SBCD - ECOLI - GREMLIN Contacts

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SBCD - Nuclease SbcCD subunit D

UniProt:	P0AG76	Sequences: MRILHTSDWHLGQNFYSKSREAEHQAFLDWLLETAQTHQVDAIIVAGDVFDTGSPPSYARTLYNRFVVNLQQTGCHLVVLAGNHDSVATLNESRDIMAFLNTTVVASAGHAPQILPRRDGTPGAVLCPIPFLRPRDIITSQAGLNGIEKQQHLLAAITDYYQQHYADACKLRGDQPLPIIATGHLTTVGASKSDAVRDIYIGTLDAFPAQNFPPADYIALGHIHRAQIIGGMEHVRYCGSPIPLSFDECGKSKYVHLVTFSNGKLESVENLNVPVTQPMAVLKGDLASITAQLEQWRDVSQEPPVWLDIEITTDEYLHDIQRKIQALTESLPVEVLLVRRSREQRERVLASQQRETLSELSVEEVFNRRLALEELDESQQQRLQHLFTTTLHTLAGEHEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11094
Length:	400 (363)
Sequences:	3765 (2953)
Seq/√Len:	155.0

ECOLI - SBCD
BACSU - SBCD YHAO
HALSA - MRE11
SULSO - MRE11

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_I	182_T	5.189	1.00
38_H	269_E	4.502	1.00
254_Y	270_N	4.059	1.00
34_T	255_V	3.929	1.00
40_V	257_L	3.761	1.00
4_L	40_V	3.607	1.00
38_H	271_L	3.296	1.00
3_I	42_A	3.229	1.00
35_A	43_I	3.173	1.00
2_R	259_T	3.166	1.00
31_L	241_P	3.132	1.00
257_L	271_L	2.945	1.00
33_E	37_T	2.801	1.00
78_V	126_L	2.766	1.00
29_D	69_N	2.710	1.00
236_R	256_H	2.568	1.00
34_T	38_H	2.544	1.00
7_S	238_C	2.529	1.00
256_H	268_V	2.480	1.00
34_T	271_L	2.471	1.00
6_T	9_W	2.465	1.00
46_A	182_T	2.418	1.00
125_V	177_L	2.414	1.00
6_T	45_V	2.383	1.00
259_T	269_E	2.382	1.00
36_Q	73_T	2.315	1.00
38_H	257_L	2.174	1.00
3_I	258_V	2.136	1.00
285_D	288_S	2.128	1.00
228_I	233_E	2.111	1.00
281_V	308_D	2.102	1.00
63_Y	67_V	2.088	1.00
259_T	267_S	2.050	1.00
28_L	66_F	2.047	1.00
190_A	223_I	2.030	1.00
5_H	219_A	2.026	1.00
25_Q	62_L	1.963	1.00
42_A	78_V	1.946	1.00
30_W	274_P	1.942	1.00
42_A	126_L	1.933	1.00
283_K	310_E	1.912	1.00
284_G	288_S	1.895	1.00
44_I	126_L	1.894	1.00
116_P	125_V	1.891	1.00
181_A	215_A	1.889	1.00
249_C	281_V	1.828	1.00
31_L	255_V	1.818	1.00
118_R	123_G	1.803	1.00
76_H	103_T	1.798	1.00
27_F	31_L	1.765	1.00
35_A	75_C	1.761	1.00
123_G	177_L	1.748	1.00
226_A	256_H	1.735	1.00
33_E	69_N	1.690	1.00
11_L	63_Y	1.689	1.00
368_R	374_E	1.667	1.00
23_E	277_Q	1.663	1.00
321_Q	325_Q	1.658	1.00
255_V	273_V	1.646	1.00
35_A	70_L	1.645	1.00
49_V	79_V	1.629	1.00
218_I	235_V	1.626	1.00
6_T	31_L	1.623	1.00
35_A	40_V	1.614	1.00
246_F	308_D	1.611	1.00
126_L	180_I	1.606	1.00
181_A	218_I	1.591	1.00
