RIR4 - ECOLI - GREMLIN Contacts

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RIR4 - Ribonucleoside-diphosphate reductase 2 subunit beta

UniProt:	P37146	Sequences: MKLSRISAINWNKISDDKDLEVWNRLTSNFWLPEKVPLSNDIPAWQTLTVVEQQLTMRVFTGLTLLDTLQNVIGAPSLMPDALTPHEEAVLSNISFMEAVHARSYSSIFSTLCQTKDVDAAYAWSEENAPLQRKAQIIQQHYRGDDPLKKKIASVFLESFLFYSGFWLPMYFSSRGKLTNTADLIRLIIRDEAVHGYYIGYKYQKNMEKISLGQREELKSFAFDLLLELYDNELQYTDELYAETPWADDVKAFLCYNANKALMNLGYEPLFPAEMAEVNPAILAALSPNADENHDFFSGSGSSYVMGKAVETEDEDWNF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12381
Length:	319 (298)
Sequences:	2222 (806)
Seq/√Len:	46.7

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_R	235_Q	5.866	1.00
238_D	251_K	5.059	1.00
50_V	53_Q	4.318	1.00
234_L	255_C	4.153	1.00
36_V	104_S	4.111	1.00
259_N	272_P	4.041	1.00
57_M	117_D	3.831	1.00
132_Q	136_Q	3.758	1.00
54_Q	58_R	3.517	1.00
279_N	282_I	3.341	1.00
227_L	270_L	3.294	1.00
49_T	52_E	3.203	1.00
223_F	270_L	3.098	1.00
230_Y	271_F	3.089	1.00
156_F	226_L	2.908	1.00
223_F	268_E	2.577	1.00
223_F	262_L	2.562	1.00
278_V	282_I	2.346	1.00
234_L	251_K	2.340	1.00
216_E	220_S	2.322	1.00
158_E	192_E	2.318	1.00
149_K	221_F	2.288	1.00
277_E	282_I	2.283	1.00
224_D	228_E	2.273	1.00
230_Y	258_A	2.257	1.00
223_F	267_Y	2.239	1.00
129_A	133_R	2.221	1.00
152_I	222_A	2.212	1.00
98_E	158_E	2.208	1.00
45_W	53_Q	2.146	1.00
216_E	219_K	2.139	1.00
255_C	273_A	2.097	1.00
231_D	235_Q	2.090	1.00
192_E	195_H	2.089	1.00
151_K	202_K	2.061	1.00
227_L	271_F	2.052	1.00
203_Y	210_I	1.987	0.99
67_D	105_Y	1.981	0.99
172_F	178_L	1.959	0.99
27_T	32_L	1.955	0.99
104_S	184_L	1.920	0.99
38_L	107_S	1.872	0.99
92_S	95_S	1.859	0.99
11_W	89_A	1.857	0.99
57_M	113_C	1.853	0.99
26_L	97_M	1.849	0.99
70_Q	142_Y	1.846	0.99
42_I	46_Q	1.812	0.99
220_S	224_D	1.800	0.99
222_A	267_Y	1.792	0.99
98_E	192_E	1.765	0.98
223_F	227_L	1.743	0.98
18_K	205_K	1.729	0.98
92_S	99_A	1.716	0.98
33_P	104_S	1.702	0.98
16_D	84_T	1.628	0.97
90_V	198_Y	1.619	0.97
187_L	190_R	1.613	0.97
203_Y	267_Y	1.602	0.97
24_N	34_E	1.577	0.97
45_W	57_M	1.567	0.97
209_K	213_G	1.555	0.97
249_D	252_A	1.482	0.95
263_M	269_P	1.437	0.95
101_H	195_H	1.432	0.95
227_L	231_D	1.427	0.94
134_K	233_E	1.395	0.94
221_F	224_D	1.372	0.93
162_F	188_I	1.372	0.93
93_N	97_M	1.370	0.93
