CODA - ECOLI - GREMLIN Contacts

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CODA - Cytosine deaminase

UniProt:	P25524	Sequences: MSNNALQTIINARLPGEEGLWQIHLQDGKISAIDAQSGVMPITENSLDAEQGLVIPPFVEPHIHLDTTQTAGQPNWNQSGTLFEGIERWAERKALLTHDDVKQRAWQTLKWQIANGIQHVRTHVDVSDATLTALKAMLEVKQEVAPWIDLQIVAFPQEGILSYPNGEALLEEALRLGADVVGAIPHFEFTREYGVESLHKTFALAQKYDRLIDVHCDEIDDEQSRFVETVAALAHHEGMGARVTASHTTAMHSYNGAYTSRLFRLLKMSGINFVANPLVNIHLQGRFDTYPKRRGITRVKEMLESGINVCFGHDDVFDPWYPLGTANMLQVLHMGLHVCQLMGYGQINDGLNLITHHSARTLNLQDYGIAAGNSANLIILPAENGFDALRRQVPVRYSVRGGKVIASTQPAQTTVYLEQPEAIDYKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11326
Length:	427 (347)
Sequences:	33008 (25230)
Seq/√Len:	1354.4

ECOLI - CODA YAHJ GUAD SSNA IADA PHNM PHYDA ALLB
BACSU - HUTI YTCJ ALLB PYRC NAGA
HALSA - MTAD Q9HQE0 HUTI Q9HNZ2 Q9HHS1 PYRC
SULSO - Q97V65 Q7LXN1 Q97W09 Q97VT3 Q97WS6 Q980B7 Q97XD4 PYRC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
399_V	404_V	4.841	1.00
9_I	49_A	4.234	1.00
52_G	396_R	3.910	1.00
26_Q	31_S	3.740	1.00
397_Y	404_V	3.722	1.00
49_A	379_I	3.446	1.00
370_A	373_N	3.309	1.00
55_I	380_L	3.249	1.00
346_Q	349_D	3.183	1.00
57_P	118_Q	3.113	1.00
12_A	49_A	3.106	1.00
367_Y	374_S	3.092	1.00
10_I	46_S	2.829	1.00
300_K	304_E	2.793	1.00
374_S	401_G	2.691	1.00
32_A	371_A	2.665	1.00
364_L	367_Y	2.424	1.00
28_G	374_S	2.389	1.00
55_I	378_I	2.363	1.00
8_T	24_H	2.316	1.00
235_H	269_S	2.295	1.00
264_R	305_S	2.283	1.00
308_N	360_R	2.279	1.00
34_D	37_S	2.252	1.00
204_L	207_K	2.196	1.00
352_N	356_H	2.193	1.00
23_I	54_V	2.171	1.00
54_V	379_I	2.112	1.00
22_Q	37_S	2.111	1.00
369_I	377_L	2.107	1.00
45_N	407_S	2.095	1.00
29_K	374_S	2.075	1.00
377_L	399_V	2.065	1.00
349_D	352_N	2.052	1.00
25_L	377_L	2.023	1.00
7_Q	399_V	2.023	1.00
381_P	396_R	2.001	1.00
52_G	381_P	1.983	1.00
54_V	377_L	1.918	1.00
398_S	406_A	1.908	1.00
28_G	401_G	1.893	1.00
52_G	379_I	1.863	1.00
12_A	54_V	1.834	1.00
404_V	407_S	1.803	1.00
41_P	44_E	1.791	1.00
24_H	44_E	1.770	1.00
113_I	405_I	1.767	1.00
10_I	22_Q	1.762	1.00
14_L	21_W	1.747	1.00
11_N	48_D	1.746	1.00
360_R	365_Q	1.702	1.00
264_R	268_M	1.691	1.00
357_H	360_R	1.644	1.00
378_I	395_V	1.627	1.00
114_A	406_A	1.625	1.00
55_I	58_F	1.617	1.00
147_W	151_Q	1.617	1.00
