SBCD - BACSU - GREMLIN Contacts

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SBCD - Nuclease SbcCD subunit D

UniProt:	P23479	Sequences: MRILHTADWHLGKTLEGRSRLSEQADVLDELNTIVKDEQIDAIVMAGDAFDTVNPPALAEQLFYESLSALSDRGKRPIVVIAGNHDNPDRLSAASPLTHENGIHLIGYPTTEPIHIEVPSAGELLAVGALAYPSEARLNEVLSDTFDEKLLRDHYDVKIRQAFEHMTSRFRTDAVKIAASHIYVAGGNQTDSERPIEVGGAYTVAAESLPADAAYVALGHLHRPQTIKRARTLARYSGSPLAYSFSEAGYAKSVTIVDAKPGEEATWQEVLLSSGKPLVKWKAANGLSEVYSWLDEGRDQNAWIDLEIRVADQLSLEEIHRLRKAHPGFIHIRPVFEEQNKDRERIEVKHVSIEDRFKKFYEKQTGGAVPDEEMVKLFLELASGVEEEDAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	391 (356)
Sequences:	3909 (3060)
Seq/√Len:	162.2

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_V	179_A	5.085	1.00
38_E	268_Q	4.365	1.00
253_S	269_E	3.741	1.00
34_I	254_V	3.704	1.00
4_L	40_I	3.477	1.00
40_I	256_I	3.416	1.00
38_E	270_V	3.205	1.00
31_L	240_P	3.121	1.00
251_A	271_L	3.111	1.00
3_I	42_A	3.047	1.00
256_I	270_V	2.947	1.00
35_V	43_I	2.933	1.00
2_R	258_D	2.871	1.00
79_V	127_V	2.736	1.00
33_T	37_D	2.732	1.00
358_K	375_V	2.631	1.00
34_I	270_V	2.545	1.00
352_S	355_D	2.518	1.00
6_T	45_M	2.501	1.00
34_I	38_E	2.459	1.00
235_R	255_T	2.430	1.00
7_A	237_S	2.404	1.00
258_D	268_Q	2.404	1.00
46_A	179_A	2.387	1.00
255_T	267_W	2.374	1.00
29_D	69_A	2.331	1.00
38_E	256_I	2.297	1.00
126_A	174_A	2.277	1.00
6_T	9_W	2.240	1.00
3_I	257_V	2.224	1.00
63_F	67_L	2.200	1.00
120_S	123_E	2.058	1.00
187_G	221_L	1.996	1.00
5_H	217_A	1.978	1.00
42_A	79_V	1.962	1.00
28_L	66_S	1.956	1.00
44_V	127_V	1.921	1.00
280_K	305_D	1.916	1.00
286_G	289_E	1.895	1.00
36_K	73_R	1.888	1.00
77_P	104_H	1.857	1.00
42_A	127_V	1.853	1.00
30_E	273_S	1.840	1.00
178_A	213_A	1.823	1.00
258_D	266_T	1.814	1.00
25_A	62_L	1.800	1.00
226_T	232_T	1.770	1.00
362_E	368_A	1.760	1.00
259_A	265_A	1.759	1.00
254_V	272_L	1.723	1.00
117_E	126_A	1.713	1.00
33_T	69_A	1.710	1.00
245_F	305_D	1.699	1.00
35_V	70_L	1.696	1.00
6_T	31_L	1.686	1.00
376_K	380_E	1.671	1.00
255_T	269_E	1.665	1.00
282_K	307_E	1.662	1.00
23_E	303_W	1.649	1.00
20_R	23_E	1.638	1.00
27_V	240_P	1.638	1.00
31_L	254_V	1.637	1.00
35_V	76_R	1.625	1.00
224_P	255_T	1.620	1.00
178_A	216_V	1.612	1.00
119_P	124_L	1.604	1.00
216_V	234_A	1.604	1.00
5_H	215_Y	1.598	1.00
