HOLB - BACSU - GREMLIN Contacts

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HOLB - DNA polymerase III subunit delta'

UniProt:	P37540	Sequences: MAISWKEMNELQPRVMKLLYNSIEKDRLSHAYLFEGKKGTGKLDAALLLAKSFFCLEGGAEPCESCRNCKRIESGNHPDLHLVQPDGLSIKKAQIQALQEEFSKTGLESHKKLYIISHADQMTANAANSLLKFLEEPNKDTMAVLITEQPQRLLDTIISRCQTLPFQPLQPKAIEDRLIEQDVSPHMARLLANMTNNVAEAVELSRNDEFAESRAKVIKLYEVLHQRKGHAFFFIQDQWMPFFKEKTHQEMGLDMLLLIYRDVLSIQIGNEDKLIYQDLFQSIKQHALQSTQQSVTNQILAVLEAKKRLHSNVNVQGLMEHLVLMLQEG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	329 (296)
Sequences:	16117 (10249)
Seq/√Len:	595.7

ECOLI - DPO3X HOLB
BACSU - HOLB DPO3X
HALSA - Q9HN59

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
175_E	189_R	3.658	1.00
13_P	173_A	3.447	1.00
170_Q	173_A	3.390	1.00
179_I	185_P	3.208	1.00
179_I	188_A	2.691	1.00
174_I	192_A	2.664	1.00
175_E	179_I	2.603	1.00
171_P	193_N	2.563	1.00
45_A	166_F	2.543	1.00
171_P	192_A	2.534	1.00
175_E	188_A	2.494	1.00
92_K	96_Q	2.306	1.00
280_F	284_K	2.156	1.00
249_Q	253_L	2.151	1.00
231_A	234_F	2.125	1.00
34_F	166_F	2.059	1.00
90_I	94_Q	2.036	1.00
72_I	80_L	2.031	1.00
51_K	73_E	2.017	1.00
72_I	79_D	2.000	1.00
237_D	241_P	1.994	1.00
8_M	45_A	1.982	1.00
278_D	281_Q	1.981	1.00
177_R	198_V	1.939	1.00
246_K	249_Q	1.918	1.00
184_S	187_M	1.916	1.00
8_M	48_L	1.872	1.00
215_A	219_K	1.849	1.00
20_Y	24_E	1.841	1.00
233_F	236_Q	1.817	1.00
175_E	192_A	1.802	1.00
29_S	32_Y	1.801	1.00
178_L	201_A	1.797	1.00
304_E	308_R	1.752	1.00
169_L	198_V	1.722	1.00
176_D	179_I	1.710	1.00
71_R	108_E	1.701	1.00
13_P	176_D	1.683	1.00
6_K	20_Y	1.683	1.00
33_L	119_A	1.667	1.00
279_L	282_S	1.665	1.00
53_F	142_M	1.646	1.00
83_V	129_S	1.641	1.00
173_A	176_D	1.639	1.00
72_I	77_H	1.620	1.00
70_K	79_D	1.608	1.00
249_Q	252_G	1.591	1.00
233_F	237_D	1.539	1.00
297_N	301_A	1.534	1.00
236_Q	240_M	1.533	1.00
253_L	257_L	1.531	1.00
171_P	189_R	1.528	1.00
281_Q	284_K	1.502	1.00
100_E	104_K	1.493	1.00
35_E	163_T	1.471	1.00
174_I	201_A	1.465	1.00
195_T	201_A	1.460	1.00
216_K	219_K	1.459	1.00
285_Q	289_Q	1.449	1.00
183_V	188_A	1.444	1.00
4_S	7_E	1.444	1.00
284_K	288_L	1.442	1.00
265_S	269_G	1.435	1.00
71_R	77_H	1.430	1.00
74_S	77_H	1.430	1.00
93_A	97_A	1.426	1.00
225_H	228_K	1.405	1.00
239_W	242_F	1.401	1.00
280_F	283_I	1.395	1.00
33_L	161_C	1.386	1.00