336_L	350_G	1.588	1.00
366_D	373_N	1.578	1.00
352_N	357_H	1.568	1.00
18_E	21_W	1.548	1.00
24_H	32_A	1.530	1.00
310_C	361_T	1.511	1.00
199_H	203_A	1.500	1.00
23_I	369_I	1.493	1.00
146_P	151_Q	1.483	1.00
199_H	236_H	1.463	1.00
9_I	25_L	1.460	1.00
303_L	349_D	1.456	1.00
30_I	369_I	1.451	1.00
195_V	199_H	1.444	1.00
356_H	360_R	1.440	1.00
351_L	355_T	1.436	1.00
265_L	269_S	1.434	1.00
397_Y	407_S	1.433	1.00
135_K	139_E	1.431	1.00
33_I	371_A	1.431	1.00
203_A	207_K	1.409	1.00
22_Q	36_Q	1.406	1.00
298_R	301_E	1.399	1.00
356_H	373_N	1.383	1.00
7_Q	25_L	1.379	1.00
23_I	377_L	1.377	1.00
232_A	236_H	1.373	1.00
379_I	399_V	1.363	1.00
8_T	22_Q	1.357	1.00
206_Q	243_V	1.356	1.00
142_Q	145_A	1.341	1.00
136_A	139_E	1.326	1.00
53_L	382_A	1.304	1.00
200_K	203_A	1.300	1.00
263_F	305_S	1.296	1.00
327_N	330_Q	1.293	1.00
171_E	175_R	1.284	1.00
13_R	18_E	1.281	1.00
112_Q	120_V	1.279	1.00
49_A	54_V	1.278	1.00
400_R	405_I	1.276	1.00
21_W	35_A	1.272	1.00
204_L	208_Y	1.262	1.00
59_V	358_S	1.256	1.00
253_S	301_E	1.255	1.00
275_A	279_V	1.255	1.00
13_R	19_G	1.251	1.00
379_I	397_Y	1.251	1.00
186_H	189_F	1.242	1.00
61_P	310_C	1.241	1.00
11_N	51_Q	1.235	1.00
172_E	176_L	1.234	1.00
25_L	399_V	1.233	1.00
302_M	307_I	1.230	1.00
229_T	233_L	1.211	1.00
196_E	199_H	1.210	1.00
380_L	395_V	1.203	1.00
213_D	246_S	1.193	1.00
11_N	20_L	1.192	1.00
365_Q	373_N	1.192	1.00
55_I	351_L	1.192	1.00
61_P	358_S	1.190	1.00
265_L	268_M	1.188	1.00
64_H	247_H	1.185	1.00
13_R	20_L	1.185	1.00
24_H	31_S	1.178	1.00
9_I	377_L	1.175	1.00
276_N	279_V	1.171	1.00
17_E	356_H	1.169	1.00
14_L	23_I	1.163	1.00
179_D	184_I	1.161	1.00
61_P	362_L	1.152	1.00
169_L	172_E	1.147	1.00
272_N	308_N	1.147	1.00
21_W	34_D	1.144	1.00
248_T	273_F	1.141	1.00
272_N	361_T	1.139	1.00
136_A	140_V	1.139	1.00
220_D	224_S	1.138	1.00
59_V	119_H	1.137	1.00
332_L	354_I	1.134	1.00
171_E	208_Y	1.132	1.00
310_C	357_H	1.131	1.00
333_H	337_H	1.118	1.00
145_A	151_Q	1.115	1.00
22_Q	38_G	1.114	1.00
11_N	50_E	1.110	1.00
9_I	399_V	1.099	1.00
381_P	394_P	1.098	1.00
45_N	404_V	1.089	1.00
47_L	399_V	1.085	1.00
121_R	362_L	1.084	1.00
106_W	110_K	1.074	1.00
149_D	153_V	1.073	1.00
34_D	38_G	1.071	1.00
31_S	371_A	1.068	1.00
245_A	248_T	1.068	1.00
310_C	358_S	1.068	1.00
