DPO42 - BACSU - GREMLIN Contacts

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DPO42 - DNA polymerase IV 2

UniProt:	P54560	Sequences: MMKEKVIFLVDMQSFYASVEKAENPHLKNRPVIVSGDPEKRGGVVLAACPLAKQKGVVNASRLWEAQEKCPEAVVLRPRMQRYIDVSLQITAILEEYTDLVEPYSIDEQFMDITGSQKLFGTPMEIAKSIQGRIMREIGVYARVGIGPNKALAKIACDNFAKKNKNGIFTLTKENMKTEMWPLPVGSMFGVGSRMKHHLNRMGISTIGGLAAFPLDLLKKKWGINGHVLWMTANGIDYSPVSTSSLDGQKAIGHGMTLPRDYEHFDKEIKVVLLELSEEVCRRSRNAGVMGQTVSVSCRGADFDWPTGFNRQVKLAEPTNSTQDVYEAVRRLFLTFWDGKPVRRLGVNLSQLSSDDIWQLNLFQDYAKKMSLGYVMDGIKNRFGDTAIIRAASLTAAGQAFERAAKIGGHYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	412 (357)
Sequences:	8804 (6297)
Seq/√Len:	333.3

ECOLI - UMUC DPO4
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
96_E	133_R	3.942	1.00
133_R	137_E	2.999	1.00
186_G	196_K	2.934	1.00
270_K	330_R	2.908	1.00
96_E	137_E	2.805	1.00
33_I	73_A	2.764	1.00
264_H	268_E	2.676	1.00
291_G	349_L	2.643	1.00
23_E	82_R	2.605	1.00
200_N	205_S	2.351	1.00
253_G	348_N	2.349	1.00
135_M	166_N	2.319	1.00
86_V	89_Q	2.314	1.00
12_M	142_A	2.304	1.00
63_L	75_V	2.290	1.00
129_S	133_R	2.256	1.00
270_K	334_L	2.219	1.00
205_S	209_G	2.194	1.00
79_R	82_R	2.191	1.00
186_G	200_N	2.167	1.00
29_N	51_L	2.162	1.00
97_Y	133_R	2.144	1.00
202_M	221_K	2.099	1.00
208_G	212_A	2.085	1.00
102_E	150_K	2.073	1.00
132_G	136_R	2.063	1.00
134_I	142_A	2.062	1.00
231_M	236_I	2.039	1.00
21_K	49_C	2.032	1.00
230_W	234_N	2.005	1.00
30_R	74_V	2.002	1.00
98_T	111_M	1.994	1.00
204_I	210_L	1.977	1.00
181_W	208_G	1.977	1.00
265_F	334_L	1.967	1.00
219_K	227_H	1.961	1.00
181_W	211_A	1.949	1.00
8_F	113_I	1.917	1.00
204_I	213_F	1.886	1.00
12_M	90_I	1.881	1.00
280_V	349_L	1.867	1.00
23_E	79_R	1.854	1.00
65_E	69_K	1.843	1.00
12_M	140_V	1.823	1.00
293_T	351_Q	1.820	1.00
215_L	227_H	1.803	1.00
284_S	349_L	1.762	1.00
131_Q	166_N	1.747	1.00
91_T	109_Q	1.739	1.00
228_V	232_T	1.710	1.00
172_T	175_N	1.699	1.00
321_S	324_D	1.659	1.00
361_N	364_Q	1.651	1.00
274_L	326_Y	1.641	1.00
295_S	350_S	1.630	1.00
95_E	101_V	1.626	1.00
33_I	75_V	1.621	1.00
82_R	85_D	1.618	1.00
320_N	355_D	1.615	1.00
277_S	325_V	1.606	1.00
313_V	331_R	1.588	1.00
51_L	54_Q	1.585	1.00
33_I	45_V	1.573	1.00
17_A	32_V	1.570	1.00
297_S	346_G	1.566	1.00
104_Y	110_F	1.566	1.00
