DPO3B - BACSU - GREMLIN Contacts

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DPO3B - DNA polymerase III subunit beta

UniProt:	P05649	Sequences: MKFTIQKDRLVESVQDVLKAVSSRTTIPILTGIKIVASDDGVSFTGSDSDISIESFIPKEEGDKEIVTIEQPGSIVLQARFFSEIVKKLPMATVEIEVQNQYLTIIRSGKAEFNLNGLDADEYPHLPQIEEHHAIQIPTDLLKNLIRQTVFAVSTSETRPILTGVNWKVEQSELLCTATDSHRLALRKAKLDIPEDRSYNVVIPGKSLTELSKILDDNQELVDIVITETQVLFKAKNVLFFSRLLDGNYPDTTSLIPQDSKTEIIVNTKEFLQAIDRASLLAREGRNNVVKLSAKPAESIEISSNSPEIGKVVEAIVADQIEGEELNISFSPKYMLDALKVLEGAEIRVSFTGAMRPFLIRTPNDETIVQLILPVRTY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	378 (363)
Sequences:	3540 (2437)
Seq/√Len:	127.9

ECOLI - DPO3B
BACSU - DPO3B

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_F	96_I	4.259	1.00
32_G	76_V	3.697	1.00
36_V	74_S	3.593	1.00
265_I	346_E	3.285	1.00
267_N	270_E	3.212	1.00
251_D	254_S	3.158	1.00
231_V	242_S	3.148	1.00
272_L	336_L	3.110	1.00
136_Q	221_L	3.108	1.00
2_K	97_E	3.031	1.00
277_R	314_E	3.021	1.00
136_Q	223_D	2.854	1.00
167_W	176_C	2.760	1.00
41_G	56_F	2.729	1.00
153_V	205_G	2.698	1.00
299_S	315_A	2.692	1.00
88_K	276_D	2.613	1.00
37_A	69_I	2.516	1.00
59_K	69_I	2.493	1.00
173_E	188_K	2.485	1.00
35_I	42_V	2.467	1.00
350_S	361_R	2.412	1.00
38_S	72_P	2.387	1.00
263_E	348_R	2.374	1.00
295_K	325_E	2.291	1.00
263_E	350_S	2.280	1.00
152_A	185_A	2.250	1.00
264_I	294_A	2.219	1.00
170_E	198_S	2.194	1.00
278_A	312_V	2.181	1.00
177_T	252_T	2.180	1.00
166_N	200_N	2.157	1.00
223_D	234_K	2.130	1.00
2_K	70_E	2.105	1.00
80_R	84_E	2.079	1.00
35_I	82_F	2.078	1.00
292_L	335_M	2.074	1.00
293_S	327_N	2.063	1.00
21_V	79_A	1.988	1.00
85_I	113_F	1.971	1.00
318_A	321_I	1.971	1.00
300_I	318_A	1.970	1.00
134_A	223_D	1.967	1.00
346_E	363_P	1.956	1.00
338_A	370_Q	1.951	1.00
265_I	348_R	1.923	1.00
36_V	43_S	1.914	1.00
148_Q	187_R	1.882	1.00
95_E	107_R	1.880	1.00
142_L	222_V	1.864	1.00
77_L	103_L	1.840	1.00
33_I	44_F	1.810	1.00
202_V	245_L	1.808	1.00
267_N	346_E	1.793	1.00
161_I	247_G	1.785	1.00
135_I	224_I	1.779	1.00
145_L	176_C	1.771	1.00
161_I	202_V	1.751	1.00
224_I	233_F	1.715	1.00
35_I	44_F	1.698	1.00
37_A	59_K	1.697	1.00
211_L	233_F	1.685	1.00
261_K	324_E	1.684	1.00
207_S	242_S	1.675	1.00
14_V	83_S	1.671	1.00
330_F	358_F	1.671	1.00
38_S	41_G	1.670	1.00
266_V	271_F	1.641	1.00
