YOBU - BACSU - GREMLIN Contacts

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YOBU - Putative transcriptional regulator protein YobU

UniProt:	O34637	Sequences: MGFSHITHLDLKRFAGLSQRTSNALEMTEERRIPALWDQLWKQDMSALLSQAEKDKSIIALYSNYEQETNGFYTFSVGTFQEYDDILPGPYENIDLPASAYAVFTSRIGPIEEIVLETWKEIWTWDKRHLRTFTGDFEMYDQNAAVPQRAQVNIYVAIKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (149)
Sequences:	983 (802)
Seq/√Len:	65.7

BACSU - YOBU

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
134_T	157_A	5.124	1.00
39_Q	43_Q	3.166	1.00
18_S	74_T	3.147	1.00
130_L	159_K	3.035	1.00
12_K	96_L	2.940	1.00
64_N	74_T	2.905	1.00
63_S	76_S	2.863	1.00
22_S	72_F	2.568	1.00
13_R	95_D	2.247	1.00
11_L	98_A	2.205	1.00
11_L	95_D	2.094	1.00
108_I	151_Q	2.043	1.00
101_Y	137_F	1.986	1.00
8_H	100_A	1.884	1.00
110_P	113_E	1.882	1.00
104_F	156_V	1.879	1.00
122_I	154_I	1.858	1.00
106_S	152_V	1.827	1.00
38_D	42_K	1.787	1.00
20_R	72_F	1.772	1.00
19_Q	39_Q	1.741	1.00
62_Y	65_Y	1.719	0.99
135_G	157_A	1.686	0.99
102_A	125_W	1.666	0.99
113_E	117_E	1.619	0.99
14_F	61_L	1.617	0.99
144_A	147_P	1.613	0.99
118_T	122_I	1.554	0.99
10_D	98_A	1.520	0.99
22_S	27_M	1.510	0.99
105_T	151_Q	1.501	0.99
15_A	81_Q	1.500	0.99
104_F	125_W	1.495	0.99
36_L	77_V	1.487	0.99
19_Q	36_L	1.479	0.98
131_R	136_D	1.440	0.98
32_R	35_A	1.434	0.98
66_E	71_G	1.429	0.98
64_N	94_I	1.426	0.98
15_A	91_Y	1.400	0.98
99_S	134_T	1.399	0.98
49_L	81_Q	1.391	0.98
123_W	131_R	1.362	0.97
126_D	129_H	1.349	0.97
62_Y	123_W	1.329	0.97
13_R	93_N	1.308	0.97
23_N	123_W	1.301	0.97
121_E	124_T	1.280	0.96
60_A	77_V	1.274	0.96
105_T	153_N	1.272	0.96
10_D	85_D	1.257	0.96
27_M	32_R	1.249	0.96
123_W	136_D	1.243	0.95
12_K	80_F	1.225	0.95
109_G	112_E	1.201	0.95
69_T	133_F	1.196	0.94
9_L	99_S	1.177	0.94
44_D	47_A	1.174	0.94
119_W	131_R	1.169	0.94
65_Y	131_R	1.153	0.93
21_T	136_D	1.143	0.93
146_V	149_R	1.141	0.93
125_W	129_H	1.117	0.92
18_S	76_S	1.106	0.92
67_Q	71_G	1.092	0.91
106_S	154_I	1.090	0.91
115_V	152_V	1.087	0.91
5_H	103_V	1.078	0.91
103_V	139_M	1.058	0.90
63_S	74_T	1.047	0.89
76_S	92_E	1.032	0.89
36_L	75_F	1.026	0.88
118_T	121_E	1.026	0.88
41_W	46_S	1.024	0.88
132_T	158_I	1.023	0.88
62_Y	131_R	1.014	0.88
16_G	76_S	1.012	0.88
61_L	94_I	0.999	0.87
33_I	104_F	0.997	0.87
88_P	93_N	0.977	0.86
62_Y	119_W	0.962	0.85
75_F	140_Y	0.959	0.85
66_E	72_F	0.944	0.84
34_P	125_W	0.934	0.83
37_W	79_T	0.928	0.83
23_N	73_Y	0.927	0.83
60_A	140_Y	0.923	0.82
6_I	102_A	0.920	0.82
13_R	83_Y	0.919	0.82
97_P	135_G	0.903	0.81
106_S	118_T	0.902	0.81
100_A	121_E	0.898	0.81
14_F	78_G	0.891	0.80
19_Q	32_R	0.890	0.80
18_S	92_E	0.885	0.80
142_Q	154_I	0.865	0.78
64_N	131_R	0.864	0.78
6_I	158_I	0.855	0.77
125_W	157_A	0.853	0.77
121_E	125_W	0.853	0.77
104_F	154_I	0.852	0.77
17_L	45_M	0.838	0.76
20_R	74_T	0.838	0.76
20_R	66_E	0.835	0.76
58_I	77_V	0.832	0.75
35_A	38_D	0.829	0.75
54_K	57_S	0.819	0.74
21_T	131_R	0.817	0.74
62_Y	133_F	0.812	0.74
84_D	93_N	0.807	0.73
14_F	76_S	0.806	0.73
7_T	103_V	0.805	0.73
112_E	116_L	0.804	0.73