26_L	94_I	1.366	0.93
248_D	252_A	1.357	0.93
42_I	111_T	1.357	0.93
27_T	33_P	1.355	0.93
133_R	228_E	1.349	0.93
55_L	240_L	1.341	0.92
140_Q	228_E	1.336	0.92
251_K	255_C	1.331	0.92
183_D	302_S	1.329	0.92
162_F	192_E	1.323	0.92
33_P	36_V	1.321	0.92
62_G	236_Y	1.312	0.91
52_E	177_K	1.299	0.91
63_L	70_Q	1.286	0.91
295_D	298_S	1.286	0.91
93_N	96_F	1.279	0.90
22_V	88_E	1.252	0.89
136_Q	140_Q	1.247	0.89
242_A	247_A	1.233	0.89
205_K	209_K	1.228	0.89
160_F	226_L	1.225	0.88
71_N	99_A	1.222	0.88
24_N	103_R	1.220	0.88
46_Q	114_Q	1.220	0.88
166_F	304_Y	1.208	0.88
53_Q	57_M	1.206	0.88
108_I	181_T	1.203	0.87
234_L	238_D	1.201	0.87
43_P	46_Q	1.200	0.87
167_W	237_T	1.198	0.87
98_E	162_F	1.196	0.87
162_F	166_F	1.190	0.87
134_K	236_Y	1.187	0.87
219_K	268_E	1.165	0.86
117_D	120_A	1.157	0.85
294_H	299_G	1.149	0.85
144_G	149_K	1.147	0.85
206_N	209_K	1.140	0.84
136_Q	268_E	1.139	0.84
305_V	310_V	1.134	0.84
24_N	32_L	1.131	0.84
235_Q	238_D	1.120	0.83
174_S	281_A	1.120	0.83
8_A	13_K	1.117	0.83
48_L	178_L	1.116	0.83
300_S	306_M	1.116	0.83
210_I	213_G	1.109	0.83
298_S	301_G	1.100	0.82
40_N	44_A	1.095	0.82
173_S	182_A	1.082	0.81
56_T	181_T	1.079	0.81
278_V	281_A	1.052	0.79
33_P	100_V	1.046	0.79
88_E	92_S	1.043	0.79
17_D	21_E	1.038	0.78
18_K	21_E	1.038	0.78
36_V	187_L	1.031	0.78
219_K	223_F	1.020	0.77
51_V	243_E	1.002	0.76
230_Y	255_C	1.001	0.76
148_L	203_Y	0.995	0.75
204_Q	207_M	0.988	0.75
200_G	264_N	0.988	0.75
224_D	231_D	0.987	0.75
20_L	24_N	0.987	0.75
196_G	261_A	0.981	0.74
33_P	107_S	0.979	0.74
170_M	189_I	0.968	0.73
259_N	269_P	0.967	0.73
101_H	191_D	0.967	0.73
27_T	100_V	0.966	0.73
101_H	304_Y	0.966	0.73
133_R	137_I	0.949	0.72
196_G	260_K	0.942	0.71
169_P	185_I	0.934	0.71
252_A	273_A	0.928	0.70
231_D	234_L	0.928	0.70
46_Q	224_D	0.920	0.69
50_V	248_D	0.917	0.69
167_W	281_A	0.917	0.69
221_F	225_L	0.915	0.69
165_G	188_I	0.909	0.69
46_Q	51_V	0.907	0.68
166_F	192_E	0.905	0.68
156_F	229_L	0.905	0.68
160_F	164_S	0.900	0.68
20_L	103_R	0.896	0.67
223_F	269_P	0.893	0.67
256_Y	260_K	0.884	0.66
183_D	187_L	0.882	0.66
212_L	268_E	0.875	0.66
30_F	93_N	0.872	0.65
158_E	166_F	0.872	0.65
154_S	199_I	0.869	0.65
75_A	80_P	0.864	0.65
248_D	251_K	0.864	0.65
138_I	157_L	0.863	0.65
166_F	195_H	0.863	0.65
268_E	272_P	0.862	0.64
237_T	254_L	0.860	0.64
