DPO4 - SULSO - GREMLIN Contacts

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DPO4 - DNA polymerase IV

UniProt:	Q97W02	Sequences: MIVLFVDFDYFYAQVEEVLNPSLKGKPVVVCVFSGRFEDSGAVATANYEARKFGVKAGIPIVEAKKILPNAVYLPMRKEVYQQVSSRIMNLLREYSEKIEIASIDEAYLDISDKVRDYREAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRLIRELDIADVPGIGNITAEKLKKLGINKLVDTLSIEFDKLKGMIGEAKAKYLISLARDEYNEPIRTRVRKSIGRIVTMKRNSRNLEEIKPYLFRAIEESYYKLDKRIPKAIHVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKIRRIGVRFSKFIEAIGLDKFFDT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	352 (335)
Sequences:	8883 (6330)
Seq/√Len:	345.8

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
94_E	131_K	3.896	1.00
181_A	191_A	2.948	1.00
257_N	260_E	2.848	1.00
131_K	135_K	2.817	1.00
94_E	135_K	2.761	1.00
29_V	71_A	2.714	1.00
19_L	80_V	2.661	1.00
262_K	316_V	2.632	1.00
281_P	337_F	2.592	1.00
246_G	336_R	2.351	1.00
195_K	200_N	2.342	1.00
84_V	87_R	2.323	1.00
61_I	73_Y	2.304	1.00
8_F	140_V	2.295	1.00
127_E	131_K	2.248	1.00
77_R	80_V	2.206	1.00
181_A	195_K	2.173	1.00
200_N	204_D	2.149	1.00
130_N	134_E	2.145	1.00
133_L	161_N	2.145	1.00
25_G	49_E	2.137	1.00
95_Y	131_K	2.103	1.00
262_K	320_Q	2.100	1.00
197_L	216_M	2.067	1.00
203_V	207_S	2.064	1.00
226_I	230_R	2.058	1.00
132_I	140_V	2.047	1.00
100_E	148_K	2.040	1.00
227_S	232_E	2.025	1.00
96_S	109_L	2.012	1.00
17_E	47_N	2.007	1.00
214_K	223_K	1.998	1.00
176_R	206_L	1.952	1.00
176_R	203_V	1.916	1.00
4_L	111_I	1.899	1.00
26_K	72_V	1.891	1.00
8_F	88_I	1.870	1.00
129_K	161_N	1.856	1.00
199_I	208_I	1.850	1.00
272_S	337_F	1.845	1.00
199_I	205_T	1.837	1.00
8_F	138_I	1.836	1.00
167_D	170_E	1.831	1.00
19_L	77_R	1.825	1.00
258_L	320_Q	1.819	1.00
63_E	67_I	1.792	1.00
210_F	223_K	1.774	1.00
224_Y	228_L	1.751	1.00
89_M	107_A	1.735	1.00
276_L	337_F	1.722	1.00
283_A	339_K	1.721	1.00
93_R	99_I	1.684	1.00
172_K	176_R	1.633	1.00
49_E	52_K	1.627	1.00
122_Y	126_L	1.582	1.00
29_V	43_V	1.580	1.00
80_V	83_Q	1.580	1.00
13_A	28_V	1.572	1.00
285_H	338_S	1.571	1.00
102_A	108_Y	1.547	1.00
129_K	163_I	1.523	1.00
287_V	334_G	1.519	1.00
59_I	67_I	1.514	1.00
247_R	272_S	1.496	1.00
83_Q	87_R	1.481	1.00
18_V	84_V	1.480	1.00
124_L	128_I	1.476	1.00
266_F	312_Y	1.470	1.00
120_E	123_N	1.470	1.00
300_R	317_K	1.463	1.00
146_K	171_V	1.460	1.00
197_L	217_I	1.450	1.00
191_A	195_K	1.449	1.00
223_K	227_S	1.448	1.00
307_S	343_A	1.439	1.00
192_E	196_K	1.433	1.00
255_S	261_I	1.433	1.00
125_G	144_I	1.433	1.00
125_G	142_V	1.426	1.00
29_V	73_Y	1.422	1.00
20_N	23_L	1.415	1.00
