YNEB - BACSU - GREMLIN Contacts

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YNEB - Resolvase homolog YneB

UniProt:	Q45057	Sequences: MKALIYARVSTNKEQQETSLKRQEEELTAIAAENGMEVVKVISEKASGYEMDRDGVFELLDEIKNADIDVILVQDETRLGRGNAKIALLHCIYREGVKVYTTAHRGELELSEADSMVLEIVSIVEEYQRKIHNMKIRRGMKRAVKNGFKPQKNLKNQHGNSGKEKIEVPISEIVRLRANKLTFAEIAATLRGFGYDVSKATVHRRFQEYIENEETAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	217 (211)
Sequences:	118 (94)
Seq/√Len:	6.4

BACSU - YNEB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_E	43_S	4.540	0.98
203_H	207_Q	3.666	0.92
76_E	161_S	3.011	0.81
114_D	123_I	2.700	0.73
96_G	187_A	2.642	0.71
168_V	173_I	2.483	0.66
179_N	185_E	2.466	0.65
44_E	159_G	2.464	0.65
63_I	68_I	2.435	0.64
2_K	37_E	2.384	0.63
188_A	191_R	2.333	0.61
57_F	89_L	2.282	0.59
112_E	203_H	2.261	0.58
168_V	197_V	2.132	0.54
164_E	185_E	2.124	0.53
165_K	180_K	2.117	0.53
30_I	102_T	2.079	0.52
91_C	95_E	2.043	0.50
98_K	107_E	2.020	0.49
114_D	137_R	2.014	0.49
117_V	121_V	1.945	0.47
188_A	193_F	1.916	0.46
44_E	161_S	1.849	0.43
4_L	178_A	1.841	0.43
112_E	207_Q	1.812	0.42
67_D	177_R	1.808	0.42
158_H	174_V	1.808	0.42
72_L	107_E	1.797	0.41
42_I	55_G	1.728	0.39
148_F	195_Y	1.683	0.37
24_E	51_M	1.670	0.37
100_Y	166_I	1.618	0.35
40_K	58_E	1.617	0.35
14_E	166_I	1.616	0.35
187_A	191_R	1.606	0.35
151_Q	173_I	1.593	0.34
21_K	71_I	1.592	0.34
64_K	193_F	1.584	0.34
134_M	137_R	1.566	0.33
101_T	113_A	1.564	0.33
84_A	173_I	1.554	0.33
70_V	170_I	1.540	0.33
4_L	170_I	1.523	0.32
73_V	196_D	1.516	0.32
174_V	206_F	1.510	0.32
123_I	131_I	1.510	0.32
89_L	131_I	1.487	0.31
92_I	203_H	1.468	0.30
30_I	113_A	1.468	0.30
83_N	115_S	1.462	0.30
89_L	122_S	1.459	0.30
104_H	122_S	1.451	0.30
63_I	71_I	1.445	0.30
57_F	69_D	1.427	0.29
37_E	191_R	1.410	0.29
25_E	142_R	1.409	0.28
91_C	193_F	1.396	0.28
51_M	123_I	1.391	0.28
40_K	144_V	1.383	0.28
42_I	85_K	1.378	0.28
88_L	95_E	1.350	0.27
45_K	101_T	1.345	0.27
76_E	179_N	1.326	0.26
103_A	179_N	1.307	0.26
15_Q	131_I	1.279	0.25
113_A	119_E	1.275	0.25
51_M	164_E	1.261	0.24
65_N	148_F	1.248	0.24
5_I	44_E	1.244	0.24
173_I	193_F	1.241	0.24
113_A	121_V	1.228	0.23
33_E	38_V	1.227	0.23
30_I	73_V	1.226	0.23
55_G	208_E	1.226	0.23
89_L	211_E	1.223	0.23
63_I	84_A	1.222	0.23
54_D	109_E	1.216	0.23
144_V	168_V	1.216	0.23
121_V	193_F	1.214	0.23
43_S	51_M	1.204	0.23
35_G	157_Q	1.188	0.22
54_D	174_V	1.180	0.22
84_A	95_E	1.151	0.21
52_D	191_R	1.147	0.21
165_K	168_V	1.145	0.21
84_A	193_F	1.143	0.21
116_M	138_R	1.141	0.21
67_D	71_I	1.136	0.21
107_E	117_V	1.135	0.21
164_E	206_F	1.134	0.21
55_G	142_R	1.130	0.21
71_I	99_V	1.123	0.21
15_Q	115_S	1.117	0.21
49_Y	54_D	1.090	0.20
141_K	145_K	1.089	0.20
115_S	156_N	1.085	0.20
50_E	145_K	1.079	0.20