125_L	177_I	1.587	1.00
49_A	80_V	1.572	1.00
257_V	267_W	1.564	1.00
124_L	174_A	1.559	1.00
35_V	40_I	1.556	1.00
27_V	31_L	1.553	1.00
127_V	177_I	1.538	1.00
4_L	256_I	1.536	1.00
126_A	176_K	1.532	1.00
11_L	63_F	1.520	1.00
375_V	379_L	1.516	1.00
79_V	129_A	1.506	1.00
4_L	254_V	1.499	1.00
23_E	276_K	1.488	1.00
22_S	26_D	1.485	1.00
36_K	69_A	1.484	1.00
224_P	253_S	1.482	1.00
9_W	45_M	1.481	1.00
4_L	34_I	1.478	1.00
7_A	46_A	1.470	1.00
160_R	164_E	1.445	1.00
29_D	33_T	1.437	1.00
293_W	296_E	1.412	1.00
242_A	277_P	1.409	1.00
29_D	66_S	1.400	1.00
15_L	20_R	1.398	1.00
1_M	258_D	1.388	1.00
128_G	213_A	1.379	1.00
235_R	267_W	1.377	1.00
248_A	280_K	1.366	1.00
163_F	166_M	1.365	1.00
80_V	105_L	1.365	1.00
367_G	370_P	1.365	1.00
27_V	272_L	1.364	1.00
106_I	129_A	1.360	1.00
213_A	216_V	1.350	1.00
354_E	379_L	1.338	1.00
81_I	179_A	1.326	1.00
13_K	243_Y	1.322	1.00
67_L	78_I	1.322	1.00
4_L	35_V	1.321	1.00
224_P	269_E	1.321	1.00
2_R	38_E	1.307	1.00
62_L	66_S	1.296	1.00
171_R	174_A	1.294	1.00
282_K	309_R	1.294	1.00
280_K	307_E	1.294	1.00
355_D	358_K	1.271	1.00
320_H	323_R	1.268	1.00
45_M	78_I	1.266	1.00
279_V	302_A	1.264	1.00
239_S	243_Y	1.263	1.00
25_A	29_D	1.239	1.00
229_R	233_L	1.229	1.00
56_P	59_A	1.226	1.00
30_E	33_T	1.220	1.00
127_V	179_A	1.208	1.00
161_Q	164_E	1.200	1.00
288_S	292_S	1.194	1.00
128_G	176_K	1.184	1.00
323_R	327_P	1.183	1.00
158_K	162_A	1.177	1.00
48_D	85_H	1.175	1.00
32_N	66_S	1.172	1.00
317_E	320_H	1.164	1.00
63_F	80_V	1.159	1.00
24_Q	243_Y	1.156	1.00
49_A	63_F	1.154	1.00
13_K	51_D	1.150	1.00
161_Q	165_H	1.144	1.00
44_V	257_V	1.142	1.00
257_V	265_A	1.120	1.00
175_V	259_A	1.113	1.00
260_K	264_E	1.111	1.00
162_A	165_H	1.110	1.00
25_A	65_E	1.108	1.00
51_D	243_Y	1.098	1.00
26_D	29_D	1.098	1.00
30_E	272_L	1.096	1.00
125_L	175_V	1.093	1.00
377_L	381_L	1.092	1.00
319_I	323_R	1.083	0.99
94_A	98_T	1.083	0.99
33_T	36_K	1.072	0.99
27_V	241_L	1.069	0.99
3_I	44_V	1.066	0.99
307_E	335_V	1.065	0.99
351_V	359_K	1.062	0.99
291_Y	294_L	1.061	0.99
36_K	72_D	1.055	0.99
292_S	295_D	1.055	0.99
129_A	179_A	1.053	0.99
370_P	373_E	1.052	0.99
34_I	37_D	1.049	0.99
118_V	123_E	1.048	0.99
378_F	382_A	1.047	0.99
115_H	126_A	1.042	0.99
256_I	268_Q	1.039	0.99