61_S	69_K	1.544	1.00
124_M	128_K	1.538	1.00
177_K	181_W	1.524	1.00
313_V	335_T	1.524	1.00
22_A	86_V	1.520	1.00
122_T	125_E	1.519	1.00
24_N	27_L	1.513	1.00
131_Q	168_I	1.513	1.00
85_D	89_Q	1.506	1.00
254_H	280_V	1.497	1.00
97_Y	129_S	1.489	1.00
152_L	171_L	1.481	1.00
197_H	201_R	1.481	1.00
215_L	231_M	1.463	1.00
213_F	217_L	1.461	1.00
206_T	209_G	1.438	1.00
202_M	222_W	1.435	1.00
281_C	322_T	1.434	1.00
226_G	230_W	1.432	1.00
293_T	350_S	1.424	1.00
127_A	146_I	1.421	1.00
126_I	130_I	1.420	1.00
175_N	178_T	1.407	1.00
262_Y	269_I	1.406	1.00
10_V	142_A	1.405	1.00
148_P	176_M	1.405	1.00
265_F	270_K	1.399	1.00
8_F	144_V	1.393	1.00
329_V	347_V	1.393	1.00
55_K	72_E	1.390	1.00
146_I	168_I	1.378	1.00
21_K	28_K	1.375	1.00
196_K	200_N	1.374	1.00
33_I	57_V	1.371	1.00
264_H	267_K	1.370	1.00
127_A	144_V	1.367	1.00
128_K	132_G	1.363	1.00
227_H	231_M	1.360	1.00
94_L	111_M	1.359	1.00
124_M	170_T	1.358	1.00
62_R	65_E	1.355	1.00
277_S	347_V	1.352	1.00
215_L	230_W	1.351	1.00
20_E	83_Y	1.351	1.00
19_V	86_V	1.349	1.00
147_G	152_L	1.335	1.00
19_V	82_R	1.331	1.00
281_C	325_V	1.317	1.00
284_S	291_G	1.316	1.00
263_E	341_P	1.313	1.00
299_R	305_W	1.305	1.00
255_G	346_G	1.299	1.00
213_F	218_L	1.298	1.00
93_I	137_E	1.295	1.00
260_R	268_E	1.286	1.00
65_E	68_E	1.286	1.00
32_V	76_L	1.280	1.00
14_S	18_S	1.277	1.00
278_E	322_T	1.273	1.00
177_K	211_A	1.268	1.00
110_F	189_F	1.268	1.00
290_M	353_S	1.267	1.00
292_Q	351_Q	1.266	1.00
50_P	54_Q	1.264	1.00
315_L	328_A	1.261	1.00
27_L	32_V	1.245	1.00
218_L	230_W	1.244	1.00
113_I	126_I	1.241	1.00
215_L	219_K	1.240	1.00
258_L	272_V	1.237	1.00
254_H	283_R	1.237	1.00
8_F	127_A	1.227	1.00
17_A	21_K	1.224	1.00
93_I	133_R	1.222	1.00
21_K	51_L	1.221	1.00
55_K	70_C	1.214	1.00
10_V	94_L	1.205	1.00
252_I	287_A	1.205	1.00
194_R	197_H	1.204	1.00
313_V	328_A	1.203	1.00
92_A	95_E	1.200	1.00
81_Q	85_D	1.189	1.00
159_N	169_F	1.185	1.00
328_A	331_R	1.184	1.00
326_Y	330_R	1.179	1.00
254_H	279_E	1.173	1.00
258_L	262_Y	1.171	1.00
94_L	109_Q	1.171	1.00
82_R	86_V	1.167	1.00
295_S	312_Q	1.152	1.00
217_L	221_K	1.150	1.00
93_I	138_I	1.150	1.00
24_N	76_L	1.147	1.00
45_V	57_V	1.143	1.00
128_K	131_Q	1.137	1.00
214_P	217_L	1.135	1.00
209_G	212_A	1.128	1.00
299_R	344_R	1.127	1.00
324_D	328_A	1.125	1.00