22_Q	34_D	1.063	1.00
24_H	41_P	1.062	1.00
162_S	165_N	1.061	1.00
211_L	363_N	1.057	1.00
12_A	379_I	1.052	1.00
301_E	304_E	1.051	1.00
21_W	33_I	1.050	1.00
353_L	357_H	1.043	1.00
252_H	255_N	1.035	1.00
61_P	274_V	1.032	1.00
119_H	367_Y	1.031	1.00
293_R	297_T	1.031	1.00
32_A	38_G	1.027	1.00
170_L	174_L	1.026	1.00
174_L	210_R	1.020	1.00
168_A	172_E	1.018	1.00
301_E	305_S	1.018	1.00
205_A	212_I	1.018	1.00
267_K	307_I	1.013	1.00
130_T	133_A	1.012	1.00
143_E	146_P	1.011	1.00
59_V	367_Y	1.009	1.00
386_F	394_P	1.007	1.00
169_L	173_A	0.997	1.00
253_S	298_R	0.997	1.00
171_E	204_L	0.990	1.00
147_W	153_V	0.989	1.00
266_L	273_F	0.987	1.00
146_P	149_D	0.980	1.00
15_P	351_L	0.978	1.00
329_L	333_H	0.976	1.00
189_F	192_E	0.971	1.00
59_V	359_A	0.969	1.00
24_H	43_T	0.950	1.00
205_A	210_R	0.947	1.00
172_E	175_R	0.946	1.00
164_P	167_E	0.946	1.00
330_Q	333_H	0.942	1.00
248_T	251_M	0.941	1.00
185_P	189_F	0.932	1.00
7_Q	45_N	0.932	1.00
274_V	310_C	0.931	1.00
30_I	377_L	0.930	1.00
106_W	143_E	0.930	1.00
232_A	235_H	0.929	1.00
215_H	314_D	0.926	1.00
148_I	152_I	0.926	1.00
175_R	208_Y	0.926	1.00
267_K	309_V	0.924	1.00
231_A	235_H	0.923	1.00
378_I	398_S	0.923	1.00
178_A	182_G	0.918	1.00
47_L	397_Y	0.916	1.00
179_D	182_G	0.911	1.00
133_A	137_M	0.910	1.00
181_V	184_I	0.909	1.00
185_P	188_E	0.908	1.00
102_K	139_E	0.908	1.00
247_H	314_D	0.908	1.00
187_F	190_T	0.906	1.00
9_I	47_L	0.901	1.00
9_I	54_V	0.900	1.00
168_A	171_E	0.899	1.00
109_L	113_I	0.895	1.00
160_I	163_Y	0.894	1.00
10_I	48_D	0.892	1.00
131_L	135_K	0.890	1.00
209_D	242_R	0.889	1.00
233_L	237_E	0.884	1.00
267_K	270_G	0.877	1.00
13_R	53_L	0.873	1.00
43_T	46_S	0.870	1.00
231_A	234_A	0.868	1.00
267_K	305_S	0.865	1.00
133_A	140_V	0.862	1.00
133_A	138_L	0.859	1.00
59_V	362_L	0.859	1.00
332_L	350_G	0.858	1.00
171_E	207_K	0.857	1.00
329_L	332_L	0.855	1.00
133_A	136_A	0.854	1.00
35_A	38_G	0.843	1.00
280_N	283_L	0.841	1.00
113_I	400_R	0.841	1.00
157_Q	161_L	0.839	1.00
65_L	108_T	0.836	1.00
132_T	135_K	0.834	1.00
328_M	354_I	0.832	1.00
24_H	34_D	0.829	1.00
325_T	330_Q	0.828	1.00
113_I	406_A	0.826	1.00
229_T	232_A	0.826	1.00
158_E	161_L	0.825	1.00
163_Y	167_E	0.824	1.00
134_L	137_M	0.824	1.00
147_W	152_I	0.823	1.00
354_I	358_S	0.821	1.00