9_W	49_A	1.038	0.99
42_A	177_I	1.037	0.99
44_V	217_A	1.031	0.99
120_S	175_V	1.028	0.99
292_S	296_E	1.027	0.99
205_A	208_S	1.024	0.99
73_R	76_R	1.021	0.99
5_H	218_L	1.019	0.99
347_E	350_H	1.017	0.99
44_V	177_I	1.013	0.99
245_F	278_L	1.012	0.99
224_P	235_R	1.008	0.99
305_D	331_H	1.006	0.99
85_H	222_H	1.000	0.99
32_N	70_L	0.999	0.99
177_I	259_A	0.998	0.99
117_E	124_L	0.997	0.99
185_A	203_T	0.994	0.99
184_V	227_I	0.990	0.99
48_D	84_N	0.987	0.99
357_F	378_F	0.983	0.99
48_D	222_H	0.978	0.99
376_K	379_L	0.973	0.99
36_K	76_R	0.969	0.99
204_V	208_S	0.966	0.99
359_K	362_E	0.966	0.99
287_L	291_Y	0.958	0.99
289_E	293_W	0.953	0.99
307_E	333_R	0.952	0.99
323_R	326_H	0.949	0.99
43_I	78_I	0.949	0.99
181_H	220_H	0.938	0.99
82_A	107_G	0.925	0.98
239_S	252_K	0.925	0.98
318_E	321_R	0.924	0.98
322_L	325_A	0.923	0.98
82_A	131_A	0.919	0.98
190_T	193_E	0.919	0.98
354_E	357_F	0.915	0.98
64_Y	96_P	0.915	0.98
121_A	124_L	0.902	0.98
176_K	214_A	0.899	0.98
166_M	169_R	0.898	0.98
23_E	241_L	0.897	0.98
94_A	97_L	0.897	0.98
215_Y	235_R	0.891	0.98
66_S	69_A	0.890	0.98
359_K	363_K	0.889	0.98
12_G	59_A	0.885	0.98
226_T	235_R	0.883	0.98
369_V	373_E	0.883	0.98
335_V	339_Q	0.881	0.98
288_S	291_Y	0.873	0.98
26_D	275_G	0.871	0.98
282_K	335_V	0.868	0.98
70_L	78_I	0.865	0.98
56_P	60_E	0.864	0.97
354_E	358_K	0.857	0.97
158_K	161_Q	0.857	0.97
325_A	328_G	0.852	0.97
9_W	28_L	0.851	0.97
159_I	162_A	0.851	0.97
50_F	63_F	0.847	0.97
159_I	163_F	0.845	0.97
371_D	375_V	0.843	0.97
10_H	222_H	0.841	0.97
6_T	240_P	0.839	0.97
360_F	364_Q	0.839	0.97
254_V	270_V	0.838	0.97
358_K	362_E	0.834	0.97
37_D	270_V	0.833	0.97
332_I	337_E	0.832	0.97
22_S	25_A	0.832	0.97
12_G	55_P	0.830	0.97
20_R	241_L	0.827	0.97
223_R	250_Y	0.826	0.97
21_L	58_L	0.817	0.96
5_H	237_S	0.817	0.96
368_A	371_D	0.811	0.96
131_A	236_Y	0.811	0.96
9_W	240_P	0.807	0.96
180_S	218_L	0.807	0.96
347_E	351_V	0.806	0.96
118_V	121_A	0.806	0.96
3_I	259_A	0.803	0.96
84_N	222_H	0.803	0.96
277_P	302_A	0.798	0.96
330_I	334_P	0.797	0.96
324_K	327_P	0.797	0.96
69_A	73_R	0.794	0.96
42_A	257_V	0.790	0.96
165_H	169_R	0.788	0.96
46_A	81_I	0.788	0.96
21_L	62_L	0.787	0.96
123_E	175_V	0.785	0.96
85_H	181_H	0.785	0.96
217_A	235_R	0.784	0.96
57_A	60_E	0.784	0.96