277_S	281_C	1.123	1.00
100_L	243_T	1.122	1.00
198_H	221_K	1.119	1.00
35_S	63_L	1.111	1.00
9_L	157_C	1.109	1.00
156_A	171_L	1.109	1.00
223_G	226_G	1.108	1.00
315_L	319_T	1.107	1.00
211_A	234_N	1.097	1.00
20_E	79_R	1.094	1.00
262_Y	268_E	1.091	1.00
22_A	82_R	1.081	1.00
330_R	334_L	1.078	1.00
91_T	103_P	1.074	1.00
45_V	48_A	1.069	1.00
41_R	67_Q	1.065	1.00
155_I	183_L	1.065	1.00
10_V	111_M	1.064	1.00
57_V	73_A	1.061	1.00
272_V	275_E	1.059	1.00
372_L	375_V	1.056	1.00
97_Y	130_I	1.054	1.00
293_T	312_Q	1.051	1.00
269_I	333_F	1.050	1.00
116_S	120_F	1.048	1.00
255_G	297_S	1.045	1.00
261_D	301_A	1.034	1.00
292_Q	353_S	1.027	1.00
22_A	139_G	1.025	1.00
45_V	66_A	1.024	1.00
327_E	331_R	1.024	1.00
197_H	200_N	1.022	1.00
277_S	326_Y	1.021	1.00
293_T	314_K	1.021	1.00
296_V	332_L	1.015	1.00
281_C	285_R	1.012	1.00
48_A	59_N	1.001	1.00
277_S	329_V	0.998	1.00
314_K	351_Q	0.998	1.00
188_M	207_I	0.997	1.00
17_A	47_A	0.989	1.00
163_K	169_F	0.982	1.00
290_M	320_N	0.982	1.00
289_V	354_S	0.979	1.00
46_L	78_P	0.979	1.00
125_E	129_S	0.978	1.00
147_G	153_A	0.975	1.00
90_I	138_I	0.972	1.00
116_S	126_I	0.972	1.00
14_S	50_P	0.970	1.00
23_E	86_V	0.966	1.00
15_F	19_V	0.962	1.00
80_M	84_I	0.961	1.00
64_W	68_E	0.961	1.00
292_Q	318_P	0.955	1.00
104_Y	189_F	0.943	1.00
91_T	95_E	0.943	1.00
158_D	187_S	0.942	1.00
273_L	345_L	0.941	1.00
273_L	296_V	0.936	1.00
322_T	373_G	0.932	1.00
298_C	345_L	0.930	1.00
285_R	320_N	0.929	1.00
198_H	201_R	0.928	1.00
261_D	343_R	0.927	1.00
35_S	43_G	0.925	1.00
295_S	348_N	0.923	1.00
290_M	355_D	0.913	1.00
116_S	121_G	0.913	1.00
61_S	65_E	0.907	1.00
280_V	347_V	0.907	1.00
300_G	340_K	0.904	1.00
21_K	32_V	0.900	1.00
222_W	226_G	0.899	1.00
331_R	335_T	0.897	1.00
135_M	139_G	0.893	1.00
182_P	208_G	0.893	1.00
322_T	326_Y	0.892	1.00
94_L	130_I	0.892	1.00
127_A	168_I	0.891	1.00
256_M	272_V	0.886	1.00
217_L	220_K	0.880	1.00
225_N	228_V	0.880	1.00
191_V	226_G	0.879	1.00
128_K	168_I	0.878	1.00
323_Q	327_E	0.876	1.00
318_P	353_S	0.874	1.00
20_E	24_N	0.870	1.00
273_L	329_V	0.869	1.00
292_Q	314_K	0.866	1.00
89_Q	92_A	0.855	1.00
151_A	232_T	0.854	1.00
204_I	209_G	0.851	1.00
210_L	218_L	0.851	1.00
371_S	374_Y	0.849	1.00
261_D	341_P	0.848	1.00
61_S	66_A	0.845	1.00
47_A	53_K	0.844	1.00
