YJCR - BACSU - GREMLIN Contacts

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YJCR - Uncharacterized protein YjcR

UniProt:	O31640	Sequences: MAEKHIQAYKDYVKGMKYKDLAEKYGVSVNTIKSWKQRHGWERKKGAPIEKSVHTKKGGQPGNKNALGNNGGAPQKNQNAVTHGFFSKFLPEETLEIMEEIQERSPADMIWDQIQIQYAAILRAQKIMFVSDKEEMIKELKKKRSLISEVSEIEDGLVISFSTWFRYRLYSETNT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	175 (167)
Sequences:	183 (153)
Seq/√Len:	11.8

BACSU - YJCR YQAS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
144_R	155_D	4.089	0.99
137_I	166_R	4.061	0.99
18_Y	33_K	3.324	0.98
18_Y	30_N	3.198	0.97
135_E	166_R	3.131	0.96
34_S	38_R	3.120	0.96
29_V	33_K	2.689	0.92
104_R	112_D	2.328	0.85
160_S	166_R	2.325	0.85
19_K	30_N	2.270	0.83
161_F	164_W	2.235	0.82
30_N	33_K	2.213	0.81
8_A	16_M	2.171	0.80
78_Q	81_V	2.163	0.80
135_E	160_S	2.146	0.79
142_K	157_L	2.130	0.79
73_A	79_N	2.060	0.76
109_M	113_Q	2.058	0.76
8_A	12_Y	1.966	0.73
5_H	39_H	1.875	0.69
55_T	60_Q	1.840	0.67
136_M	160_S	1.819	0.67
64_K	67_L	1.790	0.65
31_T	38_R	1.768	0.64
6_I	10_K	1.750	0.63
141_K	157_L	1.729	0.62
12_Y	15_G	1.696	0.61
19_K	33_K	1.684	0.60
12_Y	34_S	1.676	0.60
55_T	59_G	1.646	0.58
66_A	71_G	1.625	0.57
137_I	160_S	1.606	0.57
21_L	32_I	1.578	0.55
18_Y	29_V	1.576	0.55
136_M	166_R	1.472	0.50
9_Y	12_Y	1.451	0.49
161_F	165_F	1.403	0.46
58_G	63_N	1.389	0.46
8_A	15_G	1.374	0.45
33_K	38_R	1.367	0.45
85_F	101_I	1.350	0.44
16_M	24_K	1.325	0.43
5_H	9_Y	1.323	0.43
31_T	34_S	1.312	0.42
120_A	123_R	1.304	0.42
157_L	160_S	1.275	0.40
132_D	135_E	1.269	0.40
33_K	37_Q	1.252	0.39
30_N	37_Q	1.186	0.36
157_L	162_S	1.175	0.35
141_K	162_S	1.174	0.35
138_K	141_K	1.174	0.35
7_Q	11_D	1.169	0.35
5_H	14_K	1.164	0.35
135_E	139_E	1.157	0.35
9_Y	13_V	1.157	0.35
30_N	34_S	1.154	0.35
18_Y	37_Q	1.146	0.34
16_M	30_N	1.143	0.34
5_H	12_Y	1.133	0.34
58_G	65_N	1.127	0.33
9_Y	34_S	1.121	0.33
21_L	25_Y	1.114	0.33
8_A	39_H	1.106	0.32
12_Y	30_N	1.098	0.32
15_G	30_N	1.095	0.32
136_M	139_E	1.094	0.32
21_L	35_W	1.093	0.32
33_K	42_E	1.088	0.32
166_R	169_L	1.088	0.32
27_V	32_I	1.087	0.32
142_K	155_D	1.080	0.31
159_I	164_W	1.074	0.31
140_L	160_S	1.074	0.31
67_L	72_G	1.062	0.31
159_I	165_F	1.060	0.30
12_Y	31_T	1.058	0.30
18_Y	34_S	1.052	0.30
109_M	119_A	1.043	0.30
120_A	174_N	1.032	0.29
146_L	155_D	1.030	0.29
65_N	68_G	1.018	0.29
15_G	39_H	1.013	0.28
89_F	110_I	1.002	0.28
22_A	32_I	0.998	0.28
18_Y	42_E	0.989	0.28
15_G	34_S	0.984	0.27
123_R	128_M	0.981	0.27
25_Y	33_K	0.977	0.27
19_K	29_V	0.974	0.27
11_D	28_S	0.967	0.27
115_Q	119_A	0.965	0.27
65_N	74_P	0.965	0.27
19_K	38_R	0.962	0.26
28_S	31_T	0.959	0.26
141_K	159_I	0.954	0.26
18_Y	36_K	0.948	0.26
142_K	160_S	0.935	0.25
8_A	18_Y	0.926	0.25
34_S	39_H	0.923	0.25
60_Q	65_N	0.923	0.25
12_Y	18_Y	0.920	0.25
18_Y	27_V	0.917	0.25
5_H	25_Y	0.904	0.24
66_A	69_N	0.900	0.24
161_F	168_R	0.890	0.24
155_D	160_S	0.874	0.23
149_E	155_D	0.870	0.23
140_L	157_L	0.869	0.23
137_I	141_K	0.869	0.23
86_F	118_Y	0.864	0.23
25_Y	39_H	0.864	0.23
97_I	106_P	0.860	0.23
141_K	144_R	0.853	0.22
66_A	72_G	0.852	0.22
158_V	162_S	0.849	0.22
7_Q	16_M	0.845	0.22
136_M	157_L	0.844	0.22
12_Y	33_K	0.838	0.22
28_S	37_Q	0.832	0.22
147_I	155_D	0.826	0.22
136_M	162_S	0.824	0.21
35_W	39_H	0.820	0.21
31_T	47_A	0.818	0.21
19_K	42_E	0.808	0.21
138_K	162_S	0.806	0.21