7_K	11_V	1.640	1.00
301_E	313_V	1.618	1.00
175_L	188_K	1.587	1.00
256_I	369_V	1.567	1.00
265_I	320_Q	1.556	1.00
274_A	302_I	1.549	1.00
39_D	72_P	1.547	1.00
48_D	206_K	1.546	1.00
144_N	343_E	1.532	1.00
17_V	44_F	1.499	1.00
97_E	107_R	1.496	1.00
164_G	202_V	1.495	1.00
4_T	68_T	1.488	1.00
292_L	300_I	1.478	1.00
4_T	95_E	1.477	1.00
271_F	339_L	1.474	1.00
339_L	347_I	1.468	1.00
2_K	95_E	1.462	1.00
170_E	253_T	1.452	1.00
263_E	322_E	1.447	1.00
267_N	345_A	1.441	1.00
43_S	54_E	1.418	1.00
37_A	42_V	1.416	1.00
168_K	200_N	1.414	1.00
55_S	238_V	1.408	1.00
173_E	190_K	1.397	1.00
172_S	190_K	1.396	1.00
166_N	202_V	1.388	1.00
301_E	315_A	1.385	1.00
344_G	362_T	1.352	1.00
168_K	253_T	1.342	1.00
203_I	231_V	1.341	1.00
220_E	236_K	1.338	1.00
138_P	141_L	1.338	1.00
54_E	239_L	1.333	1.00
260_S	350_S	1.331	1.00
113_F	312_V	1.324	1.00
329_S	377_T	1.324	1.00
289_V	375_V	1.314	1.00
164_G	245_L	1.296	1.00
279_S	332_P	1.285	1.00
138_P	221_L	1.279	1.00
75_I	117_G	1.272	1.00
234_K	239_L	1.271	1.00
179_T	250_P	1.270	1.00
200_N	248_N	1.265	1.00
43_S	56_F	1.264	1.00
42_V	59_K	1.251	1.00
201_V	226_I	1.245	1.00
269_K	273_Q	1.242	1.00
159_R	181_S	1.240	1.00
82_F	96_I	1.231	1.00
4_T	93_T	1.228	1.00
47_S	52_S	1.214	0.99
44_F	57_I	1.208	0.99
183_R	337_D	1.205	0.99
30_L	124_P	1.203	0.99
298_E	320_Q	1.201	0.99
276_D	340_K	1.193	0.99
293_S	301_E	1.190	0.99
255_L	371_L	1.190	0.99
69_I	73_G	1.186	0.99
262_T	321_I	1.178	0.99
17_V	46_G	1.174	0.99
177_T	186_L	1.166	0.99
145_L	187_R	1.164	0.99
146_I	212_S	1.160	0.99
134_A	225_V	1.159	0.99
110_K	315_A	1.141	0.99
41_G	58_P	1.141	0.99
151_F	370_Q	1.136	0.99
348_R	361_R	1.133	0.99
34_K	45_T	1.130	0.99
172_S	192_D	1.127	0.99
35_I	75_I	1.121	0.99
10_L	96_I	1.119	0.99
293_S	303_S	1.109	0.99
320_Q	346_E	1.108	0.99
146_I	208_L	1.104	0.99
14_V	33_I	1.101	0.99
338_A	360_I	1.098	0.99
165_V	208_L	1.096	0.99
321_I	325_E	1.093	0.99
10_L	82_F	1.091	0.99
36_V	45_T	1.088	0.99
46_G	123_Y	1.088	0.99
184_L	257_P	1.084	0.99
119_D	122_E	1.077	0.99
37_A	72_P	1.072	0.99
145_L	189_A	1.069	0.99
74_S	121_D	1.065	0.99
166_N	177_T	1.062	0.99
165_V	178_A	1.061	0.99
291_K	327_N	1.059	0.99
4_T	70_E	1.059	0.99
114_N	311_K	1.056	0.99
98_V	103_L	1.051	0.98
13_S	55_S	1.047	0.98
261_K	352_T	1.047	0.98
148_Q	343_E	1.032	0.98