319_T	324_D	0.843	1.00
58_V	61_S	0.842	1.00
273_L	333_F	0.842	1.00
16_Y	80_M	0.841	1.00
255_G	344_R	0.838	1.00
323_Q	369_K	0.834	1.00
300_G	306_P	0.833	1.00
211_A	233_A	0.832	1.00
224_I	228_V	0.831	1.00
14_S	21_K	0.828	1.00
150_K	241_V	0.827	1.00
231_M	238_Y	0.826	1.00
306_P	311_R	0.822	1.00
146_I	170_T	0.819	1.00
313_V	332_L	0.818	1.00
370_M	374_Y	0.817	1.00
101_V	109_Q	0.816	1.00
33_I	70_C	0.815	1.00
21_K	29_N	0.812	1.00
84_I	88_L	0.809	1.00
34_V	76_L	0.808	1.00
274_L	330_R	0.808	1.00
311_R	336_F	0.804	1.00
289_V	352_L	0.803	1.00
48_A	57_V	0.802	1.00
195_M	198_H	0.800	1.00
237_D	240_P	0.784	1.00
216_D	220_K	0.783	1.00
93_I	97_Y	0.783	1.00
295_S	310_N	0.780	1.00
144_V	168_I	0.779	1.00
277_S	322_T	0.778	1.00
271_V	275_E	0.778	1.00
89_Q	138_I	0.778	1.00
198_H	222_W	0.771	1.00
177_K	212_A	0.770	1.00
70_C	73_A	0.770	1.00
17_A	49_C	0.770	1.00
100_L	112_D	0.768	1.00
131_Q	144_V	0.766	1.00
135_M	141_Y	0.765	1.00
208_G	211_A	0.765	1.00
355_D	370_M	0.763	1.00
273_L	326_Y	0.762	1.00
98_T	101_V	0.759	1.00
218_L	222_W	0.758	1.00
149_N	152_L	0.755	1.00
164_N	167_G	0.755	1.00
184_P	200_N	0.755	1.00
285_R	322_T	0.753	1.00
294_V	328_A	0.752	1.00
27_L	74_V	0.752	1.00
87_S	91_T	0.747	0.99
113_I	127_A	0.747	0.99
129_S	132_G	0.746	0.99
52_A	73_A	0.744	0.99
195_M	222_W	0.744	0.99
66_A	70_C	0.743	0.99
283_R	287_A	0.739	0.99
279_E	282_R	0.739	0.99
185_V	200_N	0.739	0.99
102_E	241_V	0.738	0.99
184_P	187_S	0.736	0.99
298_C	336_F	0.734	0.99
103_P	106_I	0.733	0.99
91_T	101_V	0.730	0.99
110_F	150_K	0.728	0.99
93_I	96_E	0.726	0.99
317_E	324_D	0.721	0.99
116_S	119_L	0.721	0.99
325_V	329_V	0.715	0.99
271_V	274_L	0.713	0.99
48_A	53_K	0.711	0.99
16_Y	78_P	0.710	0.99
278_E	282_R	0.709	0.99
7_I	112_D	0.708	0.99
125_E	128_K	0.702	0.99
45_V	75_V	0.701	0.99
63_L	70_C	0.701	0.99
270_K	274_L	0.700	0.99
46_L	59_N	0.700	0.99
12_M	15_F	0.699	0.99
50_P	53_K	0.697	0.99
202_M	213_F	0.695	0.99
7_I	241_V	0.695	0.99
67_Q	71_P	0.694	0.99
93_I	134_I	0.693	0.99
118_K	121_G	0.687	0.99
123_P	127_A	0.687	0.99
191_V	229_L	0.687	0.99
132_G	135_M	0.685	0.99
67_Q	75_V	0.683	0.99
202_M	217_L	0.683	0.99
214_P	234_N	0.682	0.99
210_L	230_W	0.682	0.99
36_G	43_G	0.681	0.99
30_R	72_E	0.681	0.99
16_Y	106_I	0.681	0.99
124_M	168_I	0.681	0.99