28_T	34_P	0.803	0.73
61_L	67_Q	0.797	0.72
61_L	96_L	0.791	0.72
40_L	58_I	0.790	0.72
58_I	62_Y	0.786	0.71
17_L	40_L	0.779	0.70
37_W	103_V	0.779	0.70
65_Y	119_W	0.776	0.70
132_T	157_A	0.773	0.70
15_A	93_N	0.770	0.70
7_T	158_I	0.767	0.69
144_A	150_A	0.766	0.69
103_V	155_Y	0.757	0.68
147_P	150_A	0.753	0.68
118_T	154_I	0.753	0.68
23_N	65_Y	0.739	0.66
51_Q	85_D	0.737	0.66
19_Q	123_W	0.736	0.66
65_Y	136_D	0.736	0.66
21_T	65_Y	0.735	0.66
119_W	136_D	0.724	0.65
59_I	63_S	0.717	0.64
6_I	100_A	0.715	0.64
60_A	75_F	0.714	0.64
101_Y	155_Y	0.699	0.62
17_L	43_Q	0.697	0.62
65_Y	73_Y	0.693	0.61
111_I	114_I	0.693	0.61
37_W	60_A	0.689	0.61
106_S	114_I	0.686	0.61
106_S	109_G	0.685	0.61
9_L	137_F	0.676	0.60
17_L	36_L	0.672	0.59
65_Y	123_W	0.668	0.59
115_V	154_I	0.657	0.57
84_D	89_G	0.654	0.57
34_P	103_V	0.653	0.57
104_F	118_T	0.653	0.57
21_T	73_Y	0.652	0.57
75_F	138_E	0.651	0.57
109_G	114_I	0.648	0.56
138_E	154_I	0.646	0.56
105_T	141_D	0.644	0.56
28_T	157_A	0.634	0.55
57_S	141_D	0.633	0.55
106_S	119_W	0.629	0.54
9_L	12_K	0.624	0.54
61_L	156_V	0.623	0.53
30_E	34_P	0.621	0.53
43_Q	48_L	0.608	0.52
103_V	125_W	0.608	0.52
61_L	135_G	0.605	0.51
117_E	120_K	0.605	0.51
141_D	151_Q	0.600	0.51
56_K	83_Y	0.599	0.51
15_A	117_E	0.598	0.50
122_I	141_D	0.596	0.50
17_L	142_Q	0.593	0.50
10_D	51_Q	0.591	0.50
79_T	103_V	0.589	0.49
26_E	31_R	0.586	0.49
17_L	55_D	0.585	0.49
73_Y	136_D	0.585	0.49
21_T	119_W	0.583	0.49
12_K	149_R	0.582	0.49
28_T	31_R	0.577	0.48
79_T	91_Y	0.576	0.48
61_L	78_G	0.575	0.48
46_S	122_I	0.574	0.48
141_D	153_N	0.571	0.47
8_H	98_A	0.567	0.47
13_R	139_M	0.565	0.47
85_D	113_E	0.564	0.46
40_L	78_G	0.560	0.46
40_L	43_Q	0.559	0.46
64_N	123_W	0.557	0.46
35_A	95_D	0.556	0.46
119_W	126_D	0.551	0.45
14_F	46_S	0.548	0.45
105_T	115_V	0.547	0.44
85_D	89_G	0.546	0.44
95_D	130_L	0.544	0.44
98_A	121_E	0.543	0.44
76_S	94_I	0.541	0.44
28_T	116_L	0.537	0.43
140_Y	154_I	0.537	0.43
80_F	159_K	0.536	0.43
15_A	89_G	0.535	0.43
34_P	111_I	0.531	0.43
78_G	151_Q	0.530	0.43
83_Y	158_I	0.527	0.42
88_P	91_Y	0.526	0.42
123_W	133_F	0.526	0.42
7_T	11_L	0.524	0.42
58_I	61_L	0.522	0.42
64_N	111_I	0.521	0.42
81_Q	106_S	0.518	0.41
35_A	113_E	0.517	0.41
126_D	133_F	0.516	0.41
59_I	80_F	0.515	0.41
23_N	131_R	0.513	0.41
21_T	71_G	0.511	0.40
57_S	139_M	0.509	0.40
34_P	138_E	0.509	0.40
89_G	92_E	0.506	0.40
14_F	118_T	0.503	0.39
40_L	137_F	0.502	0.39
23_N	26_E	0.501	0.39
108_I	150_A	0.501	0.39
125_W	135_G	0.501	0.39
22_S	76_S	0.500	0.39

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
3gk6A	1	0.9125	100	0.407	Contact Map
3lurA	1	0.9563	100	0.431	Contact Map
1d5yA	1	0.9437	99.9	0.535	Contact Map
1jyhA	1	0.9187	99.9	0.554	Contact Map
3e0hA	1	0.925	99.9	0.579	Contact Map
1r8eA	2	0.9187	99.8	0.601	Contact Map
3b49A	1	0.9437	99.5	0.701	Contact Map
4b0yA	1	0.925	60.1	0.922	Contact Map
4h40A	2	0.3187	23.9	0.939	Contact Map
2fcgF	1	0.1562	4.7	0.955	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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