37_A	73_G	1.029	0.98
271_F	292_L	1.024	0.98
91_M	108_S	1.021	0.98
2_K	71_Q	1.018	0.98
275_I	290_V	1.015	0.98
131_E	225_V	1.012	0.98
257_P	359_L	1.010	0.98
34_K	74_S	1.006	0.98
40_D	58_P	1.005	0.98
155_T	205_G	0.999	0.98
295_K	301_E	0.987	0.98
264_I	321_I	0.986	0.98
296_P	325_E	0.986	0.98
29_I	76_V	0.985	0.98
167_W	174_L	0.984	0.98
89_L	94_V	0.975	0.97
265_I	363_P	0.970	0.97
168_K	175_L	0.970	0.97
32_G	118_L	0.968	0.97
184_L	256_I	0.967	0.97
183_R	334_Y	0.965	0.97
18_L	83_S	0.963	0.97
110_K	317_V	0.961	0.97
107_R	112_E	0.960	0.97
103_L	117_G	0.956	0.97
89_L	108_S	0.956	0.97
210_E	213_K	0.955	0.97
15_Q	87_K	0.953	0.97
152_A	178_A	0.945	0.97
6_Q	92_A	0.940	0.97
6_Q	9_R	0.940	0.97
6_Q	93_T	0.939	0.97
185_A	370_Q	0.938	0.97
268_T	272_L	0.938	0.97
151_F	341_V	0.936	0.97
359_L	371_L	0.935	0.97
76_V	120_A	0.934	0.97
224_I	231_V	0.933	0.97
338_A	341_V	0.923	0.96
20_A	46_G	0.920	0.96
127_P	230_Q	0.916	0.96
90_P	277_R	0.911	0.96
68_T	93_T	0.910	0.96
362_T	365_D	0.906	0.96
331_S	334_Y	0.906	0.96
13_S	44_F	0.904	0.96
154_S	157_E	0.900	0.96
30_L	49_S	0.899	0.96
274_A	316_I	0.895	0.96
33_I	46_G	0.895	0.96
175_L	253_T	0.891	0.96
268_T	347_I	0.890	0.96
13_S	57_I	0.887	0.96
207_S	240_F	0.884	0.96
69_I	72_P	0.883	0.95
180_D	183_R	0.883	0.95
348_R	363_P	0.883	0.95
248_N	251_D	0.872	0.95
172_S	193_I	0.870	0.95
40_D	72_P	0.865	0.95
294_A	300_I	0.863	0.95
184_L	250_P	0.861	0.95
150_V	165_V	0.860	0.95
295_K	299_S	0.860	0.95
178_A	185_A	0.859	0.95
17_V	20_A	0.858	0.95
169_V	199_Y	0.856	0.95
188_K	367_T	0.854	0.95
353_G	356_R	0.853	0.95
84_E	87_K	0.852	0.95
277_R	280_L	0.852	0.95
92_A	108_S	0.852	0.95
149_T	185_A	0.851	0.94
264_I	349_V	0.851	0.94
344_G	364_N	0.848	0.94
349_V	358_F	0.847	0.94
10_L	94_V	0.844	0.94
170_E	173_E	0.840	0.94
139_T	215_L	0.839	0.94
9_R	58_P	0.838	0.94
294_A	351_F	0.838	0.94
291_K	329_S	0.835	0.94
82_F	86_V	0.834	0.94
8_D	91_M	0.834	0.94
17_V	33_I	0.831	0.94
11_V	83_S	0.831	0.94
3_F	10_L	0.829	0.94
21_V	242_S	0.829	0.94
206_K	210_E	0.828	0.94
25_T	31_T	0.826	0.94
232_L	239_L	0.822	0.93
202_V	247_G	0.820	0.93
165_V	176_C	0.819	0.93
225_V	232_L	0.818	0.93
58_P	237_N	0.816	0.93
146_I	165_V	0.813	0.93
268_T	345_A	0.811	0.93
275_I	332_P	0.802	0.93
166_N	252_T	0.801	0.93
289_V	329_S	0.801	0.93