97_A	101_E	1.376	1.00
178_L	188_A	1.373	1.00
278_D	283_I	1.371	1.00
250_E	254_D	1.367	1.00
221_Y	224_L	1.364	1.00
72_I	75_G	1.363	1.00
75_G	79_D	1.356	1.00
119_A	153_L	1.353	1.00
189_R	193_N	1.353	1.00
74_S	79_D	1.347	1.00
230_H	234_F	1.346	1.00
248_H	251_M	1.334	1.00
237_D	240_M	1.333	1.00
76_N	79_D	1.330	1.00
100_E	103_S	1.326	1.00
8_M	16_M	1.324	1.00
281_Q	285_Q	1.322	1.00
278_D	282_S	1.314	1.00
15_V	164_L	1.314	1.00
221_Y	227_R	1.296	1.00
70_K	75_G	1.295	1.00
262_D	266_I	1.287	1.00
253_L	256_L	1.284	1.00
103_S	107_L	1.277	1.00
90_I	123_T	1.276	1.00
234_F	238_Q	1.276	1.00
93_A	96_Q	1.275	1.00
218_I	221_Y	1.273	1.00
217_V	221_Y	1.258	1.00
263_V	267_Q	1.256	1.00
294_S	297_N	1.256	1.00
238_Q	242_F	1.254	1.00
231_A	235_I	1.250	1.00
236_Q	239_W	1.239	1.00
35_E	165_P	1.238	1.00
264_L	267_Q	1.238	1.00
232_F	236_Q	1.232	1.00
185_P	189_R	1.220	1.00
291_T	294_S	1.216	1.00
264_L	268_I	1.215	1.00
111_K	142_M	1.210	1.00
171_P	175_E	1.209	1.00
268_I	271_E	1.201	1.00
266_I	270_N	1.200	1.00
234_F	237_D	1.188	1.00
70_K	73_E	1.187	1.00
252_G	256_L	1.182	1.00
80_L	115_I	1.175	1.00
174_I	198_V	1.173	1.00
279_L	283_I	1.172	1.00
215_A	225_H	1.170	1.00
70_K	74_S	1.157	1.00
256_L	260_Y	1.154	1.00
294_S	298_Q	1.153	1.00
14_R	167_Q	1.153	1.00
221_Y	225_H	1.152	1.00
86_D	89_S	1.146	1.00
72_I	76_N	1.136	1.00
98_L	101_E	1.130	1.00
182_D	214_R	1.123	1.00
251_M	255_M	1.121	1.00
90_I	125_N	1.120	1.00
235_I	239_W	1.114	1.00
229_G	233_F	1.114	1.00
246_K	253_L	1.113	1.00
51_K	55_C	1.107	1.00
77_H	80_L	1.105	1.00
16_M	20_Y	1.103	1.00
85_P	89_S	1.099	1.00
282_S	285_Q	1.085	1.00
286_H	289_Q	1.084	1.00
222_E	226_Q	1.083	1.00
92_K	125_N	1.080	1.00
214_R	220_L	1.077	1.00
190_L	193_N	1.073	1.00
19_L	49_L	1.070	1.00
265_S	268_I	1.062	1.00
71_R	74_S	1.062	1.00
267_Q	271_E	1.062	1.00
101_E	105_T	1.062	1.00
272_D	276_Y	1.061	1.00
287_A	291_T	1.058	1.00
299_I	303_L	1.058	1.00
217_V	220_L	1.057	1.00
75_G	78_P	1.053	1.00
92_K	129_S	1.052	1.00
215_A	218_I	1.052	1.00
273_K	276_Y	1.047	1.00
288_L	291_T	1.046	1.00
71_R	79_D	1.037	1.00
298_Q	301_A	1.034	1.00
21_N	24_E	1.034	1.00
97_A	100_E	1.030	1.00
219_K	222_E	1.023	1.00
222_E	225_H	1.021	1.00
192_A	201_A	1.017	1.00
220_L	228_K	1.015	1.00
219_K	223_V	1.012	1.00
307_K	311_S	1.005	1.00
221_Y	228_K	1.003	1.00
246_K	250_E	0.998	1.00
