HOLA - ECOLI - GREMLIN Contacts

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HOLA - DNA polymerase III subunit delta

UniProt:	P28630	Sequences: MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTDWNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLALAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEGSEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQAVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	343 (296)
Sequences:	10838 (6979)
Seq/√Len:	405.6

ECOLI - HOLA DPO3X
BACSU - YQEN DPO3X

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
225_K	228_R	4.410	1.00
152_A	164_D	3.439	1.00
152_A	167_N	3.337	1.00
148_P	168_Q	3.212	1.00
198_T	201_R	3.203	1.00
161_E	196_K	2.989	1.00
143_E	146_Q	2.861	1.00
165_A	199_L	2.750	1.00
199_L	203_E	2.722	1.00
163_D	166_A	2.684	1.00
163_D	196_K	2.563	1.00
10_R	14_N	2.410	1.00
163_D	198_T	2.339	1.00
169_V	199_L	2.222	1.00
221_L	253_E	2.218	1.00
155_A	162_L	2.202	1.00
153_A	157_Q	2.174	1.00
152_A	156_K	2.149	1.00
155_A	185_L	2.099	1.00
148_P	167_N	2.091	1.00
310_L	314_Q	2.076	1.00
307_R	311_T	2.067	1.00
148_P	152_A	2.064	1.00
160_L	189_S	2.058	1.00
162_L	167_N	2.049	1.00
200_P	204_Q	2.027	1.00
60_D	63_A	2.023	1.00
23_L	139_C	1.974	1.00
150_W	178_L	1.958	1.00
261_K	295_Q	1.936	1.00
151_V	181_L	1.898	1.00
147_L	181_L	1.893	1.00
142_P	178_L	1.872	1.00
238_L	313_K	1.815	1.00
220_A	228_R	1.810	1.00
309_E	313_K	1.788	1.00
166_A	202_V	1.764	1.00
63_A	66_S	1.717	1.00
34_S	139_C	1.679	1.00
103_L	107_D	1.673	1.00
148_P	171_C	1.662	1.00
58_N	62_N	1.659	1.00
18_R	21_Y	1.657	1.00
149_R	152_A	1.655	1.00
169_V	203_E	1.625	1.00
77_R	109_L	1.619	1.00
200_P	203_E	1.603	1.00
58_N	92_A	1.595	1.00
220_A	232_I	1.586	1.00
154_R	182_A	1.560	1.00
166_A	199_L	1.556	1.00
262_R	295_Q	1.555	1.00
149_R	153_A	1.545	1.00
260_L	287_G	1.543	1.00
219_D	285_M	1.541	1.00
144_Q	172_Y	1.524	1.00
151_V	167_N	1.523	1.00
147_L	171_C	1.516	1.00
171_C	181_L	1.509	1.00
254_L	301_A	1.499	1.00
59_T	63_A	1.487	1.00
284_G	288_E	1.483	1.00
184_A	187_R	1.482	1.00
144_Q	168_Q	1.479	1.00
63_A	67_L	1.477	1.00
271_A	274_D	1.466	1.00
164_D	168_Q	1.456	1.00
79_T	111_I	1.426	1.00
253_E	289_A	1.414	1.00
294_S	297_Q	1.410	1.00
288_E	292_R	1.403	1.00
174_Y	181_L	1.403	1.00
192_W	201_R	1.402	1.00
218_V	254_L	1.398	1.00
201_R	204_Q	1.398	1.00
72_S	107_D	1.392	1.00
222_L	293_L	1.391	1.00
99_T	102_G	1.377	1.00
173_C	206_V	1.367	1.00
52_T	81_L	1.355	1.00
283_R	287_G	1.338	1.00
219_D	223_M	1.333	1.00
150_W	153_A	1.331	1.00
170_L	184_A	1.319	1.00
24_L	136_Q	1.319	1.00
234_Q	238_L	1.311	1.00
252_R	256_L	1.308	1.00
270_R	274_D	1.306	1.00
145_A	149_R	1.301	1.00
169_V	173_C	1.291	1.00
11_A	14_N	1.275	1.00
151_V	185_L	1.270	1.00
167_N	171_C	1.255	1.00
91_A	95_E	1.254	1.00
163_D	199_L	1.245	1.00
146_Q	149_R	1.238	1.00
148_P	164_D	1.227	1.00
53_F	56_D	1.218	1.00