141_L	144_N	0.801	0.93
262_T	323_G	0.800	0.92
232_L	241_F	0.800	0.92
234_K	237_N	0.799	0.92
150_V	208_L	0.793	0.92
361_R	366_E	0.793	0.92
47_S	123_Y	0.791	0.92
274_A	314_E	0.788	0.92
174_L	191_L	0.783	0.92
203_I	208_L	0.782	0.92
359_L	369_V	0.781	0.92
183_R	331_S	0.778	0.91
96_I	103_L	0.776	0.91
231_V	244_L	0.773	0.91
262_T	326_L	0.771	0.91
160_P	163_T	0.769	0.91
33_I	79_A	0.768	0.91
355_M	376_R	0.768	0.91
207_S	233_F	0.766	0.91
77_L	104_T	0.765	0.91
45_T	54_E	0.764	0.91
85_I	281_L	0.763	0.91
158_T	162_L	0.763	0.91
21_V	123_Y	0.761	0.90
299_S	317_V	0.761	0.90
15_Q	83_S	0.760	0.90
141_L	189_A	0.759	0.90
90_P	314_E	0.759	0.90
142_L	176_C	0.758	0.90
328_I	351_F	0.755	0.90
186_L	253_T	0.751	0.90
286_R	308_E	0.749	0.90
164_G	204_P	0.748	0.90
38_S	43_S	0.747	0.90
272_L	340_K	0.747	0.90
264_I	318_A	0.746	0.90
17_V	53_I	0.742	0.89
153_V	178_A	0.742	0.89
322_E	348_R	0.741	0.89
290_V	332_P	0.740	0.89
12_E	16_D	0.739	0.89
71_Q	97_E	0.738	0.89
85_I	115_L	0.737	0.89
7_K	94_V	0.736	0.89
292_L	302_I	0.734	0.89
1_M	73_G	0.734	0.89
262_T	324_E	0.734	0.89
260_S	263_E	0.733	0.89
342_L	362_T	0.732	0.89
226_I	231_V	0.732	0.89
243_R	246_D	0.731	0.89
162_L	250_P	0.729	0.89
209_T	213_K	0.728	0.88
74_S	120_A	0.728	0.88
145_L	149_T	0.726	0.88
147_R	343_E	0.725	0.88
42_V	57_I	0.725	0.88
56_F	237_N	0.723	0.88
136_Q	193_I	0.723	0.88
135_I	191_L	0.717	0.88
102_Y	114_N	0.716	0.88
133_H	360_I	0.716	0.88
270_E	317_V	0.715	0.88
192_D	221_L	0.714	0.87
53_I	214_I	0.713	0.87
35_I	77_L	0.709	0.87
140_D	144_N	0.707	0.87
175_L	186_L	0.706	0.87
249_Y	252_T	0.706	0.87
225_V	234_K	0.701	0.87
71_Q	98_V	0.700	0.86
5_I	10_L	0.699	0.86
300_I	316_I	0.698	0.86
19_K	210_E	0.695	0.86
10_L	35_I	0.694	0.86
53_I	240_F	0.693	0.86
362_T	366_E	0.692	0.86
113_F	278_A	0.682	0.85
50_D	243_R	0.680	0.85
215_L	222_V	0.679	0.85
16_D	238_V	0.679	0.85
328_I	358_F	0.678	0.85
167_W	203_I	0.677	0.85
294_A	326_L	0.676	0.85
100_N	340_K	0.676	0.85
338_A	372_I	0.675	0.84
342_L	347_I	0.675	0.84
179_T	373_L	0.672	0.84
326_L	351_F	0.671	0.84
250_P	255_L	0.669	0.84
266_V	300_I	0.668	0.84
133_H	197_R	0.666	0.84
177_T	255_L	0.665	0.84
139_T	220_E	0.663	0.83
336_L	340_K	0.659	0.83
276_D	373_L	0.659	0.83
264_I	300_I	0.658	0.83
49_S	52_S	0.657	0.83
27_I	49_S	0.653	0.82