98_L	106_G	0.998	1.00
287_A	292_Q	0.998	1.00
122_M	126_A	0.997	1.00
158_I	163_T	0.996	1.00
98_L	103_S	0.993	1.00
258_L	262_D	0.992	1.00
301_A	305_A	0.989	1.00
267_Q	270_N	0.989	1.00
288_L	292_Q	0.989	1.00
172_K	175_E	0.987	1.00
255_M	259_I	0.982	1.00
172_K	176_D	0.982	1.00
286_H	305_A	0.979	1.00
188_A	192_A	0.971	1.00
252_G	255_M	0.970	1.00
304_E	307_K	0.968	1.00
215_A	221_Y	0.967	1.00
218_I	222_E	0.966	1.00
238_Q	241_P	0.964	1.00
106_G	138_N	0.955	1.00
214_R	221_Y	0.953	1.00
224_L	228_K	0.951	1.00
175_E	185_P	0.950	1.00
251_M	254_D	0.943	1.00
77_H	109_S	0.942	1.00
257_L	261_R	0.941	1.00
123_T	126_A	0.934	1.00
43_L	117_S	0.934	1.00
70_K	77_H	0.930	1.00
103_S	106_G	0.930	1.00
266_I	271_E	0.927	1.00
242_F	246_K	0.925	1.00
12_Q	15_V	0.923	1.00
70_K	76_N	0.919	1.00
285_Q	288_L	0.915	1.00
5_W	51_K	0.914	1.00
261_R	265_S	0.912	1.00
73_E	76_N	0.912	1.00
276_Y	279_L	0.911	1.00
216_K	221_Y	0.910	1.00
292_Q	296_T	0.907	1.00
191_L	201_A	0.901	1.00
300_L	304_E	0.894	1.00
36_G	42_K	0.894	1.00
91_K	94_Q	0.893	1.00
215_A	222_E	0.891	1.00
71_R	76_N	0.885	1.00
99_Q	102_F	0.879	1.00
83_V	86_D	0.877	1.00
235_I	240_M	0.872	1.00
277_Q	281_Q	0.867	1.00
264_L	306_K	0.860	1.00
91_K	123_T	0.855	1.00
305_A	308_R	0.854	1.00
215_A	220_L	0.850	1.00
98_L	105_T	0.845	1.00
172_K	189_R	0.843	1.00
290_S	295_V	0.841	1.00
284_K	287_A	0.837	1.00
263_V	270_N	0.836	1.00
218_I	225_H	0.836	1.00
228_K	231_A	0.835	1.00
18_L	164_L	0.835	1.00
231_A	240_M	0.833	1.00
303_L	307_K	0.832	1.00
301_A	304_E	0.831	1.00
290_S	298_Q	0.828	1.00
49_L	144_V	0.826	1.00
229_G	232_F	0.823	1.00
263_V	268_I	0.821	1.00
276_Y	312_N	0.821	1.00
223_V	226_Q	0.819	1.00
230_H	233_F	0.816	1.00
231_A	238_Q	0.815	1.00
264_L	271_E	0.814	1.00
214_R	219_K	0.813	1.00
257_L	260_Y	0.809	1.00
242_F	245_E	0.809	1.00
102_F	114_Y	0.809	1.00
248_H	252_G	0.808	1.00
245_E	248_H	0.804	1.00
13_P	17_K	0.801	1.00
236_Q	242_F	0.801	1.00
235_I	238_Q	0.798	1.00
297_N	300_L	0.797	1.00
286_H	290_S	0.794	1.00
306_K	310_H	0.793	1.00
254_D	258_L	0.785	1.00
191_L	204_L	0.781	1.00
218_I	226_Q	0.774	1.00
94_Q	97_A	0.772	1.00
115_I	146_I	0.772	1.00
99_Q	105_T	0.772	1.00
303_L	306_K	0.772	1.00
191_L	205_S	0.769	1.00
21_N	25_K	0.768	1.00
71_R	75_G	0.766	1.00
13_P	16_M	0.764	1.00
178_L	205_S	0.762	1.00
223_V	227_R	0.762	1.00