27_F	241_P	1.591	1.00
23_E	306_W	1.590	1.00
9_W	45_V	1.588	1.00
385_H	389_T	1.572	1.00
280_A	305_V	1.572	1.00
261_S	264_K	1.568	1.00
256_H	270_N	1.561	1.00
78_V	128_P	1.558	1.00
258_V	268_V	1.558	1.00
376_D	379_Q	1.544	1.00
36_Q	69_N	1.542	1.00
5_H	217_Y	1.532	1.00
124_A	180_I	1.531	1.00
243_P	278_P	1.511	1.00
4_L	255_V	1.507	1.00
125_V	179_I	1.496	1.00
15_F	20_R	1.493	1.00
226_A	254_Y	1.487	1.00
29_D	66_F	1.481	1.00
4_L	257_L	1.480	1.00
155_A	159_D	1.467	1.00
22_A	26_A	1.464	1.00
20_R	23_E	1.464	1.00
119_D	122_P	1.462	1.00
79_V	104_V	1.444	1.00
2_R	38_H	1.440	1.00
283_K	312_T	1.424	1.00
158_T	162_Q	1.422	1.00
381_Q	385_H	1.418	1.00
155_A	158_T	1.417	1.00
358_S	361_S	1.414	1.00
105_V	128_P	1.411	1.00
4_L	34_T	1.394	1.00
7_S	46_A	1.393	1.00
127_C	215_A	1.392	1.00
215_A	218_I	1.384	1.00
56_P	59_A	1.377	1.00
384_Q	388_T	1.351	1.00
36_Q	72_Q	1.343	1.00
93_S	97_M	1.340	1.00
4_L	35_A	1.329	1.00
24_H	244_L	1.326	1.00
62_L	66_F	1.322	1.00
80_L	182_T	1.318	1.00
122_P	178_P	1.315	1.00
377_E	380_Q	1.310	1.00
226_A	270_N	1.305	1.00
49_V	63_Y	1.289	1.00
364_E	380_Q	1.289	1.00
1_M	259_T	1.289	1.00
159_D	163_Q	1.286	1.00
63_Y	79_V	1.283	1.00
45_V	77_L	1.280	1.00
13_Q	244_L	1.278	1.00
240_S	244_L	1.278	1.00
174_D	177_L	1.276	1.00
281_V	310_E	1.268	1.00
48_D	84_H	1.261	1.00
67_V	77_L	1.259	1.00
338_V	341_S	1.243	1.00
29_D	33_E	1.242	1.00
27_F	273_V	1.241	1.00
3_I	44_I	1.234	1.00
69_N	72_Q	1.231	1.00
32_L	70_L	1.229	1.00
261_S	265_L	1.227	1.00
178_P	260_F	1.195	1.00
116_P	123_G	1.192	1.00
208_P	211_N	1.186	1.00
30_W	33_E	1.181	1.00
25_Q	65_R	1.179	1.00
34_T	37_T	1.175	1.00
33_E	36_Q	1.174	1.00
30_W	273_V	1.147	1.00
44_I	258_V	1.145	1.00
334_E	337_L	1.142	1.00
25_Q	29_D	1.138	1.00
236_R	268_V	1.138	1.00
376_D	380_Q	1.135	1.00
361_S	364_E	1.130	1.00
127_C	179_I	1.116	1.00
13_Q	51_D	1.116	1.00
336_L	340_R	1.112	1.00
365_V	369_R	1.111	1.00
216_D	263_G	1.109	0.99
246_F	279_M	1.107	0.99
126_L	182_T	1.097	0.99
335_V	338_V	1.091	0.99
32_L	66_F	1.091	0.99
291_A	294_E	1.089	0.99
380_Q	384_Q	1.088	0.99
319_D	322_R	1.083	0.99
128_P	182_T	1.078	0.99
240_S	253_K	1.064	0.99
288_S	292_Q	1.057	0.99
9_W	49_V	1.055	0.99
27_F	242_I	1.054	0.99
51_D	244_L	1.041	0.99
382_R	385_H	1.041	0.99
44_I	180_I	1.040	0.99