142_L	146_I	0.652	0.82
172_S	195_E	0.651	0.82
167_W	201_V	0.650	0.82
77_L	82_F	0.649	0.82
1_M	37_A	0.649	0.82
112_E	313_V	0.648	0.82
76_V	118_L	0.647	0.82
276_D	336_L	0.647	0.82
49_S	181_S	0.646	0.82
160_P	243_R	0.646	0.82
261_K	353_G	0.645	0.82
7_K	90_P	0.644	0.82
269_K	343_E	0.643	0.81
75_I	98_V	0.643	0.81
87_K	114_N	0.640	0.81
250_P	373_L	0.639	0.81
81_F	310_G	0.636	0.81
98_V	117_G	0.636	0.81
22_S	25_T	0.633	0.80
140_D	220_E	0.631	0.80
112_E	311_K	0.629	0.80
3_F	35_I	0.626	0.80
11_V	15_Q	0.626	0.80
293_S	325_E	0.626	0.80
3_F	37_A	0.625	0.80
104_T	107_R	0.624	0.79
53_I	238_V	0.623	0.79
100_N	347_I	0.621	0.79
186_L	252_T	0.621	0.79
153_V	165_V	0.619	0.79
41_G	237_N	0.618	0.79
275_I	372_I	0.618	0.79
7_K	86_V	0.617	0.79
81_F	88_K	0.616	0.79
45_T	52_S	0.616	0.79
49_S	252_T	0.615	0.79
29_I	118_L	0.614	0.78
36_V	72_P	0.614	0.78
5_I	57_I	0.612	0.78
182_H	288_N	0.610	0.78
34_K	120_A	0.608	0.78
333_K	337_D	0.608	0.78
168_K	246_D	0.608	0.78
296_P	322_E	0.607	0.78
355_M	373_L	0.606	0.78
56_F	72_P	0.605	0.77
289_V	332_P	0.604	0.77
7_K	91_M	0.603	0.77
289_V	377_T	0.601	0.77
49_S	243_R	0.597	0.76
158_T	246_D	0.597	0.76
204_P	242_S	0.596	0.76
271_F	302_I	0.596	0.76
139_T	216_D	0.593	0.76
278_A	302_I	0.593	0.76
162_L	255_L	0.591	0.76
99_Q	104_T	0.590	0.76
351_F	358_F	0.590	0.76
249_Y	342_L	0.589	0.75
139_T	235_A	0.589	0.75
104_T	112_E	0.588	0.75
166_N	249_Y	0.586	0.75
137_I	141_L	0.586	0.75
148_Q	362_T	0.585	0.75
224_I	245_L	0.584	0.75
171_Q	195_E	0.583	0.75
204_P	244_L	0.583	0.75
86_V	94_V	0.582	0.75
298_E	322_E	0.582	0.75
17_V	55_S	0.581	0.75
21_V	46_G	0.580	0.74
99_Q	134_A	0.580	0.74
143_K	217_D	0.580	0.74
211_L	240_F	0.579	0.74
211_L	230_Q	0.578	0.74
171_Q	196_D	0.577	0.74
174_L	189_A	0.575	0.74
42_V	244_L	0.575	0.74
159_R	202_V	0.574	0.74
260_S	359_L	0.571	0.73
4_T	106_I	0.569	0.73
30_L	47_S	0.569	0.73
146_I	211_L	0.568	0.73
198_S	293_S	0.564	0.72
88_K	373_L	0.563	0.72
118_L	122_E	0.563	0.72
27_I	50_D	0.562	0.72
153_V	208_L	0.560	0.72
361_R	369_V	0.560	0.72
132_H	237_N	0.559	0.72
99_Q	316_I	0.559	0.72
90_P	108_S	0.558	0.72
157_E	357_P	0.555	0.71
172_S	198_S	0.555	0.71
163_T	245_L	0.555	0.71
307_P	310_G	0.554	0.71
208_L	243_R	0.553	0.71
48_D	156_S	0.553	0.71
148_Q	268_T	0.552	0.71
8_D	311_K	0.551	0.71
2_K	46_G	0.551	0.71