95_E	179_N	1.069	0.19
28_T	196_D	1.063	0.19
57_F	131_I	1.056	0.19
85_K	134_M	1.053	0.19
21_K	141_K	1.052	0.19
52_D	99_V	1.050	0.19
25_E	141_K	1.049	0.19
7_A	15_Q	1.045	0.19
50_E	142_R	1.036	0.19
157_Q	170_I	1.033	0.19
5_I	41_V	1.017	0.18
149_K	209_Y	1.015	0.18
107_E	209_Y	1.003	0.18
18_T	65_N	1.002	0.18
12_N	134_M	0.999	0.18
103_A	141_K	0.998	0.18
32_A	96_G	0.995	0.18
76_E	113_A	0.991	0.18
28_T	210_I	0.991	0.18
21_K	100_Y	0.988	0.18
76_E	103_A	0.980	0.17
44_E	160_N	0.979	0.17
79_L	156_N	0.977	0.17
155_K	212_N	0.972	0.17
60_L	70_V	0.948	0.17
99_V	123_I	0.946	0.17
180_K	207_Q	0.938	0.17
33_E	160_N	0.938	0.17
86_I	179_N	0.933	0.17
24_E	97_V	0.929	0.16
29_A	166_I	0.929	0.16
12_N	37_E	0.929	0.16
111_S	117_V	0.923	0.16
52_D	83_N	0.917	0.16
4_L	62_E	0.916	0.16
54_D	97_V	0.916	0.16
36_M	72_L	0.915	0.16
142_R	158_H	0.914	0.16
85_K	107_E	0.901	0.16
40_K	165_K	0.901	0.16
64_K	84_A	0.900	0.16
158_H	161_S	0.898	0.16
18_T	68_I	0.895	0.16
88_L	117_V	0.892	0.16
76_E	85_K	0.889	0.16
51_M	101_T	0.887	0.16
59_L	174_V	0.885	0.16
7_A	89_L	0.873	0.15
99_V	134_M	0.868	0.15
166_I	191_R	0.866	0.15
68_I	95_E	0.863	0.15
146_N	168_V	0.843	0.15
62_E	73_V	0.839	0.15
73_V	109_E	0.837	0.15
134_M	188_A	0.835	0.15
111_S	121_V	0.835	0.15
17_E	193_F	0.828	0.14
18_T	185_E	0.828	0.14
46_A	121_V	0.824	0.14
98_K	165_K	0.824	0.14
59_L	68_I	0.812	0.14
76_E	142_R	0.810	0.14
104_H	193_F	0.808	0.14
107_E	121_V	0.807	0.14
56_V	88_L	0.806	0.14
12_N	180_K	0.799	0.14
142_R	193_F	0.798	0.14
37_E	71_I	0.792	0.14
45_K	171_S	0.791	0.14
2_K	71_I	0.787	0.14
57_F	88_L	0.785	0.14
84_A	122_S	0.779	0.14
40_K	52_D	0.778	0.14
98_K	197_V	0.770	0.13
107_E	111_S	0.770	0.13
86_I	137_R	0.769	0.13
57_F	121_V	0.768	0.13
51_M	93_Y	0.766	0.13
3_A	70_V	0.765	0.13
3_A	46_A	0.765	0.13
113_A	122_S	0.764	0.13
12_N	165_K	0.762	0.13
34_N	56_V	0.762	0.13
113_A	117_V	0.761	0.13
76_E	114_D	0.758	0.13
77_T	114_D	0.755	0.13
167_E	184_A	0.752	0.13
63_I	73_V	0.750	0.13
104_H	115_S	0.746	0.13
12_N	52_D	0.744	0.13
20_L	45_K	0.742	0.13
40_K	71_I	0.739	0.13
184_A	199_K	0.738	0.13
37_E	145_K	0.735	0.13
92_I	95_E	0.731	0.13
5_I	79_L	0.729	0.13
41_V	178_A	0.728	0.13
73_V	83_N	0.722	0.13
165_K	211_E	0.721	0.13
96_G	211_E	0.721	0.13
95_E	193_F	0.717	0.13
72_L	111_S	0.716	0.13
164_E	195_Y	0.710	0.12
112_E	118_L	0.709	0.12
161_S	180_K	0.709	0.12
79_L	134_M	0.699	0.12
65_N	211_E	0.698	0.12
88_L	137_R	0.695	0.12
174_V	209_Y	0.691	0.12
24_E	28_T	0.686	0.12
69_D	131_I	0.685	0.12
94_R	138_R	0.685	0.12
94_R	116_M	0.685	0.12
84_A	168_V	0.681	0.12
122_S	179_N	0.679	0.12
85_K	121_V	0.677	0.12
103_A	193_F	0.677	0.12
17_E	179_N	0.675	0.12
30_I	86_I	0.671	0.12
52_D	196_D	0.671	0.12
51_M	185_E	0.671	0.12