99_Q	103_S	0.761	1.00
56_L	110_H	0.761	1.00
250_E	253_L	0.760	1.00
290_S	293_Q	0.756	1.00
262_D	268_I	0.742	1.00
186_H	189_R	0.739	1.00
203_E	206_R	0.738	1.00
253_L	260_Y	0.733	1.00
268_I	272_D	0.730	1.00
92_K	123_T	0.730	1.00
224_L	227_R	0.729	1.00
184_S	214_R	0.726	1.00
249_Q	255_M	0.724	1.00
102_F	133_F	0.722	1.00
229_G	236_Q	0.720	1.00
275_I	279_L	0.720	1.00
22_S	29_S	0.719	1.00
220_L	224_L	0.719	1.00
18_L	21_N	0.711	1.00
84_Q	117_S	0.710	1.00
249_Q	256_L	0.709	1.00
278_D	284_K	0.708	1.00
134_L	153_L	0.707	1.00
246_K	252_G	0.707	1.00
267_Q	292_Q	0.706	1.00
214_R	217_V	0.705	1.00
266_I	269_G	0.704	1.00
19_L	164_L	0.703	1.00
264_L	270_N	0.701	1.00
9_N	177_R	0.699	1.00
35_E	150_P	0.699	1.00
220_L	225_H	0.695	1.00
187_M	190_L	0.694	1.00
246_K	260_Y	0.692	1.00
16_M	45_A	0.691	1.00
37_K	40_T	0.689	1.00
308_R	311_S	0.687	1.00
300_L	303_L	0.685	1.00
40_T	166_F	0.683	1.00
256_L	259_I	0.683	1.00
266_I	283_I	0.679	1.00
28_L	142_M	0.679	1.00
75_G	80_L	0.679	1.00
186_H	217_V	0.676	1.00
187_M	208_D	0.674	1.00
37_K	197_N	0.672	1.00
257_L	299_I	0.667	1.00
183_V	186_H	0.658	1.00
220_L	223_V	0.657	1.00
296_T	300_L	0.655	1.00
46_A	144_V	0.647	1.00
245_E	249_Q	0.644	1.00
233_F	240_M	0.643	1.00
252_G	260_Y	0.641	1.00
101_E	104_K	0.639	1.00
289_Q	294_S	0.637	1.00
26_D	53_F	0.637	1.00
32_Y	164_L	0.636	1.00
135_E	159_S	0.632	1.00
290_S	294_S	0.630	1.00
50_A	113_L	0.628	1.00
254_D	306_K	0.625	1.00
29_S	162_Q	0.621	1.00
76_N	80_L	0.621	1.00
18_L	207_N	0.619	1.00
245_E	252_G	0.619	1.00
233_F	239_W	0.619	1.00
195_T	204_L	0.619	1.00
96_Q	129_S	0.618	1.00
276_Y	280_F	0.617	1.00
221_Y	226_Q	0.615	1.00
21_N	211_A	0.613	1.00
9_N	173_A	0.611	1.00
214_R	218_I	0.609	1.00
277_Q	280_F	0.607	1.00
279_L	284_K	0.607	1.00
263_V	266_I	0.605	1.00
17_K	21_N	0.605	1.00
174_I	178_L	0.603	1.00
247_T	250_E	0.603	1.00
287_A	290_S	0.598	1.00
106_G	110_H	0.596	1.00
119_A	127_A	0.596	1.00
233_F	242_F	0.595	1.00
150_P	153_L	0.595	1.00
270_N	273_K	0.592	1.00
295_V	299_I	0.592	1.00
90_I	116_I	0.592	1.00
222_E	227_R	0.590	1.00
260_Y	263_V	0.590	1.00
292_Q	295_V	0.590	1.00
198_V	201_A	0.588	1.00
242_F	247_T	0.587	1.00
219_K	225_H	0.586	1.00
267_Q	272_D	0.585	1.00
231_A	236_Q	0.583	1.00
257_L	302_V	0.581	1.00
241_P	245_E	0.579	1.00
261_R	264_L	0.579	1.00
260_Y	295_V	0.579	1.00