42_A	109_L	1.217	1.00
151_V	171_C	1.216	1.00
287_G	291_N	1.204	1.00
261_K	298_L	1.188	1.00
302_V	306_T	1.184	1.00
250_L	289_A	1.178	1.00
168_Q	172_Y	1.177	1.00
144_Q	171_C	1.176	1.00
39_R	79_T	1.176	1.00
248_R	309_E	1.167	1.00
260_L	290_L	1.162	1.00
169_V	202_V	1.156	1.00
236_L	246_L	1.152	1.00
24_L	138_T	1.151	1.00
195_G	201_R	1.149	1.00
54_S	83_L	1.148	1.00
221_L	292_R	1.139	1.00
18_R	135_V	1.137	1.00
82_L	112_V	1.134	1.00
65_F	68_C	1.131	1.00
224_G	297_Q	1.128	1.00
228_R	232_I	1.123	1.00
284_G	287_G	1.119	1.00
102_G	133_R	1.114	1.00
61_W	65_F	1.102	1.00
241_S	245_I	1.098	1.00
66_S	69_Q	1.097	1.00
144_Q	148_P	1.095	1.00
35_Q	39_R	1.092	1.00
81_L	113_R	1.087	1.00
218_V	253_E	1.083	1.00
306_T	309_E	1.077	1.00
271_A	275_K	1.076	1.00
213_T	235_Q	1.076	1.00
258_V	298_L	1.075	1.00
238_L	309_E	1.072	1.00
281_N	284_G	1.070	1.00
186_E	190_L	1.069	1.00
232_I	235_Q	1.066	1.00
36_D	54_S	1.061	1.00
231_H	235_Q	1.057	1.00
153_A	156_K	1.048	1.00
257_L	298_L	1.046	1.00
22_L	134_S	1.045	1.00
21_Y	137_V	1.039	1.00
282_R	306_T	1.036	1.00
95_E	99_T	1.035	1.00
303_Q	306_T	1.035	1.00
45_Q	76_S	1.033	1.00
270_R	275_K	1.029	1.00
19_A	109_L	1.026	1.00
187_R	190_L	1.026	1.00
219_D	289_A	1.019	1.00
53_F	78_Q	1.018	1.00
215_F	219_D	1.015	1.00
255_L	287_G	1.013	1.00
167_N	181_L	1.011	1.00
51_H	55_I	1.008	1.00
170_L	202_V	1.007	1.00
145_A	148_P	1.006	1.00
184_A	206_V	1.006	1.00
280_Q	283_R	1.001	1.00
20_A	101_T	1.001	1.00
237_R	243_P	0.999	1.00
147_L	178_L	0.995	1.00
216_H	232_I	0.993	1.00
273_F	281_N	0.992	1.00
162_L	166_A	0.988	1.00
62_N	96_Q	0.988	1.00
251_Q	302_V	0.985	1.00
169_V	172_Y	0.980	1.00
304_L	308_T	0.980	1.00
242_E	320_V	0.976	1.00
280_Q	284_G	0.973	1.00
216_H	228_R	0.970	1.00
307_R	310_L	0.970	1.00
90_N	93_I	0.968	1.00
155_A	160_L	0.966	1.00
141_T	175_E	0.963	1.00
59_T	62_N	0.961	1.00
282_R	309_E	0.956	1.00
154_R	158_L	0.956	1.00
17_L	109_L	0.956	1.00
98_L	129_A	0.951	1.00
256_L	259_N	0.949	1.00
279_W	282_R	0.944	1.00
59_T	64_I	0.938	1.00
245_I	248_R	0.937	1.00
95_E	98_L	0.932	1.00
297_Q	301_A	0.923	1.00
150_W	154_R	0.915	1.00
85_P	110_L	0.912	1.00
235_Q	238_L	0.910	1.00
312_L	315_D	0.909	1.00
236_L	241_S	0.907	1.00
261_K	264_S	0.903	1.00
242_E	245_I	0.900	1.00
261_K	294_S	0.897	1.00
88_G	93_I	0.896	1.00
68_C	80_L	0.895	1.00
257_L	261_K	0.893	1.00
300_Q	304_L	0.881	1.00
118_S	124_A	0.880	1.00
257_L	290_L	0.876	1.00
255_L	259_N	0.876	1.00
215_F	253_E	0.875	1.00
38_V	42_A	0.875	1.00
220_A	225_K	0.875	1.00
259_N	263_Q	0.873	1.00
191_L	205_A	0.872	1.00
305_L	309_E	0.868	1.00
23_L	34_S	0.864	1.00
129_A	133_R	0.863	1.00
233_L	289_A	0.861	1.00
233_L	237_R	0.859	1.00
260_L	286_M	0.853	1.00
147_L	151_V	0.845	1.00
32_Q	36_D	0.842	1.00
162_L	197_L	0.841	1.00
69_Q	103_L	0.838	1.00
247_L	308_T	0.835	1.00
53_F	67_L	0.834	1.00
216_H	235_Q	0.834	1.00
282_R	285_M	0.834	1.00
