YABD - BACSU - GREMLIN Contacts

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YABD - Uncharacterized deoxyribonuclease YabD

UniProt:	P37545	Sequences: MLFDTHAHLNAEQYDTDLEEVIERAKAEKVERIVVVGFDRPTITRAMEMIEEYDFIYAAIGWHPVDAIDMTEEDLAWIKELSAHEKVVAIGEMGLDYHWDKSPKDIQKEVFRNQIALAKEVNLPIIIHNRDATEDVVTILKEEGAEAVGGIMHCFTGSAEVARECMKMNFYLSFGGPVTFKNAKKPKEVVKEIPNDRLLIETDCPFLTPHPFRGKRNEPSYVKYVAEQIAELKEMTFEEIASITTENAKRLFRIN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	255 (251)
Sequences:	7136 (5017)
Seq/√Len:	316.7

ECOLI - YJJV YCFH TATD
BACSU - YABD
SULSO - Q981A2 Q97ZA2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_K	120_E	3.272	1.00
112_R	142_E	2.943	1.00
159_A	192_E	2.863	1.00
228_Q	231_E	2.722	1.00
51_E	84_H	2.493	1.00
97_Y	135_D	2.460	1.00
115_I	125_I	2.327	1.00
24_R	218_E	2.320	1.00
150_G	170_F	2.222	1.00
246_E	250_R	2.190	1.00
227_E	237_F	2.185	1.00
141_K	164_E	2.129	1.00
187_K	228_Q	2.051	1.00
26_K	55_F	2.042	1.00
129_N	136_V	1.937	1.00
108_K	135_D	1.918	1.00
82_S	90_I	1.916	1.00
59_A	89_A	1.866	1.00
195_N	233_K	1.847	1.00
116_A	143_E	1.829	1.00
195_N	243_I	1.823	1.00
235_M	240_I	1.807	1.00
242_S	246_E	1.792	1.00
112_R	143_E	1.791	1.00
17_D	216_R	1.786	1.00
7_A	33_I	1.776	1.00
23_E	27_A	1.772	1.00
97_Y	104_K	1.766	1.00
50_I	58_A	1.747	1.00
190_V	229_I	1.745	1.00
15_D	18_L	1.735	1.00
195_N	235_M	1.731	1.00
134_E	138_T	1.728	1.00
159_A	163_R	1.708	1.00
109_E	113_N	1.695	1.00
141_K	168_M	1.680	1.00
59_A	126_I	1.662	1.00
226_A	237_F	1.645	1.00
32_R	57_Y	1.631	1.00
44_T	77_W	1.631	1.00
58_A	87_V	1.630	1.00
32_R	249_K	1.621	1.00
164_E	167_K	1.620	1.00
152_M	165_C	1.611	1.00
5_T	248_A	1.594	1.00
154_C	175_G	1.584	1.00
93_M	114_Q	1.566	1.00
184_K	188_E	1.555	1.00
200_I	226_A	1.555	1.00
48_E	52_E	1.525	1.00
93_M	125_I	1.521	1.00
113_N	116_A	1.519	1.00
163_R	167_K	1.504	1.00
163_R	192_E	1.496	1.00
19_E	52_E	1.495	1.00
178_V	229_I	1.479	1.00
79_K	121_V	1.477	1.00
174_F	190_V	1.472	1.00
108_K	138_T	1.440	1.00
129_N	133_T	1.432	1.00
3_F	32_R	1.422	1.00
75_L	113_N	1.420	1.00
171_Y	250_R	1.419	1.00
151_I	251_L	1.417	1.00
188_E	191_K	1.415	1.00
162_A	172_L	1.415	1.00
227_E	231_E	1.404	1.00
158_S	161_V	1.401	1.00
223_K	227_E	1.388	1.00
111_F	127_I	1.379	1.00
137_V	164_E	1.368	1.00
171_Y	197_R	1.360	1.00
39_D	42_T	1.359	1.00
245_T	249_K	1.348	1.00
112_R	139_I	1.336	1.00
138_T	142_E	1.331	1.00
108_K	112_R	1.307	1.00
25_A	33_I	1.306	1.00