201_K	204_D	1.413	1.00
210_F	226_I	1.406	1.00
300_R	321_K	1.402	1.00
276_L	281_P	1.397	1.00
208_I	212_K	1.395	1.00
283_A	338_S	1.393	1.00
222_A	226_I	1.390	1.00
4_L	142_V	1.389	1.00
170_E	173_R	1.388	1.00
16_E	81_Y	1.381	1.00
269_I	311_A	1.381	1.00
95_Y	127_E	1.369	1.00
258_L	262_K	1.368	1.00
150_F	166_I	1.367	1.00
210_F	227_S	1.360	1.00
92_L	109_L	1.360	1.00
6_V	140_V	1.357	1.00
15_V	80_V	1.348	1.00
60_P	63_E	1.341	1.00
269_I	335_V	1.333	1.00
213_L	226_I	1.327	1.00
256_R	329_K	1.327	1.00
15_V	84_V	1.325	1.00
63_E	66_K	1.322	1.00
17_E	24_K	1.321	1.00
91_L	135_K	1.316	1.00
145_S	150_F	1.313	1.00
126_L	130_N	1.312	1.00
208_I	213_L	1.312	1.00
53_F	70_N	1.311	1.00
29_V	55_V	1.305	1.00
289_V	295_I	1.301	1.00
315_S	335_V	1.282	1.00
210_F	214_K	1.275	1.00
10_Y	14_Q	1.274	1.00
282_K	339_K	1.262	1.00
23_L	28_V	1.258	1.00
90_N	93_R	1.254	1.00
111_I	124_L	1.248	1.00
247_R	275_K	1.247	1.00
108_Y	184_P	1.246	1.00
91_L	131_K	1.244	1.00
172_K	206_L	1.242	1.00
310_T	314_E	1.239	1.00
4_L	125_G	1.235	1.00
251_M	264_Y	1.231	1.00
28_V	74_L	1.225	1.00
245_I	279_R	1.224	1.00
144_I	163_I	1.223	1.00
193_K	216_M	1.222	1.00
92_L	107_A	1.219	1.00
53_F	68_L	1.218	1.00
247_R	271_E	1.218	1.00
122_Y	165_V	1.215	1.00
48_Y	52_K	1.213	1.00
285_H	299_G	1.212	1.00
6_V	92_L	1.212	1.00
316_V	320_Q	1.212	1.00
13_A	17_E	1.209	1.00
80_V	84_V	1.198	1.00
126_L	129_K	1.197	1.00
302_F	314_E	1.194	1.00
17_E	49_E	1.194	1.00
157_M	164_K	1.186	1.00
280_I	341_I	1.180	1.00
98_K	239_T	1.179	1.00
91_L	136_E	1.177	1.00
269_I	273_Y	1.177	1.00
79_E	83_Q	1.171	1.00
248_I	334_G	1.161	1.00
189_I	192_E	1.153	1.00
253_R	260_E	1.147	1.00
212_K	216_M	1.146	1.00
283_A	299_G	1.142	1.00
209_E	212_K	1.139	1.00
255_S	260_E	1.127	1.00
154_A	166_I	1.126	1.00
16_E	77_R	1.126	1.00
273_Y	277_D	1.117	1.00
43_V	55_V	1.107	1.00
20_N	74_L	1.106	1.00
251_M	255_S	1.101	1.00
18_V	80_V	1.099	1.00
273_Y	311_A	1.098	1.00
302_F	306_I	1.093	1.00
39_D	65_K	1.080	1.00
248_I	287_V	1.079	1.00
204_D	207_S	1.077	1.00
5_F	155_A	1.074	1.00
218_G	222_A	1.073	1.00
289_V	332_R	1.060	1.00
123_N	127_E	1.055	1.00
269_I	312_Y	1.052	1.00
264_Y	267_R	1.044	1.00
206_L	230_R	1.043	1.00
55_V	71_A	1.038	1.00
89_M	101_I	1.037	1.00
31_C	61_I	1.031	1.00
314_E	317_K	1.029	1.00
145_S	151_A	1.023	1.00
43_V	46_A	1.022	1.00
183_V	202_L	1.015	1.00
283_A	301_T	1.008	1.00
153_I	178_L	1.007	1.00
300_R	314_E	1.006	1.00
95_Y	128_I	1.004	1.00
312_Y	316_V	1.004	1.00
62_V	66_K	0.995	1.00
43_V	64_A	0.988	1.00
158_A	164_K	0.988	1.00
46_A	57_A	0.988	1.00
254_N	291_E	0.985	1.00