10_H	48_D	0.781	0.95
130_L	180_S	0.779	0.95
24_Q	241_L	0.779	0.95
71_S	103_I	0.777	0.95
329_F	332_I	0.774	0.95
20_R	24_Q	0.773	0.95
319_I	329_F	0.772	0.95
289_E	292_S	0.771	0.95
177_I	257_V	0.771	0.95
158_K	163_F	0.770	0.95
80_V	103_I	0.770	0.95
171_R	176_K	0.769	0.95
353_I	357_F	0.767	0.95
46_A	67_L	0.767	0.95
43_I	73_R	0.766	0.95
40_I	43_I	0.765	0.95
28_L	32_N	0.765	0.95
343_R	346_I	0.764	0.95
42_A	125_L	0.761	0.95
31_L	35_V	0.761	0.95
261_P	264_E	0.750	0.94
291_Y	325_A	0.749	0.94
299_D	302_A	0.749	0.94
46_A	237_S	0.748	0.94
134_S	137_R	0.747	0.94
218_L	236_Y	0.746	0.94
175_V	214_A	0.746	0.94
24_Q	50_F	0.745	0.94
159_I	166_M	0.741	0.94
120_S	124_L	0.740	0.94
42_A	77_P	0.737	0.94
71_S	102_G	0.735	0.94
31_L	40_I	0.735	0.94
6_T	43_I	0.735	0.94
206_A	234_A	0.732	0.94
61_Q	99_H	0.732	0.94
2_R	256_I	0.731	0.94
15_L	245_F	0.731	0.94
43_I	76_R	0.730	0.94
31_L	43_I	0.728	0.93
115_H	121_A	0.727	0.93
225_Q	229_R	0.727	0.93
181_H	222_H	0.723	0.93
51_D	252_K	0.722	0.93
286_G	291_Y	0.720	0.93
367_G	371_D	0.720	0.93
115_H	119_P	0.718	0.93
115_H	118_V	0.718	0.93
264_E	267_W	0.713	0.93
158_K	165_H	0.713	0.93
25_A	69_A	0.712	0.93
119_P	123_E	0.708	0.92
346_I	376_K	0.707	0.92
61_Q	65_E	0.705	0.92
372_E	376_K	0.701	0.92
10_H	220_H	0.700	0.92
242_A	252_K	0.699	0.92
34_I	256_I	0.696	0.92
162_A	170_F	0.696	0.92
23_E	26_D	0.696	0.92
113_P	118_V	0.696	0.92
170_F	176_K	0.696	0.92
229_R	232_T	0.693	0.92
371_D	376_K	0.691	0.92
215_Y	257_V	0.686	0.91
281_W	306_L	0.682	0.91
68_S	72_D	0.678	0.91
11_L	56_P	0.677	0.91
32_N	36_K	0.676	0.91
114_I	118_V	0.675	0.91
176_K	182_I	0.675	0.91
92_S	107_G	0.673	0.90
351_V	354_E	0.672	0.90
239_S	244_S	0.670	0.90
290_V	294_L	0.669	0.90
350_H	353_I	0.669	0.90
111_T	114_I	0.667	0.90
366_G	369_V	0.667	0.90
32_N	69_A	0.667	0.90
8_D	12_G	0.666	0.90
331_H	334_P	0.665	0.90
233_L	265_A	0.665	0.90
42_A	118_V	0.665	0.90
344_E	348_V	0.664	0.90
85_H	220_H	0.663	0.90
373_E	376_K	0.663	0.90
119_P	122_G	0.662	0.90
260_K	263_E	0.661	0.90
21_L	24_Q	0.661	0.90
367_G	373_E	0.661	0.90
69_A	72_D	0.661	0.90
84_N	132_Y	0.659	0.90
185_A	205_A	0.659	0.90
50_F	94_A	0.658	0.89
29_D	62_L	0.656	0.89
226_T	267_W	0.652	0.89
226_T	229_R	0.650	0.89
333_R	337_E	0.649	0.89