106_S	110_S	0.854	0.64
89_A	99_A	0.854	0.64
19_D	205_K	0.852	0.63
61_T	121_A	0.849	0.63
96_F	100_V	0.849	0.63
26_L	29_N	0.849	0.63
23_W	103_R	0.845	0.63
89_A	92_S	0.844	0.63
77_S	80_P	0.844	0.63
158_E	195_H	0.842	0.63
18_K	201_Y	0.841	0.62
44_A	172_F	0.839	0.62
257_N	261_A	0.838	0.62
159_S	261_A	0.834	0.62
207_M	219_K	0.829	0.61
38_L	184_L	0.827	0.61
136_Q	271_F	0.826	0.61
87_E	202_K	0.824	0.61
156_F	222_A	0.820	0.61
129_A	268_E	0.817	0.60
198_Y	202_K	0.816	0.60
16_D	205_K	0.814	0.60
92_S	221_F	0.812	0.60
36_V	190_R	0.812	0.60
148_L	221_F	0.809	0.59
81_D	150_K	0.808	0.59
67_D	181_T	0.808	0.59
259_N	262_L	0.804	0.59
37_P	40_N	0.802	0.59
120_A	127_E	0.795	0.58
24_N	28_S	0.795	0.58
237_T	251_K	0.794	0.58
143_R	146_D	0.793	0.58
255_C	271_F	0.786	0.57
292_E	299_G	0.785	0.57
292_E	303_S	0.779	0.57
71_N	95_S	0.777	0.56
173_S	186_R	0.776	0.56
134_K	295_D	0.774	0.56
8_A	12_N	0.773	0.56
123_A	127_E	0.771	0.56
38_L	180_N	0.768	0.55
44_A	47_T	0.767	0.55
209_K	212_L	0.767	0.55
107_S	110_S	0.764	0.55
195_H	304_Y	0.764	0.55
294_H	301_G	0.764	0.55
43_P	235_Q	0.760	0.55
136_Q	270_L	0.760	0.55
63_L	165_G	0.755	0.54
15_S	85_P	0.755	0.54
296_F	301_G	0.754	0.54
10_N	13_K	0.752	0.54
251_K	254_L	0.749	0.54
50_V	212_L	0.745	0.53
22_V	197_Y	0.742	0.53
203_Y	265_L	0.741	0.53
75_A	79_M	0.736	0.52
26_L	198_Y	0.735	0.52
67_D	191_D	0.734	0.52
50_V	227_L	0.733	0.52
116_K	120_A	0.731	0.52
20_L	23_W	0.731	0.52
230_Y	234_L	0.726	0.51
94_I	162_F	0.723	0.51
101_H	192_E	0.722	0.51
101_H	166_F	0.720	0.51
208_E	267_Y	0.719	0.51
164_S	254_L	0.716	0.50
32_L	100_V	0.713	0.50
67_D	195_H	0.712	0.50
201_Y	205_K	0.712	0.50
259_N	273_A	0.711	0.50
191_D	195_H	0.710	0.50
233_E	236_Y	0.709	0.50
158_E	162_F	0.708	0.50
192_E	304_Y	0.708	0.50
196_G	256_Y	0.708	0.50
37_P	180_N	0.706	0.49
70_Q	157_L	0.705	0.49
295_D	301_G	0.704	0.49
186_R	292_E	0.700	0.49
226_L	258_A	0.700	0.49
18_K	33_P	0.699	0.49
108_I	163_Y	0.698	0.49
174_S	183_D	0.695	0.48
189_I	286_L	0.693	0.48
66_L	70_Q	0.691	0.48
126_E	129_A	0.691	0.48
120_A	238_D	0.687	0.47
262_L	270_L	0.684	0.47
198_Y	201_Y	0.681	0.47
69_L	134_K	0.678	0.47
106_S	306_M	0.678	0.47
31_W	41_D	0.678	0.47
26_L	194_V	0.678	0.47
49_T	251_K	0.677	0.47
98_E	195_H	0.675	0.46
219_K	267_Y	0.672	0.46
19_D	201_Y	0.672	0.46