89_M	93_R	0.973	1.00
282_K	301_T	0.970	1.00
192_E	195_K	0.970	1.00
126_L	163_I	0.967	1.00
301_T	339_K	0.965	1.00
314_E	318_L	0.963	1.00
88_I	136_E	0.959	1.00
10_Y	48_Y	0.959	1.00
313_S	317_K	0.958	1.00
282_K	341_I	0.957	1.00
44_A	76_M	0.957	1.00
19_L	84_V	0.956	1.00
13_A	45_T	0.956	1.00
317_K	321_K	0.952	1.00
114_K	119_R	0.952	1.00
11_F	15_V	0.952	1.00
156_D	182_D	0.939	1.00
18_V	137_K	0.937	1.00
6_V	109_L	0.936	1.00
254_N	331_R	0.933	1.00
217_I	222_A	0.928	1.00
309_E	313_S	0.928	1.00
114_K	124_L	0.922	1.00
17_E	28_V	0.922	1.00
282_K	305_G	0.918	1.00
285_H	336_R	0.917	1.00
59_I	63_E	0.917	1.00
31_C	41_G	0.911	1.00
92_L	128_I	0.903	1.00
277_D	307_S	0.900	1.00
318_L	322_I	0.899	1.00
254_N	329_K	0.898	1.00
133_L	137_K	0.897	1.00
114_K	118_Y	0.895	1.00
319_L	322_I	0.893	1.00
148_K	237_I	0.893	1.00
265_L	286_V	0.887	1.00
87_R	90_N	0.885	1.00
227_S	234_N	0.884	1.00
249_V	264_Y	0.882	1.00
193_K	196_K	0.881	1.00
78_K	82_Q	0.881	1.00
177_E	203_V	0.878	1.00
212_K	215_G	0.876	1.00
205_T	213_L	0.875	1.00
102_A	184_P	0.873	1.00
59_I	64_A	0.870	1.00
280_I	307_S	0.869	1.00
265_L	333_I	0.869	1.00
305_G	341_I	0.861	1.00
10_Y	17_E	0.845	1.00
315_S	318_L	0.839	1.00
290_T	328_R	0.838	1.00
56_K	59_I	0.835	1.00
29_V	68_L	0.825	1.00
319_L	323_L	0.825	1.00
125_G	163_I	0.818	1.00
265_L	319_L	0.817	1.00
91_L	95_Y	0.816	1.00
288_A	333_I	0.815	1.00
16_E	20_N	0.814	1.00
275_K	279_R	0.813	1.00
82_Q	86_S	0.811	1.00
12_Y	78_K	0.811	1.00
280_I	343_A	0.809	1.00
149_V	228_L	0.808	1.00
206_L	229_A	0.807	1.00
290_T	296_V	0.805	1.00
199_I	204_D	0.805	1.00
26_K	70_N	0.804	1.00
265_L	312_Y	0.798	1.00
147_N	150_F	0.796	1.00
186_I	222_A	0.793	1.00
133_L	139_T	0.789	1.00
64_A	68_L	0.784	1.00
272_S	335_V	0.784	1.00
213_L	217_I	0.783	1.00
45_T	51_R	0.782	1.00
170_E	174_L	0.782	1.00
142_V	163_I	0.778	1.00
286_V	318_L	0.777	1.00
220_A	224_Y	0.776	1.00
193_K	217_I	0.775	1.00
48_Y	51_R	0.773	1.00
23_L	72_V	0.769	1.00
203_V	206_L	0.768	1.00
98_K	113_D	0.765	1.00
98_K	110_D	0.763	1.00
163_I	166_I	0.762	1.00
269_I	315_S	0.761	1.00
233_Y	236_P	0.760	1.00
306_I	310_T	0.758	1.00
197_L	208_I	0.756	1.00
87_R	136_E	0.755	1.00
180_I	195_K	0.754	1.00
100_E	237_I	0.752	1.00
96_S	99_I	0.752	1.00
261_I	319_L	0.752	1.00
127_E	130_N	0.749	1.00
17_E	25_G	0.745	1.00
89_M	99_I	0.741	1.00
85_S	89_M	0.740	1.00
190_T	193_K	0.738	1.00
270_E	274_Y	0.738	1.00
68_L	71_A	0.736	0.99
111_I	125_G	0.734	0.99
311_A	315_S	0.733	0.99
263_P	267_R	0.733	0.99
108_Y	148_K	0.730	0.99
179_D	195_K	0.726	0.99