340_K	373_L	0.550	0.70
147_R	212_S	0.549	0.70
211_L	215_L	0.548	0.70
269_K	345_A	0.548	0.70
98_V	104_T	0.546	0.70
361_R	368_I	0.545	0.70
330_F	371_L	0.545	0.70
154_S	158_T	0.544	0.70
22_S	82_F	0.544	0.70
190_K	367_T	0.542	0.69
181_S	252_T	0.542	0.69
161_I	245_L	0.542	0.69
38_S	220_E	0.542	0.69
35_I	96_I	0.542	0.69
350_S	359_L	0.541	0.69
16_D	55_S	0.540	0.69
359_L	373_L	0.539	0.69
210_E	240_F	0.539	0.69
47_S	371_L	0.538	0.69
119_D	234_K	0.538	0.69
117_G	127_P	0.536	0.69
20_A	51_I	0.535	0.68
184_L	252_T	0.534	0.68
252_T	373_L	0.534	0.68
275_I	287_N	0.532	0.68
52_S	126_L	0.531	0.68
271_F	347_I	0.531	0.68
260_S	352_T	0.530	0.68
129_I	230_Q	0.529	0.68
159_R	257_P	0.529	0.68
154_S	181_S	0.529	0.68
179_T	358_F	0.528	0.67
168_K	198_S	0.527	0.67
282_A	306_S	0.527	0.67
179_T	184_L	0.527	0.67
287_N	306_S	0.526	0.67
48_D	122_E	0.526	0.67
33_I	82_F	0.526	0.67
171_Q	270_E	0.526	0.67
10_L	44_F	0.525	0.67
20_A	44_F	0.523	0.67
294_A	321_I	0.523	0.67
129_I	232_L	0.523	0.67
339_L	360_I	0.521	0.66
266_V	347_I	0.520	0.66
29_I	288_N	0.519	0.66
95_E	296_P	0.519	0.66
42_V	320_Q	0.518	0.66
54_E	128_Q	0.518	0.66
182_H	249_Y	0.516	0.66
324_E	353_G	0.516	0.66
3_F	59_K	0.516	0.66
351_F	354_A	0.515	0.65
230_Q	377_T	0.512	0.65
57_I	82_F	0.511	0.65
177_T	184_L	0.511	0.65
181_S	356_R	0.510	0.65
150_V	212_S	0.510	0.65
189_A	229_T	0.508	0.64
6_Q	26_T	0.508	0.64
140_D	345_A	0.508	0.64
21_V	26_T	0.507	0.64
344_G	365_D	0.507	0.64
166_N	255_L	0.506	0.64
90_P	273_Q	0.506	0.64
171_Q	198_S	0.506	0.64
87_K	277_R	0.506	0.64
4_T	8_D	0.505	0.64
156_S	163_T	0.505	0.64
150_V	209_T	0.505	0.64
268_T	342_L	0.504	0.64
136_Q	354_A	0.503	0.64
295_K	298_E	0.503	0.64
106_I	259_D	0.503	0.64
39_D	223_D	0.502	0.64
162_L	179_T	0.500	0.63

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
4tr6A	2	0.9921	100	0.026	Contact Map
4tr8A	2	0.9577	100	0.028	Contact Map
4k3lA	2	0.9444	100	0.03	Contact Map
2avtA	2	0.9709	100	0.032	Contact Map
1vpkA	2	0.9656	100	0.038	Contact Map
5agvA	3	0.9603	100	0.041	Contact Map
3t0pA	2	0.963	100	0.041	Contact Map
4trtA	2	0.9444	100	0.062	Contact Map
3k4xA	1	0.8942	100	0.349	Contact Map
3ifvA	3	0.5926	100	0.573	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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