561	0.35
163_L	175_P	0.560	0.35
66_D	262_Y	0.559	0.35
21_F	24_Q	0.558	0.35
25_N	92_F	0.557	0.35
177_Y	181_Q	0.556	0.35
158_V	224_L	0.556	0.35
87_K	304_G	0.555	0.35
16_D	45_K	0.554	0.35
155_K	224_L	0.554	0.35
221_Q	224_L	0.554	0.35
130_F	246_V	0.553	0.35
62_L	298_D	0.553	0.35
274_D	280_E	0.551	0.34
139_V	143_K	0.550	0.34
53_D	58_V	0.547	0.34
217_T	220_K	0.547	0.34
21_F	204_Y	0.546	0.34
215_K	218_P	0.543	0.34
78_A	94_A	0.541	0.34
165_S	186_Q	0.540	0.33
129_R	229_L	0.539	0.33
160_S	202_G	0.539	0.33
116_E	120_E	0.538	0.33
18_T	83_G	0.538	0.33
233_Q	280_E	0.537	0.33
184_L	190_I	0.533	0.33
247_Y	268_L	0.531	0.33
213_Y	272_G	0.530	0.33
168_F	307_Y	0.530	0.33
142_Y	169_Y	0.529	0.32
60_A	121_V	0.529	0.32
49_K	151_I	0.528	0.32
49_K	129_R	0.528	0.32
133_K	139_V	0.528	0.32
224_L	273_F	0.527	0.32
160_S	170_S	0.526	0.32
165_S	202_G	0.526	0.32
297_H	303_K	0.526	0.32
259_F	296_S	0.525	0.32
157_M	213_Y	0.525	0.32
133_K	238_N	0.524	0.32
12_K	85_Q	0.523	0.32
252_L	256_V	0.522	0.32
66_D	172_F	0.520	0.32
46_Y	178_F	0.519	0.32
30_W	101_H	0.519	0.32
15_D	18_T	0.518	0.32
185_M	302_T	0.518	0.32
68_E	108_I	0.518	0.32
72_T	93_M	0.517	0.31
49_K	274_D	0.517	0.31
273_F	276_W	0.516	0.31
270_N	301_S	0.515	0.31
21_F	44_W	0.515	0.31
22_Y	32_P	0.514	0.31
164_E	194_I	0.513	0.31
155_K	231_L	0.512	0.31
265_N	268_L	0.512	0.31
262_Y	284_P	0.512	0.31
90_L	205_V	0.512	0.31
144_T	149_D	0.511	0.31
150_E	218_P	0.511	0.31
295_K	305_N	0.510	0.31
236_Y	260_I	0.508	0.31
59_L	187_S	0.508	0.31
183_K	276_W	0.507	0.31
97_E	172_F	0.506	0.31
56_M	70_G	0.506	0.31
57_K	246_V	0.505	0.30
251_G	283_N	0.505	0.30
59_L	109_F	0.504	0.30
10_W	204_Y	0.504	0.30
92_F	99_A	0.504	0.30
59_L	63_T	0.503	0.30
105_Y	164_E	0.502	0.30
213_Y	216_Q	0.501	0.30
10_W	15_D	0.500	0.30
310_A	314_P	0.500	0.30

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
4dr0A	2	0.8815	100	0.112	Contact Map
4bmoA	2	0.8754	100	0.121	Contact Map
4n83A	4	0.8602	100	0.123	Contact Map
3n37A	2	0.8571	100	0.124	Contact Map
3dhzA	2	0.8632	100	0.133	Contact Map
1mxrA	2	0.8693	100	0.153	Contact Map
1jk0A	1	0.8359	100	0.157	Contact Map
2rccA	4	0.8784	100	0.16	Contact Map
1h0oA	2	0.8328	100	0.164	Contact Map
1jk0B	1	0.7508	100	0.166	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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