91_L	132_I	0.725	0.99
262_K	266_F	0.723	0.99
298_R	322_I	0.722	0.99
290_T	294_D	0.719	0.99
144_I	165_V	0.716	0.99
190_T	217_I	0.715	0.99
249_V	271_E	0.712	0.99
99_I	107_A	0.712	0.99
302_F	305_G	0.710	0.99
65_K	69_P	0.709	0.99
172_K	207_S	0.709	0.99
3_V	110_D	0.709	0.99
129_K	142_V	0.706	0.99
248_I	332_R	0.706	0.99
65_K	73_Y	0.705	0.99
61_I	68_L	0.705	0.99
258_L	319_L	0.704	0.99
174_L	178_L	0.703	0.99
179_D	182_D	0.699	0.99
46_A	55_V	0.697	0.99
90_N	94_E	0.693	0.99
44_A	57_A	0.692	0.99
46_A	51_R	0.692	0.99
131_K	134_E	0.691	0.99
111_I	114_K	0.690	0.99
121_A	125_G	0.690	0.99
84_V	136_E	0.689	0.99
13_A	47_N	0.689	0.99
312_Y	320_Q	0.687	0.99
300_R	318_L	0.686	0.99
209_E	230_R	0.684	0.99
50_A	71_A	0.684	0.99
30_V	74_L	0.683	0.99
8_F	11_F	0.681	0.99
3_V	237_I	0.678	0.99
259_E	263_P	0.677	0.99
91_L	94_E	0.676	0.99
32_V	75_P	0.676	0.99
263_P	266_F	0.676	0.99
259_E	262_K	0.675	0.99
260_E	263_P	0.673	0.99
217_I	225_L	0.672	0.99
288_A	330_I	0.672	0.99
101_I	104_I	0.668	0.99
116_R	119_R	0.667	0.99
205_T	226_I	0.665	0.99
285_H	297_S	0.665	0.99
123_N	126_L	0.663	0.99
98_K	236_P	0.663	0.99
246_G	334_G	0.662	0.99
12_Y	76_M	0.662	0.99
266_F	270_E	0.662	0.99
79_E	82_Q	0.662	0.99
310_T	313_S	0.661	0.99
211_D	215_G	0.659	0.99
271_E	274_Y	0.655	0.99
9_D	141_T	0.655	0.99
26_K	49_E	0.653	0.99
43_V	73_Y	0.653	0.99
186_I	225_L	0.651	0.99
287_V	297_S	0.648	0.99
242_R	279_R	0.642	0.99
87_R	135_K	0.639	0.99
284_I	314_E	0.639	0.99
173_R	176_R	0.639	0.99
166_I	174_L	0.638	0.99
92_L	99_I	0.637	0.99
261_I	330_I	0.633	0.98
124_L	127_E	0.632	0.98
261_I	333_I	0.630	0.98
197_L	212_K	0.628	0.98
265_L	315_S	0.627	0.98
16_E	19_L	0.622	0.98
298_R	321_K	0.621	0.98
153_I	184_P	0.621	0.98
312_Y	318_L	0.621	0.98
176_R	207_S	0.619	0.98
31_C	76_M	0.618	0.98
155_A	158_A	0.617	0.98
298_R	318_L	0.617	0.98
210_F	230_R	0.616	0.98
178_L	182_D	0.614	0.98
296_V	322_I	0.613	0.98
62_V	65_K	0.612	0.98
122_Y	163_I	0.611	0.98
12_Y	104_I	0.610	0.98
177_E	201_K	0.609	0.98
180_I	199_I	0.608	0.98
84_V	138_I	0.607	0.98
139_T	158_A	0.607	0.98
311_A	318_L	0.605	0.98
114_K	117_D	0.604	0.98
64_A	71_A	0.604	0.98
316_V	319_L	0.604	0.98
29_V	50_A	0.604	0.98
130_N	133_L	0.603	0.98
27_P	68_L	0.603	0.98
268_A	333_I	0.601	0.98
214_K	219_E	0.601	0.98
150_F	171_V	0.600	0.98
10_Y	51_R	0.596	0.98
341_I	345_G	0.596	0.98
146_K	150_F	0.593	0.98
184_P	228_L	0.591	0.98
42_A	57_A	0.591	0.98
258_L	323_L	0.590	0.98
255_S	264_Y	0.590	0.98
222_A	225_L	0.588	0.98
311_A	320_Q	0.587	0.98
76_M	81_Y	0.586	0.97
180_I	191_A	0.586	0.97