86_V	140_V	0.681	0.99
97_Y	126_I	0.679	0.99
276_L	345_L	0.679	0.99
185_V	204_I	0.678	0.99
86_V	138_I	0.673	0.99
269_I	342_V	0.673	0.99
294_V	325_V	0.671	0.99
269_I	345_L	0.671	0.99
274_L	278_E	0.668	0.99
265_F	333_F	0.668	0.99
324_D	327_E	0.667	0.99
31_P	70_C	0.666	0.99
13_Q	143_R	0.664	0.99
262_Y	272_V	0.664	0.99
92_A	96_E	0.664	0.99
371_S	375_V	0.657	0.99
175_N	179_E	0.655	0.99
29_N	49_C	0.654	0.99
30_R	51_L	0.653	0.99
256_M	279_E	0.651	0.99
249_Q	287_A	0.651	0.99
298_C	342_V	0.648	0.99
100_L	240_P	0.645	0.98
290_M	352_L	0.644	0.98
257_T	344_R	0.642	0.98
178_T	181_W	0.642	0.98
222_W	229_L	0.635	0.98
268_E	271_V	0.635	0.98
45_V	73_A	0.634	0.98
64_W	67_Q	0.634	0.98
159_N	163_K	0.634	0.98
36_G	77_R	0.631	0.98
185_V	196_K	0.630	0.98
171_L	179_E	0.628	0.98
126_I	129_S	0.627	0.98
100_L	115_G	0.625	0.98
253_G	346_G	0.624	0.98
300_G	342_V	0.623	0.98
81_Q	84_I	0.623	0.98
321_S	369_K	0.618	0.98
44_V	59_N	0.616	0.98
182_P	206_T	0.615	0.98
19_V	22_A	0.615	0.98
141_Y	163_K	0.614	0.98
288_G	355_D	0.614	0.98
35_S	75_V	0.611	0.98
300_G	304_D	0.610	0.98
33_I	52_A	0.609	0.98
325_V	349_L	0.608	0.98
67_Q	73_A	0.607	0.98
311_R	335_T	0.607	0.98
148_P	152_L	0.606	0.98
28_K	135_M	0.606	0.98
21_K	30_R	0.605	0.98
185_V	199_L	0.605	0.98
152_L	176_M	0.605	0.98
66_A	73_A	0.604	0.98
273_L	330_R	0.603	0.98
252_I	289_V	0.601	0.98
19_V	23_E	0.599	0.98
78_P	83_Y	0.597	0.97
252_I	283_R	0.594	0.97
198_H	223_G	0.593	0.97
328_A	332_L	0.593	0.97
37_D	41_R	0.590	0.97
113_I	116_S	0.590	0.97
210_L	222_W	0.588	0.97
311_R	332_L	0.587	0.97
349_L	352_L	0.587	0.97
274_L	322_T	0.587	0.97
361_N	366_Y	0.587	0.97
94_L	101_V	0.586	0.97
84_I	106_I	0.585	0.97
14_S	53_K	0.584	0.97
8_F	146_I	0.580	0.97
89_Q	137_E	0.579	0.97
18_S	47_A	0.578	0.97
282_R	286_N	0.577	0.97
47_A	59_N	0.577	0.97
333_F	337_W	0.576	0.97
321_S	373_G	0.576	0.97
134_I	138_I	0.575	0.97
232_T	237_D	0.573	0.97
163_K	167_G	0.572	0.97
155_I	189_F	0.570	0.97
272_V	345_L	0.570	0.97
229_L	232_T	0.568	0.97
108_E	154_K	0.568	0.97
45_V	70_C	0.568	0.97
296_V	333_F	0.568	0.97
280_V	294_V	0.567	0.97
25_P	28_K	0.567	0.97
219_K	226_G	0.567	0.97
20_E	23_E	0.565	0.97
183_L	187_S	0.565	0.97
291_G	294_V	0.563	0.96
133_R	136_R	0.563	0.96
181_W	212_A	0.562	0.96