65_L	187_L	0.671	0.46
178_L	184_L	0.669	0.46
55_L	168_L	0.666	0.45
128_N	239_E	0.666	0.45
35_K	300_S	0.665	0.45
238_D	242_A	0.665	0.45
127_E	268_E	0.663	0.45
176_G	287_S	0.660	0.45
109_F	244_T	0.659	0.45
156_F	253_F	0.659	0.45
150_K	153_A	0.659	0.45
67_D	304_Y	0.657	0.45
139_Q	143_R	0.655	0.44
176_G	302_S	0.655	0.44
67_D	162_F	0.648	0.44
40_N	43_P	0.644	0.43
297_F	301_G	0.643	0.43
159_S	180_N	0.638	0.43
152_I	218_L	0.636	0.43
61_T	193_A	0.636	0.43
39_S	42_I	0.634	0.42
167_W	249_D	0.634	0.42
160_F	258_A	0.633	0.42
63_L	295_D	0.631	0.42
48_L	53_Q	0.630	0.42
152_I	265_L	0.626	0.42
165_G	169_P	0.626	0.42
255_C	259_N	0.625	0.41
162_F	195_H	0.625	0.41
64_T	109_F	0.618	0.41
140_Q	212_L	0.617	0.41
38_L	111_T	0.617	0.41
47_T	53_Q	0.616	0.41
130_P	239_E	0.615	0.40
26_L	93_N	0.612	0.40
105_Y	166_F	0.609	0.40
133_R	232_N	0.608	0.40
133_R	139_Q	0.608	0.40
133_R	238_D	0.608	0.40
269_P	272_P	0.607	0.40
268_E	273_A	0.606	0.40
67_D	256_Y	0.605	0.40
43_P	47_T	0.605	0.40
129_A	231_D	0.603	0.39
56_T	63_L	0.603	0.39
137_I	228_E	0.603	0.39
105_Y	195_H	0.601	0.39
285_A	289_N	0.601	0.39
148_L	210_I	0.600	0.39
50_V	238_D	0.600	0.39
219_K	224_D	0.600	0.39
50_V	222_A	0.600	0.39
60_F	64_T	0.598	0.39
145_D	203_Y	0.598	0.39
11_W	16_D	0.597	0.39
26_L	90_V	0.595	0.39
268_E	274_E	0.595	0.39
135_A	141_H	0.594	0.38
309_A	312_T	0.594	0.38
167_W	285_A	0.593	0.38
46_Q	120_A	0.593	0.38
58_R	240_L	0.593	0.38
96_F	99_A	0.591	0.38
76_P	79_M	0.588	0.38
67_D	106_S	0.588	0.38
19_D	87_E	0.587	0.38
205_K	208_E	0.585	0.38
238_D	254_L	0.584	0.38
154_S	196_G	0.584	0.38
30_F	66_L	0.583	0.37
50_V	129_A	0.581	0.37
191_D	304_Y	0.580	0.37
182_A	186_R	0.579	0.37
100_V	307_G	0.577	0.37
205_K	212_L	0.577	0.37
146_D	208_E	0.577	0.37
227_L	274_E	0.576	0.37
134_K	162_F	0.575	0.37
183_D	288_P	0.574	0.37
156_F	225_L	0.574	0.37
49_T	177_K	0.573	0.37
122_Y	125_S	0.573	0.37
9_I	12_N	0.572	0.36
154_S	164_S	0.570	0.36
67_D	101_H	0.569	0.36
199_I	254_L	0.567	0.36
79_M	95_S	0.567	0.36
31_W	101_H	0.567	0.36
100_V	240_L	0.563	0.36
188_I	192_E	0.562	0.36
57_M	71_N	0.562	0.36
64_T	241_Y	0.561	0.35
230_Y	254_L	0.558	0.35
283_L	286_L	0.557	0.35
67_D	199_I	0.557	0.35
112_L	289_N	0.557	0.35
141_H	221_F	0.556	0.35
70_Q	74_G	0.555	0.35
231_D	274_E	0.555	0.35
231_D	263_M	0.555	0.35