146_N	199_K	0.666	0.12
21_K	38_V	0.662	0.12
5_I	170_I	0.662	0.12
2_K	158_H	0.661	0.12
55_G	83_N	0.661	0.12
42_I	188_A	0.661	0.12
73_V	146_N	0.658	0.12
51_M	142_R	0.656	0.12
74_Q	197_V	0.652	0.12
39_V	69_D	0.651	0.12
84_A	91_C	0.650	0.12
34_N	166_I	0.648	0.12
41_V	58_E	0.647	0.11
107_E	134_M	0.646	0.11
61_D	110_L	0.646	0.11
12_N	149_K	0.646	0.11
28_T	35_G	0.645	0.11
18_T	187_A	0.643	0.11
41_V	160_N	0.633	0.11
32_A	69_D	0.630	0.11
69_D	178_A	0.628	0.11
109_E	152_K	0.628	0.11
46_A	137_R	0.627	0.11
167_E	174_V	0.623	0.11
116_M	127_Y	0.620	0.11
127_Y	138_R	0.620	0.11
56_V	166_I	0.618	0.11
68_I	73_V	0.617	0.11
14_E	83_N	0.617	0.11
65_N	85_K	0.616	0.11
73_V	76_E	0.616	0.11
5_I	70_V	0.615	0.11
15_Q	67_D	0.614	0.11
4_L	28_T	0.612	0.11
51_M	131_I	0.607	0.11
85_K	113_A	0.607	0.11
97_V	121_V	0.604	0.11
96_G	191_R	0.600	0.11
112_E	148_F	0.600	0.11
105_R	164_E	0.600	0.11
12_N	191_R	0.591	0.11
14_E	188_A	0.589	0.11
119_E	123_I	0.584	0.11
103_A	170_I	0.583	0.11
174_V	197_V	0.579	0.11
38_V	141_K	0.577	0.10
59_L	67_D	0.576	0.10
97_V	137_R	0.576	0.10
42_I	56_V	0.573	0.10
164_E	197_V	0.571	0.10
151_Q	177_R	0.569	0.10
12_N	28_T	0.568	0.10
32_A	156_N	0.564	0.10
14_E	196_D	0.564	0.10
46_A	111_S	0.559	0.10
51_M	134_M	0.559	0.10
17_E	196_D	0.556	0.10
155_K	159_G	0.556	0.10
165_K	208_E	0.554	0.10
14_E	96_G	0.552	0.10
92_I	184_A	0.551	0.10
34_N	164_E	0.550	0.10
28_T	66_A	0.550	0.10
24_E	67_D	0.540	0.10
92_I	166_I	0.538	0.10
6_Y	16_Q	0.533	0.10
11_T	16_Q	0.533	0.10
10_S	16_Q	0.533	0.10
9_V	16_Q	0.533	0.10
8_R	11_T	0.533	0.10
6_Y	11_T	0.533	0.10
6_Y	10_S	0.533	0.10
6_Y	9_V	0.533	0.10
8_R	16_Q	0.533	0.10
50_E	211_E	0.532	0.10
59_L	117_V	0.529	0.10
29_A	167_E	0.528	0.10
43_S	118_L	0.528	0.10
112_E	116_M	0.527	0.10
112_E	138_R	0.527	0.10
28_T	65_N	0.527	0.10
36_M	171_S	0.527	0.10
28_T	41_V	0.526	0.10
146_N	184_A	0.524	0.10
85_K	180_K	0.520	0.10
83_N	152_K	0.518	0.10
38_V	149_K	0.516	0.10
59_L	72_L	0.514	0.10
15_Q	98_K	0.509	0.10
61_D	99_V	0.508	0.10
101_T	190_L	0.508	0.10
30_I	137_R	0.504	0.10
166_I	187_A	0.503	0.09
115_S	193_F	0.503	0.09
114_D	132_H	0.503	0.09
12_N	39_V	0.503	0.09
85_K	122_S	0.501	0.09
18_T	156_N	0.500	0.09

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
1gdtA	2	0.8341	100	0.767	Contact Map
4bqqA	2	0.9493	99.9	0.781	Contact Map
3g13A	2	0.6912	99.9	0.787	Contact Map
3guvA	2	0.6498	99.9	0.792	Contact Map
2r0qC	3	0.8295	99.9	0.792	Contact Map
3uj3X	2	0.5622	99.9	0.8	Contact Map
3ilxA	2	0.6175	99.9	0.805	Contact Map
3lhkA	2	0.6406	99.8	0.814	Contact Map
3bvpA	4	0.6037	99.8	0.816	Contact Map
2gm5A	4	0.5668	99.8	0.829	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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