HOLB - ECOLI - GREMLIN Contacts

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HOLB - DNA polymerase III subunit delta'

UniProt:	P28631	Sequences: MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCGHCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALLTDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREVTMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQAPARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQLMSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11500
Length:	334 (293)
Sequences:	14316 (9312)
Seq/√Len:	544.0

ECOLI - HOLB DPO3X
BACSU - DPO3X HOLB
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
168_P	171_Y	3.642	1.00
173_V	188_L	3.613	1.00
8_R	171_Y	3.590	1.00
40_L	164_L	2.673	1.00
172_A	191_L	2.669	1.00
173_V	187_L	2.592	1.00
169_E	191_L	2.475	1.00
90_V	94_R	2.462	1.00
46_R	69_Q	2.355	1.00
295_H	299_Q	2.344	1.00
169_E	192_R	2.330	1.00
29_I	164_L	2.272	1.00
4_Y	40_L	2.248	1.00
240_Q	243_A	2.243	1.00
183_S	186_A	2.144	1.00
271_P	275_A	2.064	1.00
241_A	244_R	2.060	1.00
4_Y	43_A	2.054	1.00
175_W	198_P	2.028	1.00
173_V	191_L	1.988	1.00
42_Y	78_T	1.933	1.00
2_R	15_V	1.911	1.00
24_H	27_L	1.907	1.00
15_V	19_Q	1.867	1.00
208_D	211_Q	1.864	1.00
95_E	99_K	1.859	1.00
210_W	214_E	1.850	1.00
167_P	198_P	1.827	1.00
48_L	140_W	1.810	1.00
176_L	201_A	1.805	1.00
76_Y	113_W	1.798	1.00
234_A	238_H	1.792	1.00
288_A	292_D	1.792	1.00
269_D	272_G	1.730	1.00
171_Y	174_T	1.707	1.00
194_S	201_A	1.705	1.00
88_L	92_A	1.702	1.00
257_K	261_G	1.695	1.00
182_M	187_L	1.678	1.00
275_A	279_N	1.674	1.00
109_A	140_W	1.646	1.00
8_R	174_T	1.645	1.00
230_Y	234_A	1.632	1.00
211_Q	214_E	1.623	1.00
276_E	280_H	1.621	1.00
249_A	253_M	1.619	1.00
255_A	258_R	1.618	1.00
250_T	254_D	1.605	1.00
210_W	213_R	1.596	1.00
214_E	218_Q	1.584	1.00
4_Y	11_F	1.570	1.00
102_E	105_R	1.550	1.00
88_L	121_T	1.546	1.00
172_A	201_A	1.544	1.00
176_L	187_L	1.529	1.00
233_L	236_L	1.524	1.00
169_E	188_L	1.520	1.00
272_G	276_E	1.511	1.00
28_L	117_A	1.507	1.00
272_G	275_A	1.494	1.00
267_N	270_V	1.482	1.00
241_A	245_L	1.476	1.00
285_R	288_A	1.468	1.00
30_Q	161_L	1.467	1.00
253_M	257_K	1.462	1.00
91_D	95_E	1.455	1.00
28_L	159_C	1.443	1.00
113_W	144_A	1.441	1.00
181_T	211_Q	1.437	1.00
134_E	138_E	1.436	1.00
230_Y	233_L	1.435	1.00
209_N	213_R	1.432	1.00
117_A	143_L	1.427	1.00
184_Q	188_L	1.425	1.00
282_S	285_R	1.412	1.00
95_E	98_E	1.407	1.00
9_P	165_A	1.406	1.00
267_N	271_P	1.405	1.00
208_D	214_E	1.397	1.00
270_V	273_L	1.396	1.00
213_R	216_L	1.337	1.00
259_H	263_A	1.328	1.00
298_E	302_S	1.322	1.00
177_S	187_L	1.313	1.00
77_Y	80_A	1.306	1.00
309_E	313_T	1.306	1.00
242_P	246_H	1.304	1.00
217_C	220_L	1.291	1.00
75_D	80_A	1.283	1.00
255_A	259_H	1.275	1.00
88_L	123_A	1.270	1.00
74_P	81_P	1.268	1.00
69_Q	72_T	1.261	1.00
225_P	228_D	1.251	1.00