253_S	272_L	0.649	0.89
63_F	105_L	0.649	0.89
59_A	131_A	0.646	0.89
13_K	239_S	0.645	0.89
112_E	115_H	0.644	0.88
228_K	232_T	0.643	0.88
353_I	382_A	0.641	0.88
240_P	272_L	0.640	0.88
26_D	274_S	0.638	0.88
18_R	330_I	0.636	0.88
329_F	334_P	0.635	0.88
321_R	324_K	0.634	0.88
20_R	239_S	0.634	0.88
344_E	347_E	0.633	0.88
55_P	88_P	0.633	0.88
320_H	326_H	0.633	0.88
84_N	181_H	0.631	0.87
4_L	31_L	0.631	0.87
352_S	357_F	0.630	0.87
228_K	233_L	0.629	0.87
131_A	180_S	0.629	0.87
335_V	338_E	0.627	0.87
43_I	70_L	0.626	0.87
334_P	337_E	0.624	0.87
126_A	171_R	0.623	0.87
87_N	183_Y	0.621	0.87
241_L	275_G	0.620	0.87
82_A	105_L	0.619	0.86
162_A	166_M	0.618	0.86
333_R	340_N	0.618	0.86
297_G	300_Q	0.616	0.86
305_D	333_R	0.615	0.86
183_Y	198_V	0.614	0.86
343_R	359_K	0.613	0.86
322_L	328_G	0.613	0.86
6_T	254_V	0.611	0.86
51_D	55_P	0.610	0.86
158_K	166_M	0.608	0.85
7_A	200_G	0.608	0.85
279_V	283_A	0.608	0.85
23_E	239_S	0.607	0.85
329_F	335_V	0.605	0.85
107_G	110_T	0.605	0.85
50_F	60_E	0.604	0.85
132_Y	183_Y	0.604	0.85
290_V	306_L	0.602	0.85
32_N	35_V	0.599	0.85
63_F	93_A	0.599	0.85
27_V	30_E	0.598	0.85
232_T	235_R	0.596	0.84
352_S	358_K	0.596	0.84
87_N	135_E	0.595	0.84
41_D	77_P	0.595	0.84
10_H	85_H	0.594	0.84
317_E	321_R	0.594	0.84
15_L	88_P	0.592	0.84
41_D	119_P	0.592	0.84
321_R	328_G	0.592	0.84
36_K	40_I	0.588	0.84
166_M	170_F	0.585	0.83
70_L	76_R	0.585	0.83
2_R	39_Q	0.584	0.83
82_A	88_P	0.583	0.83
11_L	28_L	0.583	0.83
32_N	73_R	0.582	0.83
45_M	49_A	0.580	0.83
43_I	66_S	0.579	0.83
188_N	207_E	0.579	0.83
21_L	59_A	0.579	0.83
318_E	323_R	0.576	0.82
14_T	51_D	0.576	0.82
3_I	125_L	0.575	0.82
319_I	322_L	0.575	0.82
9_W	66_S	0.575	0.82
13_K	20_R	0.574	0.82
12_G	243_Y	0.574	0.82
78_I	93_A	0.572	0.82
367_G	379_L	0.570	0.82
55_P	87_N	0.569	0.82
356_R	360_F	0.569	0.82
217_A	237_S	0.568	0.81
3_I	177_I	0.567	0.81
329_F	336_F	0.567	0.81
353_I	364_Q	0.566	0.81
288_S	295_D	0.565	0.81
104_H	107_G	0.565	0.81
41_D	258_D	0.565	0.81
4_L	43_I	0.565	0.81
172_T	212_D	0.564	0.81
331_H	335_V	0.562	0.81
378_F	381_L	0.562	0.81
330_I	333_R	0.561	0.81
337_E	340_N	0.561	0.81
21_L	25_A	0.560	0.81
318_E	327_P	0.560	0.81
24_Q	252_K	0.559	0.80
355_D	359_K	0.558	0.80
62_L	237_S	0.556	0.80