77_W	80_E	1.299	1.00
184_K	187_K	1.299	1.00
187_K	232_L	1.294	1.00
82_S	121_V	1.292	1.00
224_Y	227_E	1.285	1.00
172_L	193_I	1.270	1.00
122_N	149_G	1.268	1.00
194_P	197_R	1.263	1.00
48_E	51_E	1.256	1.00
3_F	34_V	1.245	1.00
111_F	136_V	1.237	1.00
119_K	143_E	1.219	1.00
239_E	242_S	1.215	1.00
10_N	42_T	1.213	1.00
108_K	139_I	1.212	1.00
46_A	58_A	1.210	1.00
97_Y	108_K	1.204	1.00
34_V	88_V	1.200	1.00
235_M	239_E	1.197	1.00
65_V	99_W	1.192	1.00
3_F	245_T	1.189	1.00
236_T	239_E	1.181	1.00
229_I	240_I	1.180	1.00
212_F	221_Y	1.168	1.00
212_F	224_Y	1.167	1.00
166_M	197_R	1.166	1.00
212_F	215_K	1.166	1.00
37_G	43_I	1.164	1.00
2_L	241_A	1.162	1.00
7_A	204_C	1.161	1.00
104_K	108_K	1.151	1.00
35_V	46_A	1.145	1.00
103_P	106_I	1.144	1.00
245_T	248_A	1.143	1.00
226_A	244_T	1.131	1.00
2_L	226_A	1.128	1.00
199_L	251_L	1.125	1.00
71_T	74_D	1.120	1.00
17_D	20_E	1.118	1.00
19_E	23_E	1.118	1.00
174_F	198_L	1.117	1.00
40_R	43_I	1.115	1.00
105_D	109_E	1.110	1.00
40_R	74_D	1.091	1.00
160_E	163_R	1.091	1.00
47_M	58_A	1.089	1.00
20_E	24_R	1.087	1.00
100_D	104_K	1.082	1.00
79_K	83_A	1.081	1.00
228_Q	232_L	1.070	1.00
244_T	248_A	1.066	1.00
51_E	86_K	1.065	1.00
80_E	83_A	1.063	1.00
133_T	161_V	1.062	1.00
188_E	192_E	1.057	1.00
171_Y	251_L	1.054	1.00
67_A	110_V	1.047	1.00
14_Y	216_R	1.041	1.00
36_V	126_I	1.040	1.00
217_N	221_Y	1.036	1.00
33_I	56_I	1.022	1.00
178_V	190_V	1.018	1.00
47_M	84_H	1.014	1.00
106_I	109_E	1.012	1.00
134_E	164_E	1.008	1.00
24_R	220_S	1.005	1.00
116_A	120_E	1.005	1.00
2_L	222_V	1.004	1.00
157_G	161_V	1.004	1.00
66_D	69_D	1.002	1.00
181_K	210_H	1.001	1.00
35_V	56_I	1.000	1.00
159_A	189_V	1.000	1.00
190_V	233_K	0.997	1.00
3_F	248_A	0.994	1.00
105_D	108_K	0.994	1.00
47_M	60_I	0.992	1.00
65_V	102_S	0.986	1.00
200_I	229_I	0.984	1.00
134_E	161_V	0.983	1.00
200_I	222_V	0.975	1.00
243_I	246_E	0.972	1.00
40_R	77_W	0.972	1.00
44_T	48_E	0.962	1.00
20_E	23_E	0.958	1.00
45_R	48_E	0.957	1.00
226_A	241_A	0.944	1.00
241_A	245_T	0.940	1.00
159_A	188_E	0.934	1.00
44_T	81_L	0.925	1.00
174_F	193_I	0.925	1.00
218_E	221_Y	0.918	1.00
34_V	248_A	0.916	1.00
70_M	75_L	0.913	1.00
79_K	117_L	0.912	1.00
239_E	243_I	0.912	1.00
98_H	131_D	0.912	1.00
190_V	232_L	0.911	1.00
200_I	244_T	0.909	1.00
77_W	81_L	0.908	1.00
180_F	208_T	0.902	1.00
240_I	244_T	0.899	1.00
50_I	56_I	0.893	1.00
173_S	199_L	0.889	1.00
150_G	251_L	0.886	1.00
223_K	237_F	0.885	1.00
5_T	199_L	0.877	1.00