166_P	195_A	1.250	1.00
75_D	81_P	1.245	1.00
227_G	231_S	1.243	1.00
232_L	236_L	1.241	1.00
247_W	251_L	1.240	1.00
69_Q	80_A	1.239	1.00
262_A	266_T	1.230	1.00
290_L	294_C	1.225	1.00
296_I	315_L	1.218	1.00
91_D	94_R	1.213	1.00
283_P	287_Q	1.209	1.00
10_D	162_H	1.208	1.00
98_E	102_E	1.207	1.00
218_Q	222_Y	1.206	1.00
216_L	219_A	1.205	1.00
188_L	192_R	1.202	1.00
117_A	151_L	1.192	1.00
120_L	124_A	1.187	1.00
256_L	260_H	1.181	1.00
273_L	276_E	1.179	1.00
258_R	262_A	1.178	1.00
191_L	201_A	1.171	1.00
209_N	212_A	1.163	1.00
260_H	264_Q	1.162	1.00
215_T	219_A	1.160	1.00
231_S	234_A	1.159	1.00
295_H	298_E	1.156	1.00
73_H	81_P	1.156	1.00
82_E	86_N	1.155	1.00
255_A	261_G	1.150	1.00
208_D	213_R	1.149	1.00
256_L	259_H	1.148	1.00
258_R	261_G	1.146	1.00
172_A	198_P	1.146	1.00
173_V	184_Q	1.146	1.00
46_R	50_C	1.144	1.00
90_V	123_A	1.143	1.00
285_R	289_I	1.142	1.00
16_A	19_Q	1.142	1.00
30_Q	163_Y	1.135	1.00
278_A	283_P	1.123	1.00
208_D	212_A	1.122	1.00
169_E	173_V	1.113	1.00
98_E	101_N	1.111	1.00
232_L	235_A	1.102	1.00
78_T	82_E	1.100	1.00
248_L	252_L	1.097	1.00
253_M	256_L	1.091	1.00
279_N	282_S	1.090	1.00
90_V	127_A	1.087	1.00
218_Q	221_A	1.087	1.00
257_K	262_A	1.082	1.00
215_T	218_Q	1.082	1.00
254_D	258_R	1.082	1.00
292_D	296_I	1.081	1.00
11_F	15_V	1.074	1.00
255_A	262_A	1.074	1.00
289_I	292_D	1.072	1.00
279_N	283_P	1.071	1.00
296_I	311_L	1.068	1.00
221_A	225_P	1.067	1.00
217_C	221_A	1.066	1.00
89_G	121_T	1.062	1.00
228_D	232_L	1.062	1.00
222_Y	226_S	1.060	1.00
99_K	103_H	1.056	1.00
189_A	192_R	1.054	1.00
229_W	233_L	1.050	1.00
212_A	215_T	1.043	1.00
14_L	44_L	1.032	1.00
208_D	218_Q	1.032	1.00
8_R	12_E	1.031	1.00
222_Y	225_P	1.025	1.00
209_N	214_E	1.018	1.00
231_S	235_A	1.016	1.00
256_L	262_A	1.015	1.00
292_D	315_L	1.006	1.00
251_L	255_A	1.006	1.00
41_I	142_F	1.005	1.00
87_T	121_T	1.000	1.00
267_N	305_G	0.992	1.00
73_H	107_G	0.990	1.00
291_G	295_H	0.983	1.00
259_H	262_A	0.983	1.00
216_L	220_L	0.974	1.00
257_K	264_Q	0.972	1.00
77_Y	81_P	0.970	1.00
156_R	161_L	0.965	1.00
229_W	232_L	0.964	1.00
77_Y	99_K	0.961	1.00
190_A	201_A	0.961	1.00
287_Q	291_G	0.960	1.00
234_A	237_N	0.959	1.00
31_A	37_D	0.952	1.00
293_V	315_L	0.944	1.00
16_A	20_A	0.943	1.00
227_G	230_Y	0.942	1.00
312_I	316_L	0.937	1.00
187_L	191_L	0.933	1.00
223_S	227_G	0.930	1.00
294_C	298_E	0.930	1.00
290_L	316_L	0.928	1.00
71_G	78_T	0.927	1.00
170_Q	174_T	0.926	1.00
73_H	80_A	0.925	1.00
268_V	271_P	0.923	1.00
211_Q	218_Q	0.923	1.00
275_A	278_A	0.918	1.00
243_A	247_W	0.912	1.00
287_Q	290_L	0.907	1.00
292_D	295_H	0.907	1.00
246_H	250_T	0.903	1.00
13_K	16_A	0.897	1.00
261_G	264_Q	0.895	1.00
72_T	80_A	0.888	1.00
269_D	274_V	0.887	1.00
38_D	115_T	0.883	1.00
242_P	245_L	0.880	1.00
288_A	291_G	0.879	1.00
73_H	76_Y	0.876	1.00
8_R	11_F	0.874	1.00
281_L	289_I	0.873	1.00
