DPO4 - ECOLI - GREMLIN Contacts

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DPO4 - DNA polymerase IV

UniProt:	Q47155	Sequences: MRKIIHVDMDCFFAAVEMRDNPALRDIPIAIGGSRERRGVISTANYPARKFGVRSAMPTGMALKLCPHLTLLPGRFDAYKEASNHIREIFSRYTSRIEPLSLDEAYLDVTDSVHCHGSATLIAQEIRQTIFNELQLTASAGVAPVKFLAKIASDMNKPNGQFVITPAEVPAFLQTLPLAKIPGVGKVSAAKLEAMGLRTCGDVQKCDLVMLLKRFGKFGRILWERSQGIDERDVNSERLRKSVGVERTMAEDIHHWSECEAIIERLYPELERRLAKVKPDLLIARQGVKLKFDDFQQTTQEHVWPRLNKADLIATARKTWDERRGGRGVRLVGLHVTLLDPQMERQLVLGL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13141
Length:	351 (337)
Sequences:	8904 (6326)
Seq/√Len:	344.6

ECOLI - DPO4 UMUC
BACSU - DPO42 DPO41 UVRX
HALSA - DPO4
SULSO - DPO4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_R	129_T	3.857	1.00
179_A	189_A	2.913	1.00
260_E	317_R	2.876	1.00
129_T	133_E	2.803	1.00
92_R	133_E	2.729	1.00
30_A	69_L	2.708	1.00
255_H	258_E	2.684	1.00
20_D	78_A	2.618	1.00
283_I	336_V	2.594	1.00
193_E	198_R	2.323	1.00
244_G	335_H	2.317	1.00
9_M	138_A	2.300	1.00
131_F	159_N	2.260	1.00
82_A	85_H	2.255	1.00
59_T	71_L	2.234	1.00
260_E	321_D	2.220	1.00
198_R	202_D	2.206	1.00
125_E	129_T	2.195	1.00
75_R	78_A	2.191	1.00
93_Y	129_T	2.109	1.00
179_A	193_E	2.106	1.00
26_D	47_P	2.062	1.00
195_M	214_R	2.041	1.00
201_G	205_K	2.039	1.00
94_T	107_L	2.013	1.00
130_I	138_A	2.002	1.00
98_E	146_K	1.999	1.00
224_E	229_I	1.995	1.00
18_M	45_N	1.986	1.00
128_Q	132_N	1.974	1.00
256_W	321_D	1.959	1.00
223_W	227_Q	1.957	1.00
212_L	220_R	1.914	1.00
174_Q	204_Q	1.906	1.00
127_R	159_N	1.903	1.00
174_Q	201_G	1.890	1.00
27_I	70_T	1.884	1.00
5_I	109_V	1.878	1.00
9_M	86_I	1.869	1.00
197_L	203_V	1.852	1.00
308_N	311_D	1.850	1.00
270_L	336_V	1.834	1.00
197_L	206_C	1.811	1.00
9_M	136_L	1.792	1.00
165_T	168_E	1.784	1.00
61_M	65_L	1.770	1.00
20_D	75_R	1.767	1.00
274_L	336_V	1.757	1.00
208_L	220_R	1.725	1.00
87_R	105_A	1.724	1.00
285_R	338_L	1.720	1.00
91_S	97_I	1.676	1.00
221_I	225_R	1.647	1.00
47_P	50_K	1.622	1.00
170_P	174_Q	1.581	1.00
190_A	194_A	1.579	1.00
30_A	41_I	1.566	1.00
78_A	81_E	1.563	1.00
14_A	29_I	1.557	1.00
287_G	337_T	1.551	1.00
57_M	65_L	1.535	1.00
100_L	106_Y	1.527	1.00
127_R	161_Q	1.525	1.00
120_T	124_Q	1.499	1.00
30_A	71_L	1.499	1.00
81_E	85_H	1.488	1.00
19_R	82_A	1.480	1.00
289_K	333_G	1.478	1.00
21_N	24_L	1.471	1.00
118_S	121_L	1.470	1.00
264_E	313_I	1.467	1.00
302_H	318_K	1.464	1.00
316_A	334_L	1.452	1.00
122_I	126_I	1.448	1.00
245_V	270_L	1.445	1.00
144_P	169_V	1.444	1.00
189_A	193_E	1.437	1.00
199_T	202_D	1.432	1.00
307_L	342_Q	1.430	1.00
195_M	215_F	1.426	1.00