206_N	210_I	0.554	0.35
157_L	169_P	0.553	0.35
98_E	166_F	0.552	0.35
230_Y	259_N	0.552	0.35
231_D	238_D	0.551	0.35
93_N	99_A	0.551	0.35
162_F	304_Y	0.549	0.34
22_V	198_Y	0.549	0.34
51_V	212_L	0.547	0.34
22_V	45_W	0.546	0.34
15_S	100_V	0.545	0.34
207_M	210_I	0.545	0.34
144_G	228_E	0.545	0.34
108_I	112_L	0.544	0.34
50_V	268_E	0.543	0.34
294_H	298_S	0.543	0.34
36_V	180_N	0.540	0.34
177_K	227_L	0.539	0.33
136_Q	231_D	0.538	0.33
140_Q	143_R	0.538	0.33
55_L	243_E	0.537	0.33
93_N	100_V	0.535	0.33
149_K	218_L	0.534	0.33
101_H	162_F	0.534	0.33
43_P	224_D	0.534	0.33
159_S	196_G	0.533	0.33
153_A	225_L	0.532	0.33
66_L	104_S	0.531	0.33
122_Y	172_F	0.530	0.33
167_W	254_L	0.529	0.33
144_G	147_P	0.529	0.33
292_E	302_S	0.529	0.33
25_R	57_M	0.528	0.33
278_V	283_L	0.528	0.33
86_H	283_L	0.527	0.32
54_Q	59_V	0.527	0.32
264_N	298_S	0.527	0.32
127_E	136_Q	0.526	0.32
85_P	88_E	0.525	0.32
86_H	110_S	0.524	0.32
130_P	240_L	0.523	0.32
159_S	195_H	0.523	0.32
15_S	18_K	0.520	0.32
58_R	254_L	0.520	0.32
197_Y	261_A	0.520	0.32
253_F	282_I	0.519	0.32
60_F	181_T	0.519	0.32
139_Q	235_Q	0.517	0.32
253_F	296_F	0.516	0.31
136_Q	224_D	0.516	0.31
128_N	132_Q	0.515	0.31
64_T	188_I	0.515	0.31
105_Y	158_E	0.514	0.31
200_G	265_L	0.513	0.31
78_L	98_E	0.513	0.31
122_Y	131_L	0.512	0.31
218_L	267_Y	0.511	0.31
78_L	150_K	0.511	0.31
104_S	188_I	0.511	0.31
13_K	86_H	0.510	0.31
76_P	80_P	0.510	0.31
21_E	228_E	0.509	0.31
21_E	25_R	0.509	0.31
278_V	298_S	0.508	0.31
7_S	126_E	0.508	0.31
208_E	228_E	0.507	0.31
70_Q	199_I	0.507	0.31
91_L	199_I	0.507	0.31
233_E	266_G	0.506	0.31
263_M	272_P	0.504	0.30
66_L	282_I	0.503	0.30
98_E	105_Y	0.503	0.30
43_P	306_M	0.503	0.30
143_R	147_P	0.502	0.30
134_K	232_N	0.502	0.30
47_T	120_A	0.501	0.30
244_T	252_A	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
3n37A	2	0.884	100	0.072	Contact Map
3dhzA	2	0.8997	100	0.083	Contact Map
4dr0A	2	0.8934	100	0.086	Contact Map
4n83A	4	0.8871	100	0.091	Contact Map
4bmoA	2	0.884	100	0.091	Contact Map
2rccA	4	0.8934	100	0.101	Contact Map
1mxrA	2	0.8871	100	0.109	Contact Map
1jk0A	1	0.8621	100	0.118	Contact Map
1jk0B	1	0.7712	100	0.123	Contact Map
1syyA	2	0.8715	100	0.126	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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