36_Q	75_C	1.038	0.99
226_A	236_R	1.036	0.99
5_H	220_L	1.023	0.99
159_D	162_Q	1.012	0.99
64_N	95_D	1.012	0.99
26_A	276_T	1.005	0.99
81_A	106_A	1.004	0.99
157_I	160_Y	1.001	0.99
320_I	323_K	1.000	0.99
187_T	229_I	1.000	0.99
43_I	77_L	0.991	0.99
323_K	326_A	0.989	0.99
364_E	367_N	0.988	0.99
278_P	305_V	0.979	0.99
325_Q	328_T	0.978	0.99
289_I	293_L	0.974	0.99
193_S	196_V	0.972	0.99
48_D	83_N	0.967	0.99
42_A	180_I	0.967	0.99
110_H	113_Q	0.963	0.99
84_H	224_H	0.959	0.99
225_R	251_K	0.957	0.99
383_L	387_F	0.950	0.98
114_I	125_V	0.939	0.98
124_A	178_P	0.937	0.98
321_Q	331_L	0.936	0.98
367_N	371_A	0.934	0.98
286_L	290_T	0.931	0.98
339_R	343_E	0.931	0.98
12_G	59_A	0.928	0.98
217_Y	236_R	0.928	0.98
81_A	130_P	0.927	0.98
287_A	290_T	0.926	0.98
43_I	73_T	0.922	0.98
119_D	178_P	0.919	0.98
71_Q	101_N	0.911	0.98
44_I	219_A	0.910	0.98
180_I	258_V	0.909	0.98
260_F	265_L	0.908	0.98
324_I	331_L	0.907	0.98
262_N	265_L	0.906	0.98
337_L	340_R	0.904	0.98
188_V	206_A	0.899	0.98
12_G	55_P	0.896	0.98
326_A	329_E	0.895	0.98
178_P	216_D	0.893	0.98
56_P	60_R	0.889	0.98
363_E	383_L	0.885	0.98
228_I	236_R	0.883	0.97
61_T	98_A	0.880	0.97
180_I	260_F	0.880	0.97
50_F	93_S	0.878	0.97
130_P	237_Y	0.875	0.97
386_L	389_T	0.874	0.97
81_A	104_V	0.869	0.97
26_A	29_D	0.869	0.97
37_T	271_L	0.864	0.97
255_V	271_L	0.862	0.97
179_I	216_D	0.861	0.97
320_I	328_T	0.860	0.97
209_A	235_V	0.859	0.97
66_F	69_N	0.858	0.97
290_T	327_L	0.858	0.97
320_I	324_I	0.858	0.97
70_L	77_L	0.857	0.97
3_I	260_F	0.856	0.97
23_E	242_I	0.856	0.97
325_Q	329_E	0.855	0.97
118_R	121_T	0.854	0.97
15_F	246_F	0.851	0.97
46_A	238_C	0.848	0.97
207_F	211_N	0.847	0.97
219_A	236_R	0.845	0.97
333_V	336_L	0.843	0.97
357_L	365_V	0.842	0.97
257_L	269_E	0.838	0.97
341_S	344_Q	0.835	0.96
282_L	309_I	0.834	0.96
42_A	124_A	0.834	0.96
78_V	115_L	0.832	0.96
41_D	259_T	0.830	0.96
302_E	305_V	0.830	0.96
23_E	26_A	0.825	0.96
284_G	289_I	0.824	0.96
73_T	76_H	0.822	0.96
340_R	343_E	0.820	0.96
286_L	293_L	0.819	0.96
337_L	341_S	0.818	0.96
21_E	58_Y	0.816	0.96
369_R	373_E	0.816	0.96
287_A	291_A	0.816	0.96
310_E	339_R	0.815	0.96
24_H	50_F	0.811	0.96
31_L	35_A	0.809	0.96
5_H	238_C	0.807	0.96
50_F	63_Y	0.806	0.96
173_G	179_I	0.803	0.96
91_N	106_A	0.802	0.96
6_T	241_P	0.801	0.96
322_R	325_Q	0.798	0.95