251_Q	305_L	0.831	1.00
54_S	57_P	0.828	1.00
209_A	212_F	0.827	1.00
155_A	189_S	0.827	1.00
84_L	115_N	0.826	1.00
299_R	303_Q	0.825	1.00
131_A	136_Q	0.824	1.00
158_L	189_S	0.823	1.00
60_D	65_F	0.821	1.00
36_D	40_Q	0.821	1.00
218_V	221_L	0.817	1.00
218_V	252_R	0.813	1.00
62_N	65_F	0.810	1.00
235_Q	239_E	0.809	1.00
35_Q	113_R	0.805	1.00
256_L	286_M	0.804	1.00
214_P	245_I	0.803	1.00
26_N	29_L	0.803	1.00
226_S	229_A	0.801	1.00
102_G	129_A	0.801	1.00
254_L	298_L	0.798	1.00
98_L	102_G	0.798	1.00
273_F	283_R	0.796	1.00
32_Q	83_L	0.796	1.00
228_R	231_H	0.794	1.00
140_Q	143_E	0.785	1.00
213_T	216_H	0.784	1.00
303_Q	307_R	0.784	1.00
259_N	262_R	0.782	1.00
38_V	111_I	0.781	1.00
258_V	302_V	0.780	1.00
285_M	288_E	0.778	1.00
123_N	128_T	0.778	1.00
16_G	42_A	0.777	1.00
278_V	282_R	0.776	1.00
258_V	262_R	0.775	1.00
237_R	278_V	0.771	1.00
242_E	246_L	0.767	1.00
214_P	218_V	0.766	1.00
46_G	52_T	0.766	1.00
68_C	100_L	0.762	1.00
227_K	231_H	0.762	1.00
42_A	77_R	0.760	1.00
217_W	246_L	0.760	1.00
308_T	312_L	0.757	1.00
22_L	114_G	0.756	1.00
254_L	305_L	0.756	1.00
192_W	195_G	0.755	1.00
100_L	104_L	0.753	1.00
61_W	64_I	0.745	1.00
102_G	132_N	0.744	1.00
260_L	263_Q	0.743	1.00
293_L	298_L	0.743	1.00
276_H	284_G	0.742	1.00
223_M	292_R	0.741	1.00
23_L	35_Q	0.739	1.00
79_T	109_L	0.739	1.00
37_A	40_Q	0.735	1.00
158_L	186_E	0.734	1.00
219_D	292_R	0.734	1.00
24_L	123_N	0.731	1.00
253_E	257_L	0.730	1.00
23_L	31_L	0.729	1.00
255_L	260_L	0.725	1.00
255_L	258_V	0.717	1.00
31_L	113_R	0.716	1.00
170_L	181_L	0.715	1.00
65_F	100_L	0.715	1.00
77_R	107_D	0.712	1.00
54_S	81_L	0.710	1.00
85_P	112_V	0.710	1.00
128_T	131_A	0.707	1.00
41_V	44_A	0.703	1.00
210_A	241_S	0.703	1.00
264_S	291_N	0.700	1.00
27_D	30_L	0.698	1.00
304_L	307_R	0.698	1.00
156_K	162_L	0.697	1.00
156_K	159_N	0.693	1.00
39_R	81_L	0.691	1.00
65_F	69_Q	0.690	1.00
261_K	290_L	0.690	1.00
155_A	167_N	0.689	1.00
82_L	85_P	0.689	1.00
58_N	90_N	0.686	1.00
67_L	78_Q	0.679	0.99
58_N	96_Q	0.677	0.99
246_L	249_T	0.676	0.99
226_S	230_L	0.676	0.99
67_L	70_A	0.668	0.99
165_A	168_Q	0.667	0.99
281_N	285_M	0.667	0.99
154_R	157_Q	0.667	0.99
51_H	72_S	0.665	0.99
263_Q	287_G	0.664	0.99
202_V	206_V	0.663	0.99
311_T	315_D	0.661	0.99
174_Y	184_A	0.660	0.99
261_K	291_N	0.660	0.99
293_L	301_A	0.659	0.99
142_P	146_Q	0.655	0.99
175_E	181_L	0.654	0.99
8_Q	11_A	0.652	0.99
293_L	297_Q	0.651	0.99
101_T	130_L	0.649	0.99
254_L	293_L	0.649	0.99
182_A	186_E	0.648	0.99
58_N	61_W	0.647	0.99
28_P	179_L	0.645	0.99
245_I	249_T	0.644	0.99
83_L	113_R	0.641	0.99
258_V	295_Q	0.639	0.99
202_V	205_A	0.637	0.99
308_T	311_T	0.634	0.99
28_P	31_L	0.633	0.99
52_T	55_I	0.632	0.99
253_E	256_L	0.632	0.99
99_T	103_L	0.632	0.99
297_Q	300_Q	0.632	0.99
306_T	310_L	0.630	0.99
285_M	289_A	0.629	0.99
237_R	241_S	0.628	0.99
35_Q	83_L	0.626	0.99
311_T	316_Y	0.623	0.99
185_L	189_S	0.622	0.99