184_V	209_L	0.555	0.80
359_K	376_K	0.555	0.80
268_Q	271_L	0.554	0.80
51_D	91_L	0.554	0.80
7_A	217_A	0.554	0.80
198_V	203_T	0.554	0.80
295_D	298_R	0.553	0.80
161_Q	324_K	0.553	0.80
240_P	254_V	0.553	0.80
291_Y	295_D	0.550	0.79
318_E	326_H	0.549	0.79
12_G	56_P	0.549	0.79
194_R	221_L	0.549	0.79
227_I	255_T	0.549	0.79
209_L	234_A	0.545	0.79
48_D	181_H	0.544	0.79
175_V	261_P	0.540	0.78
98_T	101_N	0.540	0.78
375_V	378_F	0.539	0.78
99_H	114_I	0.538	0.78
225_Q	228_K	0.538	0.78
329_F	338_E	0.535	0.77
87_N	131_A	0.534	0.77
124_L	175_V	0.533	0.77
24_Q	239_S	0.533	0.77
369_V	381_L	0.531	0.77
299_D	304_I	0.531	0.77
128_G	178_A	0.531	0.77
87_N	91_L	0.530	0.77
243_Y	252_K	0.529	0.77
287_L	315_S	0.528	0.77
9_W	31_L	0.527	0.76
55_P	63_F	0.527	0.76
243_Y	360_F	0.526	0.76
35_V	77_P	0.526	0.76
112_E	116_I	0.525	0.76
66_S	70_L	0.524	0.76
286_G	309_R	0.524	0.76
235_R	269_E	0.522	0.76
105_L	109_P	0.520	0.75
319_I	325_A	0.519	0.75
132_Y	221_L	0.518	0.75
144_D	161_Q	0.518	0.75
115_H	129_A	0.518	0.75
26_D	30_E	0.518	0.75
132_Y	247_E	0.517	0.75
42_A	123_E	0.517	0.75
31_L	66_S	0.517	0.75
337_E	341_K	0.517	0.75
361_Y	365_T	0.516	0.75
242_A	274_S	0.516	0.75
251_A	269_E	0.515	0.75
125_L	259_A	0.514	0.75
373_E	377_L	0.513	0.74
201_A	204_V	0.511	0.74
255_T	258_D	0.511	0.74
84_N	220_H	0.510	0.74
361_Y	366_G	0.507	0.74
351_V	355_D	0.507	0.74
322_L	329_F	0.506	0.73
99_H	102_G	0.506	0.73
182_I	245_F	0.505	0.73
335_V	341_K	0.505	0.73
206_A	227_I	0.504	0.73
122_G	175_V	0.503	0.73
79_V	106_I	0.503	0.73
227_I	306_L	0.503	0.73
8_D	222_H	0.502	0.73
177_I	265_A	0.502	0.73
20_R	55_P	0.501	0.73
228_K	320_H	0.501	0.73
54_N	64_Y	0.501	0.73
377_L	380_E	0.500	0.73
342_D	346_I	0.500	0.73

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	0.8312	100	0.363	Contact Map
3thoB	2	0.8951	100	0.378	Contact Map
4nzvA	1	0.7877	100	0.443	Contact Map
1ii7A	2	0.7673	100	0.446	Contact Map
3av0A	1	0.867	100	0.462	Contact Map
4ykeA	2	0.7826	100	0.477	Contact Map
4fbwA	2	0.7903	100	0.492	Contact Map
3t1iA	2	0.8414	100	0.496	Contact Map
4fbkA	2	0.8031	100	0.5	Contact Map
3d03A	5	0.6598	99.9	0.716	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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