21_E	24_H	0.797	0.95
32_L	73_T	0.796	0.95
114_I	117_R	0.792	0.95
363_E	367_N	0.790	0.95
160_Y	163_Q	0.790	0.95
57_S	60_R	0.789	0.95
230_G	233_E	0.789	0.95
71_Q	102_T	0.788	0.95
285_D	290_T	0.787	0.95
48_D	224_H	0.786	0.95
385_H	388_T	0.777	0.95
34_T	257_L	0.770	0.94
184_H	222_H	0.764	0.94
378_S	381_Q	0.763	0.94
46_A	80_L	0.759	0.94
43_I	75_C	0.758	0.94
22_A	25_Q	0.756	0.94
11_L	56_P	0.755	0.94
43_I	70_L	0.750	0.94
83_N	224_H	0.746	0.93
362_V	367_N	0.743	0.93
9_W	28_L	0.741	0.93
179_I	185_L	0.737	0.93
333_V	337_L	0.737	0.93
240_S	245_S	0.736	0.93
10_H	222_H	0.734	0.93
25_Q	69_N	0.733	0.93
217_Y	258_V	0.731	0.93
248_E	253_K	0.731	0.93
377_E	381_Q	0.731	0.93
21_E	62_L	0.726	0.93
381_Q	384_Q	0.721	0.92
174_D	179_I	0.720	0.92
103_T	106_A	0.720	0.92
243_P	253_K	0.718	0.92
290_T	294_E	0.717	0.92
129_I	183_G	0.713	0.92
63_Y	92_E	0.712	0.92
286_L	317_L	0.710	0.92
156_A	161_Y	0.710	0.92
10_H	224_H	0.708	0.92
66_F	70_L	0.706	0.91
375_L	387_F	0.706	0.91
23_E	240_S	0.704	0.91
84_H	184_H	0.704	0.91
42_A	258_V	0.704	0.91
334_E	340_R	0.703	0.91
285_D	289_I	0.702	0.91
36_Q	155_A	0.697	0.91
225_R	250_G	0.694	0.91
183_G	220_L	0.694	0.91
70_L	75_C	0.690	0.91
320_I	329_E	0.690	0.91
300_S	303_P	0.689	0.90
360_L	363_E	0.685	0.90
24_H	242_I	0.684	0.90
156_A	160_Y	0.684	0.90
21_E	59_A	0.683	0.90
9_W	241_P	0.683	0.90
363_E	388_T	0.683	0.90
230_G	234_H	0.680	0.90
288_S	291_A	0.678	0.90
3_I	124_A	0.678	0.90
31_L	40_V	0.677	0.90
350_A	353_Q	0.677	0.90
365_V	368_R	0.676	0.90
335_V	341_S	0.675	0.90
201_I	205_D	0.674	0.90
335_V	339_R	0.673	0.89
382_R	386_L	0.672	0.89
86_S	134_P	0.672	0.89
265_L	268_V	0.669	0.89
40_V	43_I	0.668	0.89
27_F	30_W	0.666	0.89
4_L	43_I	0.665	0.89
83_N	131_F	0.664	0.89
241_P	273_V	0.664	0.89
328_T	331_L	0.661	0.89
51_D	253_K	0.659	0.88
158_T	211_N	0.658	0.88
360_L	364_E	0.656	0.88
11_L	28_L	0.653	0.88
323_K	327_L	0.652	0.88
251_K	272_N	0.651	0.88
120_G	124_A	0.651	0.88
79_V	102_T	0.651	0.88
31_L	43_I	0.651	0.88
15_F	87_V	0.650	0.88
338_V	342_R	0.650	0.88
50_F	60_R	0.649	0.88
361_S	370_L	0.647	0.88
220_L	237_Y	0.646	0.87
325_Q	331_L	0.645	0.87
319_D	328_T	0.644	0.87
340_R	345_R	0.643	0.87
133_R	136_D	0.643	0.87
236_R	270_N	0.643	0.87
125_V	174_D	0.639	0.87
197_R	223_I	0.636	0.87
284_G	293_L	0.636	0.87