119_H	376_N	0.818	1.00
49_A	52_G	0.811	1.00
123_H	213_D	0.811	1.00
202_F	212_I	0.805	1.00
62_H	247_H	0.802	1.00
293_R	296_I	0.799	1.00
264_R	267_K	0.797	1.00
180_V	184_I	0.796	1.00
251_M	302_M	0.796	1.00
58_F	354_I	0.795	1.00
198_L	214_V	0.794	1.00
111_W	114_A	0.794	1.00
130_T	135_K	0.793	1.00
130_T	138_L	0.792	1.00
141_K	145_A	0.792	1.00
15_P	53_L	0.791	1.00
244_T	361_T	0.791	1.00
52_G	397_Y	0.789	1.00
137_M	140_V	0.788	1.00
15_P	18_E	0.783	1.00
180_V	183_A	0.777	1.00
102_K	143_E	0.775	1.00
383_E	386_F	0.774	1.00
376_N	401_G	0.774	1.00
64_H	215_H	0.772	1.00
230_V	234_A	0.771	1.00
13_R	383_E	0.769	1.00
110_K	114_A	0.767	1.00
18_E	348_N	0.766	1.00
243_V	247_H	0.764	1.00
113_I	398_S	0.763	1.00
348_N	352_N	0.761	1.00
7_Q	47_L	0.761	1.00
156_P	159_G	0.761	1.00
251_M	298_R	0.760	1.00
327_N	333_H	0.759	1.00
107_Q	110_K	0.757	1.00
130_T	137_M	0.756	1.00
117_I	328_M	0.755	1.00
146_P	152_I	0.754	1.00
132_T	136_A	0.752	1.00
266_L	269_S	0.751	1.00
173_A	176_L	0.750	1.00
65_L	109_L	0.750	1.00
215_H	247_H	0.745	1.00
229_T	234_A	0.744	1.00
161_L	165_N	0.742	1.00
11_N	49_A	0.740	1.00
359_A	368_G	0.737	1.00
367_Y	376_N	0.736	1.00
223_Q	255_N	0.736	1.00
385_G	389_L	0.736	1.00
367_Y	373_N	0.736	1.00
188_E	191_R	0.735	1.00
149_D	152_I	0.734	1.00
60_E	313_H	0.733	1.00
20_L	50_E	0.732	1.00
163_Y	166_G	0.729	1.00
64_H	314_D	0.727	1.00
395_V	398_S	0.727	1.00
155_F	158_E	0.726	1.00
24_H	37_S	0.725	1.00
107_Q	111_W	0.724	1.00
325_T	329_L	0.723	1.00
135_K	138_L	0.723	1.00
276_N	312_G	0.721	1.00
142_Q	147_W	0.717	1.00
62_H	215_H	0.717	1.00
148_I	151_Q	0.717	1.00
23_I	33_I	0.716	1.00
156_P	162_S	0.715	1.00
65_L	120_V	0.714	1.00
63_I	112_Q	0.713	1.00
60_E	63_I	0.713	1.00
334_M	338_V	0.713	1.00
229_T	235_H	0.712	1.00
235_H	265_L	0.711	1.00
22_Q	32_A	0.711	1.00
186_H	190_T	0.710	1.00
234_A	237_E	0.706	1.00
197_S	200_K	0.701	1.00
341_L	345_G	0.701	1.00
12_A	377_L	0.700	1.00
143_E	147_W	0.692	1.00
300_K	303_L	0.692	1.00
216_C	245_A	0.690	1.00
62_H	314_D	0.686	1.00
132_T	137_M	0.686	1.00
159_G	162_S	0.685	1.00
157_Q	160_I	0.683	1.00
118_Q	398_S	0.682	1.00
17_E	351_L	0.682	1.00
308_N	357_H	0.681	1.00
21_W	369_I	0.680	1.00
37_S	40_M	0.679	1.00
359_A	373_N	0.679	1.00
275_A	278_L	0.673	1.00