301_A	340_K	0.562	0.96
319_T	325_V	0.561	0.96
189_F	232_T	0.561	0.96
281_C	329_V	0.560	0.96
306_P	336_F	0.557	0.96
35_S	78_P	0.557	0.96
94_L	98_T	0.555	0.96
215_L	226_G	0.555	0.96
269_I	337_W	0.552	0.96
177_K	234_N	0.549	0.96
88_L	92_A	0.547	0.96
193_S	197_H	0.547	0.96
301_A	343_R	0.547	0.96
178_T	182_P	0.546	0.96
63_L	67_Q	0.544	0.96
265_F	337_W	0.544	0.96
207_I	233_A	0.543	0.96
58_V	65_E	0.543	0.96
210_L	233_A	0.542	0.96
151_A	155_I	0.542	0.96
176_M	180_M	0.541	0.96
99_D	115_G	0.539	0.95
105_S	108_E	0.538	0.95
227_H	230_W	0.538	0.95
159_N	179_E	0.537	0.95
215_L	234_N	0.536	0.95
80_M	106_I	0.535	0.95
27_L	76_L	0.535	0.95
150_K	240_P	0.535	0.95
8_F	126_I	0.532	0.95
270_K	326_Y	0.532	0.95
131_Q	142_A	0.532	0.95
37_D	77_R	0.531	0.95
33_I	63_L	0.531	0.95
353_S	356_D	0.530	0.95
163_K	168_I	0.529	0.95
267_K	271_V	0.528	0.95
69_K	72_E	0.527	0.95
91_T	94_L	0.527	0.95
298_C	333_F	0.526	0.95
115_G	119_L	0.526	0.95
254_H	276_L	0.526	0.95
313_V	316_A	0.524	0.95
225_N	229_L	0.522	0.95
13_Q	50_P	0.522	0.95
279_E	283_R	0.522	0.95
179_E	183_L	0.521	0.95
333_F	336_F	0.520	0.95
323_Q	326_Y	0.520	0.95
199_L	222_W	0.518	0.94
22_A	89_Q	0.518	0.94
159_N	187_S	0.517	0.94
315_L	318_P	0.517	0.94
268_E	272_V	0.517	0.94
252_I	284_S	0.515	0.94
34_V	47_A	0.515	0.94
45_V	63_L	0.514	0.94
66_A	69_K	0.514	0.94
224_I	227_H	0.512	0.94
127_A	130_I	0.511	0.94
148_P	172_T	0.510	0.94
167_G	170_T	0.510	0.94
297_S	310_N	0.509	0.94
171_L	176_M	0.509	0.94
32_V	49_C	0.508	0.94
297_S	348_N	0.507	0.94
291_G	352_L	0.506	0.94
21_K	27_L	0.505	0.94
90_I	140_V	0.504	0.94
231_M	234_N	0.503	0.93
98_T	126_I	0.502	0.93
46_L	80_M	0.502	0.93
121_G	126_I	0.501	0.93
281_C	349_L	0.501	0.93
10_V	144_V	0.500	0.93
301_A	341_P	0.500	0.93

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	0.8083	100	0.136	Contact Map
4dezA	2	0.5607	100	0.145	Contact Map
3gqcA	3	0.8422	100	0.154	Contact Map
4q45F	1	0.8252	100	0.155	Contact Map
4tqrA	1	0.818	100	0.164	Contact Map
3pzpA	1	0.8252	100	0.175	Contact Map
3osnA	1	0.8252	100	0.183	Contact Map
1t94A	1	0.8107	100	0.184	Contact Map
4ecqA	1	0.8398	100	0.185	Contact Map
2aq4A	1	0.8325	100	0.187	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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