188_L	205_A	0.621	0.99
287_G	290_L	0.613	0.99
216_H	219_D	0.611	0.99
279_W	286_M	0.610	0.99
26_N	141_T	0.608	0.99
223_M	228_R	0.605	0.99
124_A	128_T	0.605	0.99
98_L	125_A	0.605	0.99
288_E	291_N	0.604	0.99
188_L	191_L	0.603	0.99
160_L	195_G	0.601	0.99
130_L	134_S	0.600	0.99
29_L	178_L	0.598	0.99
192_W	197_L	0.598	0.99
290_L	301_A	0.596	0.99
278_V	281_N	0.595	0.99
22_L	136_Q	0.595	0.99
68_C	108_L	0.593	0.99
234_Q	312_L	0.592	0.99
123_N	138_T	0.590	0.99
211_H	215_F	0.589	0.99
53_F	57_P	0.588	0.99
156_K	161_E	0.580	0.98
244_V	270_R	0.580	0.98
174_Y	177_N	0.578	0.98
229_A	289_A	0.576	0.98
61_W	88_G	0.576	0.98
257_L	293_L	0.573	0.98
51_H	54_S	0.573	0.98
21_Y	109_L	0.572	0.98
11_A	15_E	0.572	0.98
26_N	177_N	0.572	0.98
257_L	286_M	0.572	0.98
221_L	250_L	0.569	0.98
66_S	70_A	0.565	0.98
177_N	180_A	0.565	0.98
8_Q	12_Q	0.564	0.98
251_Q	270_R	0.563	0.98
154_R	186_E	0.562	0.98
43_A	52_T	0.562	0.98
247_L	305_L	0.559	0.98
244_V	274_D	0.557	0.98
212_F	216_H	0.556	0.98
247_L	270_R	0.556	0.98
32_Q	179_L	0.555	0.98
44_A	77_R	0.555	0.98
279_W	283_R	0.555	0.98
37_A	41_V	0.554	0.98
29_L	139_C	0.552	0.98
100_L	103_L	0.552	0.98
279_W	285_M	0.551	0.98
166_A	170_L	0.551	0.98
33_E	154_R	0.550	0.98
219_D	288_E	0.550	0.98
188_L	197_L	0.548	0.98
245_I	252_R	0.547	0.98
17_L	42_A	0.543	0.98
210_A	213_T	0.541	0.98
247_L	251_Q	0.541	0.98
188_L	202_V	0.539	0.97
257_L	289_A	0.538	0.97
215_F	218_V	0.537	0.97
230_L	304_L	0.536	0.97
31_L	139_C	0.535	0.97
90_N	127_F	0.533	0.97
36_D	103_L	0.532	0.97
256_L	278_V	0.529	0.97
243_P	246_L	0.529	0.97
80_L	108_L	0.529	0.97
197_L	204_Q	0.528	0.97
184_A	188_L	0.527	0.97
167_N	170_L	0.526	0.97
130_L	136_Q	0.526	0.97
70_A	73_L	0.526	0.97
58_N	65_F	0.524	0.97
149_R	164_D	0.523	0.97
237_R	309_E	0.523	0.97
311_T	314_Q	0.516	0.97
55_I	60_D	0.515	0.97
225_K	231_H	0.515	0.97
272_L	284_G	0.514	0.97
60_D	92_A	0.514	0.97
251_Q	255_L	0.513	0.97
250_L	305_L	0.511	0.97
217_W	229_A	0.509	0.96
231_H	234_Q	0.508	0.96
85_P	126_W	0.508	0.96
273_F	278_V	0.508	0.96
252_R	282_R	0.507	0.96
166_A	197_L	0.506	0.96
300_Q	303_Q	0.505	0.96
33_E	36_D	0.504	0.96
44_A	47_F	0.503	0.96
217_W	221_L	0.502	0.96
33_E	37_A	0.502	0.96
166_A	188_L	0.500	0.96
150_W	182_A	0.500	0.96

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)
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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
1jr3D	1	0.9825	100	0.228	Contact Map
3zh9B	1	0.9534	100	0.298	Contact Map
1jr3A	3	0.9446	100	0.426	Contact Map
1a5tA	2	0.8484	100	0.471	Contact Map
2chqA	3	0.8455	100	0.516	Contact Map
1iqpA	5	0.8484	100	0.522	Contact Map
1sxjD	1	0.8513	100	0.524	Contact Map
1sxjB	1	0.8426	100	0.538	Contact Map
3u61B	3	0.8163	100	0.544	Contact Map
1sxjC	1	0.8542	100	0.555	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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