148_L	164_I	1.424	1.00
206_C	210_M	1.423	1.00
208_L	224_E	1.418	1.00
307_L	313_I	1.411	1.00
123_A	142_V	1.393	1.00
285_R	337_T	1.391	1.00
219_G	223_W	1.385	1.00
253_I	259_C	1.383	1.00
17_E	79_Y	1.378	1.00
93_Y	125_E	1.372	1.00
220_R	224_E	1.359	1.00
208_L	223_W	1.355	1.00
268_P	309_K	1.351	1.00
7_V	138_A	1.348	1.00
256_W	260_E	1.348	1.00
168_E	171_A	1.345	1.00
90_F	107_L	1.342	1.00
5_I	140_A	1.340	1.00
120_T	163_V	1.335	1.00
124_Q	128_Q	1.335	1.00
142_V	161_Q	1.334	1.00
16_V	78_A	1.326	1.00
58_P	61_M	1.323	1.00
123_A	140_A	1.322	1.00
61_M	64_K	1.319	1.00
271_E	309_K	1.318	1.00
143_A	148_L	1.314	1.00
16_V	82_A	1.311	1.00
274_L	283_I	1.304	1.00
206_C	211_L	1.300	1.00
267_Y	334_L	1.287	1.00
18_M	25_R	1.287	1.00
11_C	15_A	1.287	1.00
249_M	262_I	1.287	1.00
30_A	53_V	1.287	1.00
51_F	68_H	1.284	1.00
211_L	223_W	1.278	1.00
282_L	340_D	1.273	1.00
208_L	212_L	1.268	1.00
254_H	328_G	1.267	1.00
109_V	122_I	1.249	1.00
106_Y	182_P	1.245	1.00
89_I	133_E	1.242	1.00
46_Y	50_K	1.241	1.00
89_I	129_T	1.237	1.00
24_L	29_I	1.235	1.00
284_A	338_L	1.232	1.00
245_V	269_E	1.227	1.00
14_A	18_M	1.223	1.00
291_K	297_Q	1.221	1.00
245_V	273_R	1.221	1.00
302_H	322_E	1.221	1.00
18_M	47_P	1.216	1.00
51_F	66_C	1.216	1.00
29_I	72_L	1.215	1.00
243_V	279_P	1.214	1.00
5_I	123_A	1.210	1.00
267_Y	312_L	1.210	1.00
170_P	204_Q	1.200	1.00
7_V	90_F	1.198	1.00
251_E	258_E	1.198	1.00
90_F	105_A	1.197	1.00
246_E	333_G	1.196	1.00
88_E	91_S	1.189	1.00
152_A	164_I	1.174	1.00
89_I	134_L	1.173	1.00
124_Q	127_R	1.171	1.00
77_D	81_E	1.163	1.00
191_K	214_R	1.155	1.00
187_V	190_A	1.147	1.00
78_A	82_A	1.146	1.00
315_T	318_K	1.141	1.00
304_W	315_T	1.135	1.00
41_I	53_V	1.132	1.00
17_E	75_R	1.125	1.00
207_D	210_M	1.121	1.00
267_Y	271_E	1.119	1.00
21_N	72_L	1.119	1.00
202_D	205_K	1.113	1.00
210_M	214_R	1.109	1.00
155_M	162_F	1.105	1.00
309_K	313_I	1.103	1.00
19_R	78_A	1.100	1.00
252_D	293_D	1.097	1.00
253_I	258_E	1.085	1.00
6_H	153_S	1.082	1.00
249_M	253_I	1.078	1.00
246_E	289_K	1.073	1.00
291_K	331_L	1.072	1.00
271_E	275_A	1.072	1.00
317_R	321_D	1.064	1.00
96_R	236_S	1.059	1.00
216_G	219_G	1.056	1.00
32_G	59_T	1.053	1.00
204_Q	227_Q	1.048	1.00
271_E	312_L	1.046	1.00
267_Y	313_I	1.046	1.00
284_A	340_D	1.044	1.00
87_R	99_P	1.040	1.00
44_A	55_S	1.040	1.00
285_R	301_E	1.037	1.00
37_R	63_L	1.037	1.00
41_I	44_A	1.032	1.00
121_L	125_E	1.025	1.00
93_Y	126_I	1.022	1.00
314_A	318_K	1.019	1.00
262_I	265_R	1.017	1.00
259_C	320_W	1.016	1.00
181_I	200_C	1.001	1.00
318_K	322_E	0.998	1.00
252_D	330_R	0.998	1.00
190_A	193_E	0.994	1.00