154_A	157_Q	0.672	1.00
273_F	307_I	0.671	1.00
340_Q	345_G	0.667	1.00
229_T	237_E	0.666	1.00
327_N	334_M	0.663	1.00
21_W	36_Q	0.662	1.00
102_K	136_A	0.661	1.00
174_L	208_Y	0.660	1.00
324_G	327_N	0.659	1.00
157_Q	162_S	0.658	1.00
17_E	348_N	0.657	1.00
331_V	335_G	0.657	1.00
213_D	244_T	0.656	1.00
142_Q	146_P	0.653	1.00
118_Q	376_N	0.651	1.00
311_F	353_L	0.648	1.00
263_F	302_M	0.648	1.00
144_V	149_D	0.646	1.00
147_W	150_L	0.643	1.00
233_L	236_H	0.641	1.00
251_M	254_Y	0.640	1.00
195_V	236_H	0.635	1.00
275_A	299_V	0.634	1.00
20_L	36_Q	0.633	1.00
145_A	152_I	0.633	1.00
272_N	310_C	0.632	1.00
32_A	37_S	0.631	1.00
145_A	148_I	0.629	1.00
244_T	272_N	0.628	1.00
334_M	337_H	0.627	1.00
381_P	384_N	0.626	1.00
311_F	335_G	0.625	1.00
170_L	173_A	0.624	1.00
10_I	36_Q	0.624	1.00
247_H	250_A	0.623	1.00
356_H	365_Q	0.618	1.00
159_G	164_P	0.618	1.00
145_A	149_D	0.616	1.00
196_E	200_K	0.616	1.00
8_T	43_T	0.616	1.00
266_L	271_I	0.614	1.00
14_L	19_G	0.614	1.00
121_R	244_T	0.613	1.00
25_L	31_S	0.612	1.00
142_Q	151_Q	0.611	1.00
66_D	125_D	0.610	1.00
53_L	380_L	0.607	1.00
250_A	253_S	0.607	1.00
219_I	223_Q	0.606	1.00
30_I	373_N	0.604	1.00
159_G	163_Y	0.604	1.00
366_D	374_S	0.603	1.00
220_D	223_Q	0.603	1.00
274_V	278_L	0.603	1.00
275_A	280_N	0.601	1.00
279_V	283_L	0.601	1.00
156_P	160_I	0.598	1.00
326_A	329_L	0.598	1.00
139_E	143_E	0.597	1.00
270_G	308_N	0.597	1.00
397_Y	406_A	0.596	1.00
160_I	165_N	0.596	1.00
160_I	166_G	0.595	1.00
245_A	266_L	0.593	1.00
150_L	153_V	0.592	1.00
102_K	106_W	0.591	1.00
20_L	33_I	0.591	1.00
330_Q	334_M	0.590	1.00
155_F	159_G	0.588	1.00
280_N	284_Q	0.587	1.00
143_E	151_Q	0.587	1.00
214_V	230_V	0.586	1.00
20_L	35_A	0.585	1.00
58_F	117_I	0.585	1.00
109_L	120_V	0.583	1.00
197_S	201_T	0.581	1.00
177_G	180_V	0.581	1.00
162_S	166_G	0.578	1.00
178_A	181_V	0.577	1.00
32_A	40_M	0.576	1.00
161_L	164_P	0.575	1.00
201_T	204_L	0.573	1.00
294_R	297_T	0.571	1.00
263_F	267_K	0.571	1.00
218_E	221_D	0.570	1.00
151_Q	154_A	0.570	1.00
263_F	301_E	0.569	1.00
232_A	254_Y	0.568	1.00
128_D	131_L	0.567	1.00
169_L	175_R	0.567	1.00
229_T	255_N	0.565	1.00
58_F	395_V	0.565	1.00
217_D	249_T	0.564	1.00
241_A	247_H	0.563	1.00
145_A	153_V	0.562	1.00
121_R	246_S	0.562	1.00
221_D	224_S	0.561	1.00