136_M	141_K	0.804	0.21
17_K	34_S	0.798	0.21
24_K	34_S	0.796	0.21
135_E	146_L	0.795	0.21
17_K	20_D	0.784	0.20
30_N	47_A	0.777	0.20
93_E	98_M	0.767	0.20
157_L	161_F	0.764	0.20
66_A	73_A	0.760	0.19
74_P	79_N	0.755	0.19
117_Q	168_R	0.750	0.19
33_K	36_K	0.747	0.19
23_E	26_G	0.741	0.19
63_N	74_P	0.740	0.19
5_H	35_W	0.740	0.19
120_A	128_M	0.736	0.19
24_K	38_R	0.736	0.19
145_S	156_G	0.728	0.18
32_I	35_W	0.727	0.18
16_M	20_D	0.723	0.18
17_K	33_K	0.720	0.18
96_E	100_E	0.719	0.18
104_R	113_Q	0.719	0.18
5_H	21_L	0.716	0.18
8_A	32_I	0.716	0.18
112_D	126_K	0.708	0.18
17_K	38_R	0.708	0.18
81_V	87_S	0.707	0.18
123_R	174_N	0.706	0.18
128_M	168_R	0.697	0.18
66_A	74_P	0.696	0.17
3_E	17_K	0.692	0.17
19_K	34_S	0.689	0.17
111_W	121_I	0.688	0.17
140_L	155_D	0.685	0.17
10_K	13_V	0.684	0.17
15_G	18_Y	0.681	0.17
93_E	120_A	0.679	0.17
20_D	32_I	0.675	0.17
128_M	174_N	0.674	0.17
48_P	51_K	0.672	0.17
164_W	168_R	0.669	0.17
82_T	102_Q	0.668	0.17
69_N	72_G	0.668	0.17
133_K	138_K	0.667	0.17
5_H	32_I	0.667	0.17
121_I	128_M	0.662	0.17
139_E	166_R	0.657	0.16
116_I	120_A	0.655	0.16
24_K	33_K	0.654	0.16
11_D	39_H	0.654	0.16
29_V	34_S	0.653	0.16
133_K	141_K	0.648	0.16
87_S	113_Q	0.647	0.16
62_G	76_K	0.647	0.16
36_K	42_E	0.645	0.16
63_N	66_A	0.644	0.16
78_Q	87_S	0.640	0.16
167_Y	170_Y	0.638	0.16
85_F	144_R	0.636	0.16
67_L	79_N	0.636	0.16
145_S	149_E	0.636	0.16
86_F	126_K	0.631	0.16
80_A	93_E	0.630	0.16
87_S	119_A	0.627	0.16
11_D	19_K	0.618	0.15
83_H	113_Q	0.617	0.15
136_M	142_K	0.615	0.15
125_Q	174_N	0.614	0.15
95_L	112_D	0.610	0.15
9_Y	32_I	0.601	0.15
100_E	126_K	0.600	0.15
133_K	137_I	0.600	0.15
121_I	124_A	0.600	0.15
15_G	32_I	0.599	0.15
53_V	57_K	0.599	0.15
141_K	155_D	0.597	0.15
5_H	8_A	0.597	0.15
12_Y	38_R	0.595	0.15
5_H	15_G	0.592	0.15
6_I	9_Y	0.591	0.15
133_K	166_R	0.591	0.15
11_D	18_Y	0.589	0.15
162_S	168_R	0.589	0.15
14_K	39_H	0.584	0.14
5_H	33_K	0.583	0.14
91_P	121_I	0.582	0.14
9_Y	57_K	0.579	0.14
34_S	45_K	0.578	0.14
24_K	29_V	0.576	0.14
160_S	172_E	0.571	0.14
18_Y	25_Y	0.568	0.14
19_K	28_S	0.567	0.14
6_I	14_K	0.567	0.14
30_N	53_V	0.567	0.14
25_Y	29_V	0.565	0.14
45_K	52_S	0.561	0.14
144_R	159_I	0.561	0.14
24_K	47_A	0.555	0.14
26_G	129_F	0.545	0.14
22_A	36_K	0.544	0.14
132_D	166_R	0.543	0.13
11_D	24_K	0.540	0.13
27_V	47_A	0.539	0.13
20_D	35_W	0.537	0.13
170_Y	174_N	0.536	0.13
62_G	66_A	0.533	0.13
8_A	11_D	0.533	0.13
141_K	160_S	0.528	0.13
70_N	86_F	0.528	0.13
8_A	17_K	0.527	0.13
17_K	28_S	0.526	0.13
7_Q	10_K	0.518	0.13
149_E	172_E	0.517	0.13
11_D	15_G	0.514	0.13
28_S	54_H	0.512	0.13
5_H	13_V	0.512	0.13
108_D	130_V	0.508	0.13
111_W	130_V	0.504	0.13
159_I	162_S	0.504	0.13
28_S	34_S	0.503	0.13
38_R	47_A	0.503	0.13
131_S	143_K	0.502	0.13
131_S	137_I	0.500	0.13

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
3mzyA	1	0.3143	95.6	0.915	Contact Map
2x48A	1	0.2171	94.8	0.919	Contact Map
2lfwA	1	0.36	94.6	0.92	Contact Map
1tc3C	1	0.2571	94.2	0.922	Contact Map
1jkoC	1	0.2114	92.6	0.926	Contact Map
2m8eA	1	0.2743	92.4	0.927	Contact Map
3korA	2	0.3257	91.6	0.928	Contact Map
1pdnC	1	0.5886	90.6	0.93	Contact Map
1xsvA	2	0.4914	90.6	0.93	Contact Map
1s7oA	3	0.5029	90.3	0.93	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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