41_I	62_A	0.985	1.00
151_I	176_L	0.983	1.00
86_I	134_L	0.982	1.00
7_V	107_L	0.978	1.00
87_R	91_S	0.976	1.00
60_G	64_K	0.975	1.00
313_I	317_R	0.973	1.00
143_A	149_A	0.971	1.00
14_A	43_T	0.968	1.00
288_V	319_T	0.968	1.00
112_S	116_H	0.965	1.00
53_V	69_L	0.963	1.00
112_S	122_I	0.956	1.00
17_E	21_N	0.955	1.00
19_R	135_Q	0.952	1.00
311_D	315_T	0.951	1.00
32_G	39_G	0.951	1.00
20_D	82_A	0.946	1.00
11_C	46_Y	0.943	1.00
252_D	328_G	0.941	1.00
156_N	162_F	0.939	1.00
42_S	74_G	0.938	1.00
131_F	135_Q	0.937	1.00
154_D	180_K	0.932	1.00
281_L	341_P	0.931	1.00
12_F	16_V	0.931	1.00
302_H	315_T	0.929	1.00
287_G	301_E	0.922	1.00
287_G	335_H	0.919	1.00
263_I	288_V	0.917	1.00
124_Q	161_Q	0.917	1.00
267_Y	316_A	0.915	1.00
112_S	117_G	0.913	1.00
146_K	234_V	0.912	1.00
123_A	161_Q	0.907	1.00
57_M	61_M	0.905	1.00
292_F	327_R	0.905	1.00
285_R	303_V	0.900	1.00
18_M	29_I	0.898	1.00
90_F	126_I	0.898	1.00
76_F	80_K	0.894	1.00
247_R	262_I	0.890	1.00
282_L	342_Q	0.890	1.00
100_L	182_P	0.887	1.00
191_K	194_A	0.885	1.00
263_I	332_V	0.881	1.00
218_F	221_I	0.878	1.00
284_A	303_V	0.878	1.00
290_L	332_V	0.875	1.00
147_F	225_R	0.862	1.00
210_M	213_K	0.860	1.00
303_V	338_L	0.858	1.00
224_E	231_E	0.857	1.00
215_F	219_G	0.854	1.00
85_H	88_E	0.853	1.00
57_M	62_A	0.850	1.00
204_Q	226_S	0.850	1.00
217_K	221_I	0.850	1.00
30_A	66_C	0.848	1.00
263_I	316_A	0.847	1.00
54_R	57_M	0.840	1.00
11_C	18_M	0.840	1.00
27_I	68_H	0.839	1.00
307_L	310_A	0.833	1.00
300_Q	322_E	0.833	1.00
270_L	334_L	0.828	1.00
203_V	211_L	0.825	1.00
13_F	76_F	0.822	1.00
184_V	219_G	0.820	1.00
140_A	161_Q	0.816	1.00
43_T	49_R	0.816	1.00
175_T	201_G	0.814	1.00
281_L	339_L	0.812	1.00
230_D	233_D	0.810	1.00
80_K	84_N	0.805	1.00
275_A	307_L	0.804	1.00
178_L	193_E	0.803	1.00
177_P	193_E	0.803	1.00
114_H	117_G	0.802	1.00
145_V	148_L	0.798	1.00
142_V	163_V	0.795	1.00
62_A	66_C	0.790	1.00
83_S	87_R	0.790	1.00
188_S	191_K	0.788	1.00
211_L	215_F	0.787	1.00
98_E	234_V	0.785	1.00
18_M	26_D	0.779	1.00
89_I	93_Y	0.777	1.00
197_L	202_D	0.775	1.00
85_H	134_L	0.773	1.00
263_I	320_W	0.773	1.00
96_R	108_D	0.771	1.00
201_G	204_Q	0.769	1.00
191_K	215_F	0.767	1.00
246_E	331_L	0.767	1.00
96_R	111_D	0.765	1.00
207_D	227_Q	0.765	1.00
177_P	180_K	0.765	1.00
46_Y	49_R	0.761	1.00
24_L	70_T	0.759	1.00
172_F	176_L	0.758	1.00
311_D	314_A	0.758	1.00
256_W	320_W	0.757	1.00
106_Y	146_K	0.754	1.00
286_Q	315_T	0.753	1.00
264_E	317_R	0.752	1.00
63_L	67_P	0.751	1.00
131_F	137_T	0.748	1.00
44_A	53_V	0.748	1.00
66_C	69_L	0.748	1.00
195_M	206_C	0.745	1.00
4_I	234_V	0.744	1.00
97_I	105_A	0.739	1.00