233_K	240_I	0.877	1.00
70_M	110_V	0.875	1.00
137_V	165_C	0.875	1.00
226_A	240_I	0.872	1.00
76_A	80_E	0.865	1.00
47_M	51_E	0.864	1.00
237_F	241_A	0.862	1.00
104_K	135_D	0.861	1.00
19_E	53_Y	0.860	1.00
38_F	42_T	0.854	1.00
74_D	77_W	0.853	1.00
83_A	121_V	0.849	1.00
9_L	219_P	0.839	1.00
67_A	106_I	0.838	1.00
75_L	79_K	0.834	1.00
36_V	59_A	0.832	1.00
195_N	240_I	0.830	1.00
22_I	53_Y	0.829	1.00
151_I	252_F	0.825	1.00
46_A	50_I	0.820	1.00
135_D	138_T	0.810	1.00
127_I	152_M	0.806	1.00
166_M	194_P	0.800	1.00
31_E	245_T	0.797	1.00
76_A	79_K	0.795	1.00
122_N	148_V	0.794	1.00
222_V	225_V	0.790	1.00
119_K	144_G	0.790	1.00
60_I	87_V	0.790	1.00
191_K	232_L	0.788	1.00
117_L	121_V	0.783	1.00
145_A	148_V	0.781	1.00
24_R	27_A	0.779	1.00
62_W	70_M	0.778	1.00
115_I	119_K	0.776	1.00
137_V	161_V	0.774	1.00
119_K	146_E	0.773	1.00
5_T	151_I	0.772	1.00
14_Y	18_L	0.771	0.99
14_Y	17_D	0.765	0.99
127_I	136_V	0.764	0.99
119_K	148_V	0.761	0.99
166_M	172_L	0.758	0.99
10_N	45_R	0.755	0.99
139_I	142_E	0.754	0.99
72_E	113_N	0.753	0.99
246_E	249_K	0.752	0.99
34_V	59_A	0.749	0.99
65_V	101_K	0.749	0.99
238_E	242_S	0.749	0.99
171_Y	199_L	0.748	0.99
100_D	103_P	0.744	0.99
90_I	93_M	0.743	0.99
133_T	165_C	0.743	0.99
226_A	230_A	0.737	0.99
129_N	157_G	0.737	0.99
87_V	123_L	0.730	0.99
191_K	234_E	0.729	0.99
2_L	223_K	0.727	0.99
43_I	81_L	0.727	0.99
2_L	245_T	0.722	0.99
28_E	223_K	0.721	0.99
133_T	157_G	0.719	0.99
112_R	116_A	0.717	0.99
141_K	167_K	0.712	0.99
70_M	74_D	0.711	0.99
119_K	145_A	0.701	0.99
235_M	243_I	0.701	0.99
198_L	233_K	0.701	0.99
15_D	45_R	0.700	0.99
229_I	233_K	0.700	0.99
60_I	81_L	0.699	0.99
198_L	240_I	0.693	0.99
12_E	15_D	0.690	0.99
194_P	233_K	0.689	0.99
42_T	46_A	0.689	0.99
139_I	143_E	0.688	0.99
22_I	33_I	0.686	0.99
23_E	26_K	0.683	0.99
18_L	21_V	0.679	0.99
37_G	46_A	0.679	0.99
151_I	173_S	0.672	0.99
11_A	206_F	0.667	0.99
106_I	110_V	0.665	0.99
186_P	189_V	0.664	0.99
101_K	104_K	0.663	0.98
2_L	237_F	0.662	0.98
177_P	207_L	0.661	0.98
149_G	253_R	0.660	0.98
177_P	180_F	0.660	0.98
89_A	126_I	0.653	0.98
122_N	253_R	0.652	0.98
137_V	141_K	0.651	0.98
243_I	250_R	0.650	0.98
115_I	139_I	0.649	0.98
43_I	78_I	0.646	0.98
166_M	193_I	0.645	0.98
115_I	143_E	0.645	0.98
165_C	172_L	0.643	0.98
22_I	26_K	0.635	0.98
39_D	69_D	0.631	0.98
5_T	126_I	0.630	0.98
155_F	161_V	0.628	0.98
26_K	31_E	0.625	0.98
162_A	166_M	0.620	0.98
43_I	60_I	0.618	0.98
57_Y	88_V	0.614	0.98