373_E	379_Q	0.636	0.87
46_A	67_V	0.634	0.86
356_T	359_E	0.633	0.86
8_D	12_G	0.631	0.86
188_V	208_P	0.631	0.86
12_G	244_L	0.630	0.86
9_W	66_F	0.630	0.86
383_L	390_T	0.628	0.86
54_S	64_N	0.628	0.86
334_E	338_V	0.628	0.86
28_L	32_L	0.625	0.86
123_G	178_P	0.621	0.85
289_I	292_Q	0.621	0.85
229_I	256_H	0.621	0.85
124_A	260_F	0.620	0.85
374_E	388_T	0.619	0.85
375_L	379_Q	0.619	0.85
20_R	24_H	0.618	0.85
43_I	66_F	0.617	0.85
61_T	65_R	0.616	0.85
41_D	76_H	0.612	0.85
122_P	260_F	0.612	0.85
186_T	223_I	0.611	0.84
6_T	43_I	0.611	0.84
187_T	212_F	0.611	0.84
84_H	222_H	0.610	0.84
86_S	90_L	0.608	0.84
130_P	183_G	0.608	0.84
20_R	242_I	0.606	0.84
323_K	328_T	0.605	0.84
131_F	186_T	0.605	0.84
32_L	35_A	0.604	0.84
45_V	49_V	0.604	0.84
288_S	294_E	0.603	0.84
348_V	351_S	0.602	0.84
10_H	48_D	0.600	0.83
24_H	253_K	0.600	0.83
15_F	279_M	0.594	0.83
127_C	181_A	0.594	0.83
308_D	337_L	0.594	0.83
309_I	324_I	0.594	0.83
345_R	361_S	0.593	0.83
121_T	178_P	0.592	0.83
2_R	257_L	0.592	0.83
119_D	123_G	0.591	0.82
345_R	348_V	0.591	0.82
77_L	92_E	0.590	0.82
108_A	137_I	0.589	0.82
287_A	323_K	0.588	0.82
313_T	316_Y	0.588	0.82
386_L	390_T	0.588	0.82
228_I	256_H	0.588	0.82
284_G	292_Q	0.586	0.82
290_T	293_L	0.586	0.82
59_A	81_A	0.585	0.82
355_E	361_S	0.585	0.82
244_L	253_K	0.584	0.82
83_N	184_H	0.584	0.82
260_F	263_G	0.583	0.82
14_N	51_D	0.582	0.81
336_L	342_R	0.582	0.81
234_H	265_L	0.580	0.81
13_Q	20_R	0.580	0.81
69_N	73_T	0.579	0.81
129_I	157_I	0.578	0.81
68_V	72_Q	0.577	0.81
26_A	275_V	0.576	0.81
387_F	390_T	0.576	0.81
21_E	25_Q	0.575	0.81
321_Q	330_S	0.575	0.81
63_Y	104_V	0.573	0.80
55_P	86_S	0.573	0.80
20_R	240_S	0.571	0.80
186_T	201_I	0.571	0.80
334_E	341_S	0.571	0.80
280_A	307_L	0.570	0.80
367_N	384_Q	0.570	0.80
184_H	224_H	0.570	0.80
375_L	380_Q	0.570	0.80
284_G	287_A	0.569	0.80
86_S	186_T	0.569	0.80
11_L	25_Q	0.568	0.80
198_D	201_I	0.568	0.80
95_D	98_A	0.567	0.80
32_L	69_N	0.566	0.80
228_I	268_V	0.565	0.80
90_L	104_V	0.563	0.79
59_A	130_P	0.563	0.79
81_A	87_V	0.563	0.79
11_L	16_Y	0.562	0.79
352_Q	356_T	0.562	0.79
29_D	62_L	0.561	0.79
322_R	326_A	0.559	0.79
161_Y	211_N	0.558	0.79
176_P	263_G	0.558	0.79
345_R	349_L	0.556	0.78
287_A	302_E	0.555	0.78
352_Q	355_E	0.555	0.78
240_S	278_P	0.555	0.78
156_A	159_D	0.554	0.78