94_T	97_I	0.737	0.99
263_I	313_I	0.736	0.99
168_E	172_F	0.736	0.99
109_V	123_A	0.736	0.99
127_R	140_A	0.733	0.99
87_R	97_I	0.729	0.99
273_R	279_P	0.729	0.99
261_A	265_R	0.728	0.99
89_I	130_I	0.727	0.99
268_P	272_R	0.727	0.99
292_F	298_T	0.727	0.99
48_A	69_L	0.727	0.99
112_S	115_C	0.720	0.99
63_L	71_L	0.720	0.99
209_V	213_K	0.717	0.99
302_H	306_R	0.717	0.99
125_E	128_Q	0.717	0.99
307_L	311_D	0.713	0.99
170_P	205_K	0.710	0.99
89_I	92_R	0.708	0.99
188_S	215_F	0.706	0.99
257_S	260_E	0.703	0.99
306_R	311_D	0.703	0.99
31_I	72_L	0.702	0.99
42_S	55_S	0.701	0.99
290_L	323_R	0.701	0.99
9_M	12_F	0.701	0.99
44_A	49_R	0.697	0.99
14_A	45_N	0.691	0.99
310_A	314_A	0.691	0.99
109_V	112_S	0.691	0.99
215_F	222_L	0.688	0.99
88_E	92_R	0.687	0.99
264_E	268_P	0.687	0.99
4_I	108_D	0.685	0.99
121_L	124_Q	0.684	0.99
290_L	329_V	0.682	0.99
164_I	172_F	0.682	0.99
203_V	223_W	0.680	0.99
59_T	66_C	0.679	0.99
261_A	264_E	0.679	0.99
282_L	307_L	0.677	0.99
275_A	309_K	0.676	0.99
247_R	269_E	0.675	0.99
286_Q	312_L	0.675	0.99
77_D	80_K	0.672	0.99
260_E	264_E	0.672	0.99
82_A	134_L	0.663	0.99
120_T	161_Q	0.662	0.99
13_F	74_G	0.661	0.99
41_I	71_L	0.660	0.99
315_T	319_T	0.659	0.99
269_E	272_R	0.658	0.99
10_D	139_S	0.656	0.99
282_L	339_L	0.656	0.99
244_G	333_G	0.656	0.99
287_G	299_T	0.655	0.99
99_P	102_L	0.653	0.99
258_E	261_A	0.653	0.99
33_G	73_P	0.652	0.99
96_R	233_D	0.651	0.99
137_T	156_N	0.651	0.99
25_R	131_F	0.649	0.99
259_C	332_V	0.646	0.99
27_I	47_P	0.645	0.99
184_V	222_L	0.644	0.99
292_F	296_Q	0.644	0.99
85_H	133_E	0.643	0.99
82_A	136_L	0.640	0.99
276_K	279_P	0.639	0.99
62_A	69_L	0.639	0.99
153_S	156_N	0.638	0.99
267_Y	309_K	0.638	0.99
298_T	301_E	0.637	0.99
32_G	71_L	0.631	0.98
257_S	261_A	0.630	0.98
60_G	63_L	0.630	0.98
195_M	210_M	0.627	0.98
30_A	48_A	0.626	0.98
90_F	97_I	0.624	0.98
128_Q	131_F	0.624	0.98
298_T	323_R	0.623	0.98
43_T	55_S	0.622	0.98
28_P	66_C	0.620	0.98
174_Q	205_K	0.619	0.98
148_L	169_V	0.619	0.98
122_I	125_E	0.618	0.98
156_N	160_G	0.617	0.98
13_F	102_L	0.617	0.98
240_R	279_P	0.617	0.98
178_L	189_A	0.616	0.98
171_A	174_Q	0.615	0.98
151_I	182_P	0.613	0.98
17_E	20_D	0.613	0.98
32_G	74_G	0.607	0.98
11_C	49_R	0.605	0.98
253_I	262_I	0.603	0.98
26_D	45_N	0.603	0.98
74_G	79_Y	0.603	0.98
259_C	329_V	0.602	0.98
176_L	180_K	0.602	0.98
175_T	199_T	0.600	0.98
178_L	197_L	0.598	0.98
300_Q	323_R	0.598	0.98
41_I	66_C	0.598	0.98
264_E	309_K	0.595	0.98
272_R	276_K	0.594	0.98
243_V	273_R	0.593	0.98
33_G	39_G	0.592	0.98
144_P	148_L	0.592	0.98
312_L	316_A	0.591	0.98
84_N	88_E	0.591	0.98