45_T	57_A	0.584	0.97
31_C	73_Y	0.584	0.97
172_K	230_R	0.584	0.97
56_K	67_I	0.582	0.97
25_G	47_N	0.582	0.97
166_I	171_V	0.581	0.97
95_Y	124_L	0.578	0.97
225_L	228_L	0.574	0.97
250_T	332_R	0.574	0.97
287_V	295_I	0.573	0.97
173_R	177_E	0.572	0.97
168_D	172_K	0.572	0.97
280_I	340_F	0.571	0.97
273_Y	337_F	0.570	0.97
157_M	174_L	0.570	0.97
113_D	117_D	0.568	0.97
304_H	310_T	0.565	0.97
146_K	167_D	0.565	0.97
32_V	41_G	0.565	0.97
43_V	68_L	0.564	0.97
132_I	136_E	0.563	0.97
162_G	165_V	0.563	0.97
245_I	275_K	0.562	0.97
314_E	320_Q	0.561	0.97
4_L	144_I	0.561	0.97
288_A	322_I	0.561	0.97
228_L	233_Y	0.558	0.97
274_Y	278_K	0.558	0.97
286_V	319_L	0.557	0.97
247_R	268_A	0.557	0.97
281_P	284_I	0.556	0.97
311_A	337_F	0.553	0.96
158_A	162_G	0.553	0.96
309_E	312_Y	0.553	0.96
290_T	330_I	0.551	0.96
214_K	222_A	0.550	0.96
21_P	24_K	0.550	0.96
205_T	229_A	0.549	0.96
23_L	74_L	0.548	0.96
291_E	329_K	0.547	0.96
86_S	90_N	0.547	0.96
82_Q	104_I	0.545	0.96
180_I	194_L	0.545	0.96
15_V	19_L	0.544	0.96
205_T	217_I	0.542	0.96
266_F	316_V	0.541	0.96
177_E	202_L	0.538	0.96
64_A	67_I	0.537	0.96
56_K	63_E	0.537	0.96
106_E	152_K	0.534	0.96
133_L	136_E	0.533	0.96
311_A	314_E	0.532	0.96
306_I	311_A	0.530	0.96
272_S	284_I	0.529	0.95
65_K	71_A	0.526	0.95
180_I	205_T	0.526	0.95
129_K	140_V	0.525	0.95
291_E	328_R	0.523	0.95
92_L	96_S	0.523	0.95
8_F	15_V	0.522	0.95
50_A	55_V	0.522	0.95
330_I	333_I	0.522	0.95
9_D	48_Y	0.521	0.95
139_T	161_N	0.521	0.95
121_A	144_I	0.520	0.95
18_V	87_R	0.519	0.95
342_E	345_G	0.518	0.95
186_I	191_A	0.518	0.95
28_V	47_N	0.516	0.95
260_E	264_Y	0.514	0.95
315_S	319_L	0.514	0.95
78_K	104_I	0.513	0.95
29_V	61_I	0.513	0.95
103_S	106_E	0.512	0.95
188_N	192_E	0.512	0.95
337_F	340_F	0.509	0.94
266_F	313_S	0.509	0.94
171_V	174_L	0.509	0.94
300_R	303_P	0.505	0.94
149_V	153_I	0.505	0.94
61_I	65_K	0.505	0.94
171_V	175_I	0.504	0.94
291_E	331_R	0.504	0.94
113_D	119_R	0.501	0.94
284_I	311_A	0.501	0.94
313_S	316_V	0.500	0.94
119_R	124_L	0.500	0.94
89_M	92_L	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
4f50A	1	0.9545	100	0.066	Contact Map
4tqrA	1	0.9716	100	0.083	Contact Map
4q45F	1	0.9517	100	0.104	Contact Map
4dezA	2	0.6562	100	0.108	Contact Map
3gqcA	3	0.9716	100	0.108	Contact Map
3pzpA	1	0.9517	100	0.13	Contact Map
1t94A	1	0.9375	100	0.134	Contact Map
3osnA	1	0.946	100	0.135	Contact Map
4ecqA	1	0.9631	100	0.139	Contact Map
3mfiA	1	0.9602	100	0.143	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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