67_A	102_S	0.612	0.97
177_P	186_P	0.611	0.97
80_E	84_H	0.609	0.97
162_A	193_I	0.608	0.97
198_L	244_T	0.607	0.97
75_L	117_L	0.607	0.97
95_L	132_A	0.606	0.97
68_I	103_P	0.605	0.97
193_I	198_L	0.605	0.97
129_N	165_C	0.604	0.97
208_T	221_Y	0.603	0.97
93_M	110_V	0.602	0.97
57_Y	86_K	0.599	0.97
2_L	200_I	0.598	0.97
22_I	56_I	0.596	0.97
17_D	21_V	0.594	0.97
184_K	191_K	0.594	0.97
73_E	76_A	0.594	0.97
21_V	216_R	0.592	0.97
196_D	250_R	0.592	0.97
185_K	188_E	0.590	0.97
196_D	243_I	0.590	0.97
126_I	252_F	0.587	0.97
164_E	168_M	0.587	0.97
28_E	220_S	0.587	0.97
162_A	189_V	0.586	0.97
152_M	173_S	0.585	0.97
68_I	106_I	0.584	0.97
133_T	137_V	0.584	0.97
43_I	58_A	0.583	0.97
82_S	87_V	0.581	0.97
116_A	119_K	0.581	0.97
166_M	192_E	0.579	0.96
10_N	38_F	0.571	0.96
137_V	168_M	0.569	0.96
199_L	248_A	0.569	0.96
171_Y	247_N	0.569	0.96
25_A	30_V	0.568	0.96
34_V	252_F	0.563	0.96
98_H	130_R	0.561	0.96
233_K	243_I	0.559	0.96
230_A	237_F	0.556	0.96
127_I	150_G	0.556	0.96
243_I	247_N	0.555	0.96
110_V	114_Q	0.555	0.96
145_A	149_G	0.554	0.95
3_F	249_K	0.551	0.95
47_M	81_L	0.550	0.95
10_N	35_V	0.549	0.95
178_V	240_I	0.548	0.95
41_P	45_R	0.547	0.95
38_F	66_D	0.547	0.95
25_A	218_E	0.547	0.95
231_E	234_E	0.543	0.95
68_I	102_S	0.540	0.95
144_G	170_F	0.539	0.95
22_I	55_F	0.536	0.95
99_W	102_S	0.536	0.95
174_F	177_P	0.532	0.94
179_T	210_H	0.531	0.94
43_I	46_A	0.528	0.94
41_P	69_D	0.527	0.94
83_A	120_E	0.527	0.94
151_I	199_L	0.527	0.94
180_F	214_G	0.526	0.94
176_G	179_T	0.524	0.94
221_Y	224_Y	0.521	0.94
247_N	250_R	0.521	0.94
113_N	117_L	0.521	0.94
47_M	50_I	0.520	0.94
72_E	76_A	0.519	0.94
186_P	190_V	0.515	0.93
97_Y	132_A	0.514	0.93
25_A	29_K	0.512	0.93
32_R	245_T	0.512	0.93
173_S	207_L	0.510	0.93
238_E	241_A	0.510	0.93
21_V	24_R	0.506	0.93
61_G	114_Q	0.506	0.93
179_T	228_Q	0.505	0.93
133_T	136_V	0.505	0.93
200_I	240_I	0.502	0.93
187_K	191_K	0.502	0.93
78_I	82_S	0.500	0.92

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
3e2vA	1	0.9765	100	0.178	Contact Map
3ipwA	1	0.9922	100	0.24	Contact Map
2xioA	1	0.9922	100	0.306	Contact Map
1j6oA	1	1	100	0.316	Contact Map
3gg7A	1	0.9451	100	0.342	Contact Map
3rcmA	1	1	100	0.358	Contact Map
2gzxA	1	0.9882	100	0.366	Contact Map
1xwyA	1	0.9922	100	0.368	Contact Map
1zzmA	1	0.9961	100	0.388	Contact Map
2y1hA	2	0.9725	100	0.394	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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