122_P	126_L	0.554	0.78
212_F	218_I	0.554	0.78
347_R	351_S	0.553	0.78
20_R	55_P	0.553	0.78
294_E	301_Q	0.553	0.78
162_Q	215_A	0.553	0.78
51_D	90_L	0.551	0.78
127_C	185_L	0.550	0.78
13_Q	240_S	0.550	0.78
92_E	133_R	0.548	0.77
357_L	360_L	0.546	0.77
322_R	328_T	0.545	0.77
192_K	198_D	0.545	0.77
43_I	71_Q	0.544	0.77
334_E	342_R	0.542	0.77
78_V	105_V	0.542	0.77
357_L	364_E	0.542	0.77
361_S	365_V	0.542	0.77
180_I	385_H	0.541	0.77
4_L	31_L	0.541	0.77
117_R	122_P	0.540	0.76
157_I	161_Y	0.540	0.76
72_Q	99_F	0.539	0.76
49_V	90_L	0.537	0.76
33_E	293_L	0.537	0.76
277_Q	305_V	0.537	0.76
282_L	324_I	0.537	0.76
34_T	273_V	0.537	0.76
361_S	367_N	0.536	0.76
336_L	339_R	0.536	0.76
359_E	362_V	0.535	0.76
3_I	126_L	0.534	0.76
2_R	39_Q	0.533	0.76
191_S	210_Q	0.532	0.75
353_Q	356_T	0.532	0.75
360_L	368_R	0.529	0.75
87_V	90_L	0.529	0.75
10_H	84_H	0.528	0.75
37_T	302_E	0.528	0.75
241_P	255_V	0.527	0.75
26_A	30_W	0.526	0.75
249_C	308_D	0.526	0.75
325_Q	330_S	0.523	0.74
3_I	180_I	0.523	0.74
12_G	15_F	0.523	0.74
365_V	370_L	0.523	0.74
333_V	338_V	0.523	0.74
254_Y	273_V	0.522	0.74
361_S	369_R	0.521	0.74
256_H	259_T	0.521	0.74
354_R	362_V	0.519	0.74
13_Q	128_P	0.519	0.74
34_T	40_V	0.519	0.74
368_R	371_A	0.518	0.73
183_G	212_F	0.518	0.73
209_A	229_I	0.518	0.73
349_L	352_Q	0.518	0.73
289_I	309_I	0.515	0.73
185_L	201_I	0.515	0.73
57_S	218_I	0.513	0.73
45_V	79_V	0.513	0.73
194_D	247_D	0.512	0.73
351_S	364_E	0.512	0.73
362_V	370_L	0.511	0.72
51_D	55_P	0.510	0.72
285_D	312_T	0.509	0.72
9_W	31_L	0.508	0.72
162_Q	303_P	0.508	0.72
120_G	123_G	0.507	0.72
351_S	367_N	0.504	0.71
6_T	255_V	0.503	0.71
367_N	370_L	0.503	0.71
358_S	367_N	0.502	0.71
338_V	345_R	0.502	0.71
269_E	272_N	0.501	0.71
217_Y	220_L	0.500	0.71
190_A	207_F	0.500	0.71

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
4ltyC	1	0.845	100	0.309	Contact Map
3thoB	2	0.875	100	0.396	Contact Map
1ii7A	2	0.7475	100	0.447	Contact Map
4nzvA	1	0.7625	100	0.451	Contact Map
4ykeA	2	0.77	100	0.467	Contact Map
3av0A	1	0.8525	100	0.467	Contact Map
3t1iA	2	0.82	100	0.488	Contact Map
4fbwA	2	0.77	100	0.489	Contact Map
4fbkA	2	0.785	100	0.491	Contact Map
3d03A	5	0.635	99.9	0.717	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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