228_D	231_S	0.872	1.00
213_R	220_L	0.864	1.00
69_Q	73_H	0.863	1.00
278_A	282_S	0.858	1.00
117_A	141_F	0.853	1.00
75_D	78_T	0.850	1.00
69_Q	81_P	0.845	1.00
170_Q	173_V	0.843	1.00
190_A	205_F	0.839	1.00
7_L	10_D	0.836	1.00
71_G	82_E	0.834	1.00
294_C	297_R	0.831	1.00
247_W	250_T	0.827	1.00
11_F	40_L	0.824	1.00
220_L	223_S	0.819	1.00
286_L	290_L	0.813	1.00
268_V	272_G	0.812	1.00
276_E	279_N	0.811	1.00
75_D	103_H	0.808	1.00
297_R	301_M	0.805	1.00
210_W	218_Q	0.804	1.00
190_A	204_L	0.801	1.00
70_A	73_H	0.800	1.00
132_L	151_L	0.796	1.00
244_R	247_W	0.795	1.00
183_S	211_Q	0.791	1.00
121_T	124_A	0.790	1.00
13_K	162_H	0.784	1.00
89_G	92_A	0.782	1.00
71_G	80_A	0.782	1.00
223_S	226_S	0.780	1.00
88_L	114_V	0.773	1.00
296_I	299_Q	0.770	1.00
74_P	77_Y	0.768	1.00
213_R	221_A	0.767	1.00
185_D	214_E	0.766	1.00
252_L	256_L	0.765	1.00
74_P	80_A	0.762	1.00
73_H	77_Y	0.760	1.00
243_A	246_H	0.757	1.00
251_L	254_D	0.755	1.00
313_T	316_L	0.753	1.00
5_P	175_W	0.753	1.00
80_A	115_T	0.752	1.00
270_V	274_V	0.750	1.00
76_Y	80_A	0.749	1.00
271_P	274_V	0.748	1.00
260_H	263_A	0.748	1.00
72_T	77_Y	0.744	1.00
111_V	142_F	0.742	1.00
216_L	221_A	0.738	1.00
224_V	227_G	0.737	1.00
244_R	316_L	0.737	1.00
194_S	204_L	0.736	1.00
112_V	139_T	0.735	1.00
212_A	220_L	0.734	1.00
212_A	219_A	0.732	1.00
277_L	296_I	0.732	1.00
281_L	286_L	0.731	1.00
220_L	226_S	0.730	1.00
239_E	242_P	0.729	1.00
13_K	207_G	0.728	1.00
100_L	112_V	0.727	1.00
14_L	162_H	0.725	1.00
233_L	237_N	0.725	1.00
281_L	284_S	0.723	1.00
249_A	257_K	0.719	1.00
203_A	206_Q	0.718	1.00
114_V	128_L	0.717	1.00
170_Q	188_L	0.717	1.00
81_P	86_N	0.714	1.00
100_L	131_T	0.713	1.00
283_P	290_L	0.712	1.00
30_Q	148_P	0.711	1.00
299_Q	302_S	0.711	1.00
245_L	252_L	0.707	1.00
148_P	151_L	0.706	1.00
93_V	97_T	0.706	1.00
69_Q	78_T	0.705	1.00
254_D	257_K	0.704	1.00
250_T	253_M	0.703	1.00
104_A	108_G	0.702	1.00
44_L	142_F	0.701	1.00
252_L	255_A	0.700	1.00
261_G	265_V	0.700	1.00
265_V	297_R	0.698	1.00
99_K	102_E	0.698	1.00
49_L	76_Y	0.695	1.00
71_G	76_Y	0.695	1.00
291_G	294_C	0.695	1.00
245_L	249_A	0.695	1.00
169_E	195_A	0.694	1.00
114_V	141_F	0.694	1.00
76_Y	81_P	0.690	1.00
21_G	48_L	0.681	1.00
9_P	12_E	0.678	1.00
217_C	225_P	0.676	1.00
23_G	140_W	0.673	1.00
210_W	220_L	0.671	1.00
92_A	95_E	0.670	1.00
51_Q	54_Q	0.668	1.00
104_A	138_E	0.668	1.00
262_A	265_V	0.664	1.00
5_P	171_Y	0.660	1.00
12_E	16_A	0.658	1.00
100_L	139_T	0.658	1.00
32_L	197_S	0.657	1.00
256_L	261_G	0.655	1.00
87_T	92_A	0.654	1.00
69_Q	76_Y	0.653	1.00
117_A	125_A	0.653	1.00
251_L	261_G	0.652	1.00
214_E	217_C	0.651	1.00
77_Y	127_A	0.649	1.00
307_N	310_L	0.648	1.00
130_K	134_E	0.647	1.00
282_S	287_Q	0.646	1.00
29_I	40_L	0.644	1.00
10_D	164_L	0.643	1.00
176_L	205_F	0.642	1.00
220_L	224_V	0.638	1.00
133_E	157_S	0.637	1.00
229_W	236_L	0.633	1.00
167_P	175_W	0.632	1.00