46_A	115_I	0.579	1.00
230_H	236_Q	0.578	1.00
259_I	262_D	0.577	1.00
104_K	107_L	0.577	1.00
242_F	252_G	0.575	1.00
116_I	130_L	0.575	1.00
169_L	173_A	0.575	1.00
217_V	224_L	0.568	1.00
232_F	239_W	0.568	1.00
33_L	153_L	0.567	1.00
214_R	224_L	0.567	1.00
272_D	275_I	0.566	1.00
262_D	265_S	0.564	1.00
183_V	209_E	0.564	1.00
28_L	49_L	0.563	1.00
17_K	20_Y	0.563	1.00
119_A	142_M	0.563	1.00
259_I	286_H	0.563	1.00
95_I	99_Q	0.562	1.00
216_K	225_H	0.560	1.00
47_L	136_E	0.559	1.00
132_K	136_E	0.559	1.00
56_L	105_T	0.558	0.99
215_A	223_V	0.557	0.99
15_V	166_F	0.556	0.99
119_A	143_A	0.556	0.99
71_R	78_P	0.556	0.99
284_K	292_Q	0.556	0.99
98_L	114_Y	0.556	0.99
102_F	141_T	0.556	0.99
296_T	299_I	0.556	0.99
72_I	78_P	0.552	0.99
245_E	253_L	0.551	0.99
265_S	270_N	0.551	0.99
169_L	177_R	0.551	0.99
214_R	222_E	0.550	0.99
280_F	286_H	0.550	0.99
190_L	194_M	0.547	0.99
219_K	227_R	0.547	0.99
106_G	109_S	0.546	0.99
229_G	235_I	0.544	0.99
249_Q	257_L	0.544	0.99
113_L	144_V	0.544	0.99
83_V	87_G	0.540	0.99
128_N	154_L	0.538	0.99
220_L	226_Q	0.537	0.99
14_R	17_K	0.537	0.99
99_Q	104_K	0.536	0.99
134_L	161_C	0.532	0.99
209_E	212_E	0.531	0.99
247_T	253_L	0.531	0.99
169_L	174_I	0.530	0.99
305_A	309_L	0.529	0.99
32_Y	142_M	0.527	0.99
201_A	205_S	0.526	0.99
48_L	51_K	0.525	0.99
102_F	106_G	0.524	0.99
188_A	201_A	0.520	0.99
34_F	45_A	0.516	0.99
113_L	142_M	0.515	0.99
263_V	271_E	0.515	0.99
216_K	220_L	0.514	0.99
52_S	55_C	0.514	0.99
293_Q	297_N	0.514	0.99
122_M	127_A	0.513	0.99
232_F	235_I	0.508	0.99
247_T	252_G	0.508	0.99
248_H	253_L	0.507	0.99
219_K	226_Q	0.506	0.99
217_V	222_E	0.505	0.99
282_S	286_H	0.504	0.99
204_L	207_N	0.500	0.99
127_A	154_L	0.500	0.99

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
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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
1a5tA	2	0.9392	100	0.359	Contact Map
1jr3A	3	0.9848	100	0.446	Contact Map
2gnoA	1	0.8389	100	0.484	Contact Map
1sxjE	1	0.8906	100	0.485	Contact Map
1iqpA	5	0.8967	100	0.488	Contact Map
2chqA	3	0.8997	100	0.496	Contact Map
3zh9B	1	0.8815	100	0.511	Contact Map
1sxjC	1	0.8967	100	0.511	Contact Map
1jr3D	1	0.8875	100	0.511	Contact Map
1sxjD	1	0.8997	100	0.512	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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