263_I	317_R	0.589	0.98
293_D	327_R	0.589	0.98
171_A	175_T	0.588	0.98
292_F	329_V	0.587	0.97
40_V	55_S	0.586	0.97
266_L	332_V	0.583	0.97
182_P	225_R	0.581	0.97
302_H	305_P	0.578	0.97
16_V	20_D	0.577	0.97
203_V	215_F	0.574	0.97
225_R	230_D	0.573	0.97
80_K	102_L	0.572	0.97
208_L	227_Q	0.571	0.97
186_K	190_A	0.571	0.97
129_T	132_N	0.571	0.97
93_Y	122_I	0.570	0.97
271_E	316_A	0.568	0.97
270_L	286_Q	0.567	0.97
130_I	134_L	0.566	0.97
178_L	192_L	0.565	0.97
340_D	344_E	0.563	0.97
63_L	69_L	0.561	0.97
248_T	331_L	0.561	0.97
243_V	281_L	0.561	0.97
200_C	226_S	0.561	0.97
169_V	172_F	0.558	0.97
90_F	94_T	0.557	0.97
155_M	172_F	0.555	0.97
169_V	173_L	0.555	0.97
117_G	122_I	0.555	0.97
302_H	319_T	0.555	0.97
222_L	225_R	0.552	0.96
16_V	19_R	0.551	0.96
22_P	25_R	0.551	0.96
203_V	226_S	0.549	0.96
147_F	151_I	0.548	0.96
104_E	150_K	0.548	0.96
5_I	142_V	0.546	0.96
280_D	342_Q	0.546	0.96
9_M	16_V	0.545	0.96
184_V	189_A	0.545	0.96
170_P	227_Q	0.543	0.96
94_T	122_I	0.542	0.96
340_D	343_M	0.539	0.96
24_L	72_L	0.539	0.96
283_I	286_Q	0.535	0.96
289_K	299_T	0.535	0.96
293_D	330_R	0.534	0.96
41_I	69_L	0.534	0.96
127_R	138_A	0.534	0.96
245_V	266_L	0.534	0.96
164_I	169_V	0.531	0.96
312_L	336_V	0.531	0.96
10_D	46_Y	0.530	0.95
95_S	111_D	0.530	0.95
30_A	59_T	0.529	0.95
46_Y	158_P	0.528	0.95
212_L	219_G	0.526	0.95
144_P	165_T	0.526	0.95
101_S	104_E	0.525	0.95
300_Q	319_T	0.525	0.95
147_F	222_L	0.524	0.95
336_V	339_L	0.524	0.95
119_A	123_A	0.523	0.95
59_T	63_L	0.523	0.95
19_R	85_H	0.523	0.95
18_M	27_I	0.523	0.95
62_A	65_L	0.522	0.95
5_I	119_A	0.522	0.95
178_L	203_V	0.521	0.95
111_D	115_C	0.520	0.95
10_D	156_N	0.519	0.95
224_E	227_Q	0.517	0.95
15_A	43_T	0.516	0.95
262_I	332_V	0.514	0.95
175_T	200_C	0.513	0.95
258_E	262_I	0.512	0.95
283_I	339_L	0.511	0.95
290_L	320_W	0.511	0.95
54_R	65_L	0.511	0.95
329_V	332_V	0.510	0.94
86_I	136_L	0.510	0.94
271_E	336_V	0.510	0.94
269_E	273_R	0.508	0.94
293_D	328_G	0.505	0.94
310_A	313_I	0.504	0.94
29_I	45_N	0.504	0.94
54_R	61_M	0.500	0.94
23_A	27_I	0.500	0.94

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
4q45F	1	0.9658	100	0.064	Contact Map
4f50A	1	0.9459	100	0.076	Contact Map
4dezA	2	0.6581	100	0.083	Contact Map
3gqcA	3	0.9715	100	0.091	Contact Map
4tqrA	1	0.9544	100	0.092	Contact Map
3pzpA	1	0.9544	100	0.113	Contact Map
3osnA	1	0.9487	100	0.114	Contact Map
4ecqA	1	0.9715	100	0.117	Contact Map
1t94A	1	0.9373	100	0.118	Contact Map
2aq4A	1	0.9544	100	0.124	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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