252_L	258_R	0.632	1.00
213_R	218_Q	0.628	1.00
244_R	248_L	0.628	1.00
269_D	273_L	0.627	1.00
187_L	201_A	0.624	1.00
216_L	222_Y	0.624	1.00
212_A	218_Q	0.624	1.00
101_N	131_T	0.622	1.00
224_V	228_D	0.622	1.00
235_A	243_A	0.621	1.00
273_L	277_L	0.621	1.00
131_T	141_F	0.617	1.00
109_A	138_E	0.617	1.00
78_T	81_P	0.616	1.00
185_D	188_L	0.616	1.00
87_T	90_V	0.614	1.00
219_A	223_S	0.613	1.00
82_E	127_A	0.605	1.00
239_E	243_A	0.604	1.00
97_T	100_L	0.599	1.00
211_Q	220_L	0.597	1.00
194_S	197_S	0.596	1.00
219_A	222_Y	0.596	1.00
116_D	146_R	0.595	1.00
27_L	162_H	0.592	1.00
35_M	164_L	0.592	1.00
217_C	222_Y	0.590	1.00
70_A	81_P	0.590	1.00
286_L	289_I	0.588	1.00
218_Q	223_S	0.584	0.99
210_W	216_L	0.583	0.99
43_A	46_R	0.582	0.99
79_L	92_A	0.582	0.99
32_L	35_M	0.581	0.99
245_L	248_L	0.579	0.99
238_H	241_A	0.577	0.99
214_E	220_L	0.574	0.99
131_T	134_E	0.574	0.99
213_R	217_C	0.570	0.99
96_V	104_A	0.569	0.99
277_L	281_L	0.568	0.99
75_D	82_E	0.568	0.99
280_H	284_S	0.567	0.99
240_Q	244_R	0.567	0.99
23_G	44_L	0.566	0.99
306_I	311_L	0.564	0.99
210_W	221_A	0.564	0.99
104_A	107_G	0.562	0.99
72_T	75_D	0.558	0.99
70_A	80_A	0.558	0.99
132_L	159_C	0.555	0.99
18_Y	44_L	0.554	0.99
284_S	288_A	0.552	0.99
208_D	215_T	0.551	0.99
281_L	285_R	0.551	0.99
90_V	121_T	0.549	0.99
118_A	146_R	0.548	0.99
258_R	266_T	0.548	0.99
249_A	252_L	0.547	0.99
217_C	224_V	0.545	0.99
41_I	113_W	0.544	0.99
75_D	104_A	0.544	0.99
172_A	176_L	0.544	0.99
247_W	257_K	0.540	0.99
76_Y	82_E	0.540	0.99
221_A	224_V	0.539	0.99
272_G	279_N	0.539	0.99
249_A	256_L	0.537	0.99
94_R	127_A	0.537	0.99
221_A	226_S	0.537	0.99
173_V	177_S	0.535	0.99
106_L	110_K	0.531	0.99
241_A	252_L	0.531	0.99
267_N	274_V	0.530	0.99
75_D	108_G	0.529	0.99
15_V	47_Y	0.528	0.99
126_N	152_L	0.528	0.99
174_T	178_R	0.526	0.99
45_S	111_V	0.525	0.99
27_L	164_L	0.524	0.99
258_R	264_Q	0.523	0.99
218_Q	226_S	0.522	0.99
96_V	112_V	0.520	0.99
18_Y	47_Y	0.517	0.99
174_T	177_S	0.516	0.99
208_D	220_L	0.516	0.99
305_G	311_L	0.514	0.99
17_S	24_H	0.514	0.99
249_A	262_A	0.511	0.99
167_P	172_A	0.511	0.99
27_L	44_L	0.508	0.99
167_P	171_Y	0.508	0.99
69_Q	75_D	0.506	0.99
247_W	255_A	0.505	0.99
235_A	247_W	0.503	0.98
47_Y	50_C	0.503	0.98
120_L	125_A	0.502	0.98
278_A	281_L	0.502	0.98
247_W	254_D	0.501	0.98
77_Y	96_V	0.500	0.98

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	0.9701	100	0.333	Contact Map
1jr3A	3	0.976	100	0.452	Contact Map
1iqpA	5	0.8802	100	0.458	Contact Map
1sxjE	1	0.8862	100	0.46	Contact Map
2chqA	3	0.8772	100	0.469	Contact Map
1sxjD	1	0.8743	100	0.478	Contact Map
1sxjC	1	0.8802	100	0.479	Contact Map
2gnoA	1	0.8323	100	0.502	Contact Map
3zh9B	1	0.8563	100	0.524	Contact Map
1jr3D	1	0.8743	100	0.532	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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