250_A	254_Y	0.561	1.00
333_H	338_V	0.560	1.00
401_G	404_V	0.560	1.00
296_I	300_K	0.560	1.00
274_V	279_V	0.558	1.00
244_T	250_A	0.558	1.00
326_A	336_L	0.556	1.00
199_H	237_E	0.556	1.00
148_I	153_V	0.556	1.00
100_D	103_Q	0.555	1.00
15_P	348_N	0.555	1.00
230_V	233_L	0.554	1.00
157_Q	163_Y	0.554	1.00
347_I	385_G	0.551	1.00
246_S	274_V	0.550	1.00
325_T	328_M	0.548	1.00
7_Q	44_E	0.547	1.00
177_G	182_G	0.545	1.00
131_L	134_L	0.545	1.00
23_I	30_I	0.545	1.00
63_I	120_V	0.545	1.00
324_G	329_L	0.545	1.00
146_P	153_V	0.544	1.00
8_T	46_S	0.544	1.00
10_I	40_M	0.544	1.00
336_L	340_Q	0.543	1.00
249_T	252_H	0.543	1.00
144_V	152_I	0.542	1.00
229_T	236_H	0.541	1.00
155_F	160_I	0.541	1.00
232_A	265_L	0.536	1.00
19_G	35_A	0.536	1.00
273_F	302_M	0.536	1.00
336_L	341_L	0.535	1.00
119_H	364_L	0.533	1.00
251_M	255_N	0.533	1.00
231_A	265_L	0.532	1.00
146_P	150_L	0.532	1.00
112_Q	326_A	0.531	1.00
254_Y	264_R	0.530	1.00
244_T	247_H	0.529	1.00
58_F	329_L	0.529	1.00
129_A	132_T	0.529	1.00
327_N	332_L	0.528	1.00
158_E	162_S	0.528	1.00
202_F	206_Q	0.527	1.00
203_A	206_Q	0.525	1.00
246_S	249_T	0.524	1.00
336_L	347_I	0.523	1.00
65_L	122_T	0.521	1.00
276_N	280_N	0.520	1.00
230_V	237_E	0.520	1.00
323_L	331_V	0.520	1.00
17_E	352_N	0.519	1.00
119_H	362_L	0.518	1.00
47_L	404_V	0.517	1.00
325_T	331_V	0.517	1.00
178_A	183_A	0.516	1.00
160_I	164_P	0.516	1.00
123_H	246_S	0.515	1.00
132_T	138_L	0.514	1.00
235_H	268_M	0.513	1.00
237_E	240_G	0.513	1.00
8_T	41_P	0.511	1.00
58_F	378_I	0.511	1.00
58_F	351_L	0.509	1.00
248_T	266_L	0.509	1.00
167_E	200_K	0.509	1.00
13_R	382_A	0.506	1.00
376_N	400_R	0.503	1.00
112_Q	117_I	0.502	1.00
8_T	44_E	0.502	1.00
147_W	376_N	0.501	1.00
297_T	301_E	0.500	1.00

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
1ra0A	4	0.9883	100	0.274	Contact Map
4r85A	4	0.9578	100	0.319	Contact Map
4dzhA	2	0.9251	100	0.338	Contact Map
4cqbA	2	0.9087	100	0.338	Contact Map
3ls9A	2	0.9297	100	0.338	Contact Map
2pajA	2	0.8478	100	0.34	Contact Map
3hpaA	2	0.911	100	0.344	Contact Map
4v1xA	5	0.9297	100	0.352	Contact Map
3lnpA	2	0.9204	100	0.353	Contact Map
4gbdA	2	0.9204	100	0.364	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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