OPCR - BACSU - GREMLIN Contacts

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OPCR - HTH-type transcriptional repressor OpcR

UniProt:	O34709	Sequences: MKKTALDIIEHAEEHLIEKIAENMHTFGMPSTVGRVLGIIYMNRKPMTLSELSEATGMSKTRMSQVVREMIDANIAEKVFEKGVRKDLYDVEQDYYQTFISLFAANWTKVVSKNKVLYKKLNRELSDLLQRDGLTPEAEEKVNQLLNELKEWLHYYDWLSRLIEFFESEEVFRYVPKTKECSSLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	185 (154)
Sequences:	652 (446)
Seq/√Len:	36.0

BACSU - OPCR YVAV GBSR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_T	58_M	3.963	1.00
48_T	88_L	3.818	1.00
84_V	88_L	3.536	1.00
34_G	37_L	3.402	1.00
137_E	140_E	2.579	1.00
45_K	51_E	2.556	1.00
45_K	81_E	2.391	1.00
46_P	87_D	2.296	0.99
20_I	37_L	2.199	0.99
59_S	65_Q	2.175	0.99
81_E	88_L	2.154	0.99
52_L	63_M	2.118	0.99
140_E	143_N	2.102	0.99
49_L	63_M	2.041	0.99
36_V	52_L	2.021	0.99
72_D	142_V	2.001	0.98
58_M	87_D	1.995	0.98
99_F	156_Y	1.941	0.98
20_I	34_G	1.856	0.97
157_D	161_R	1.821	0.97
111_V	161_R	1.747	0.96
49_L	60_K	1.721	0.96
12_A	117_L	1.628	0.94
139_E	143_N	1.581	0.93
119_K	150_K	1.575	0.93
136_P	140_E	1.568	0.93
31_S	35_R	1.542	0.93
110_V	113_K	1.538	0.92
23_N	96_Y	1.457	0.90
75_I	98_T	1.437	0.90
30_P	111_V	1.434	0.90
59_S	82_K	1.400	0.88
45_K	48_T	1.395	0.88
116_V	119_K	1.388	0.88
140_E	144_Q	1.376	0.87
50_S	86_K	1.371	0.87
82_K	99_F	1.369	0.87
39_I	47_M	1.361	0.87
79_V	88_L	1.360	0.87
29_M	86_K	1.307	0.85
12_A	83_G	1.293	0.84
103_F	149_L	1.268	0.83
35_R	84_V	1.262	0.82
135_T	138_A	1.251	0.82
58_M	99_F	1.247	0.82
97_Q	101_S	1.246	0.82
136_P	143_N	1.234	0.81
56_T	70_M	1.231	0.81
32_T	99_F	1.226	0.81
34_G	38_G	1.220	0.80
79_V	90_D	1.206	0.79
115_K	119_K	1.187	0.78
95_Y	99_F	1.187	0.78
38_G	103_F	1.179	0.78
117_L	121_L	1.177	0.78
61_T	65_Q	1.171	0.77
15_H	120_K	1.166	0.77
11_H	124_E	1.158	0.77
40_I	43_N	1.149	0.76
68_R	78_K	1.131	0.75
40_I	81_E	1.124	0.74
62_R	65_Q	1.099	0.73
21_A	31_S	1.095	0.72
102_L	149_L	1.091	0.72
23_N	49_L	1.088	0.72
111_V	122_N	1.087	0.72
119_K	123_R	1.078	0.71
94_D	108_T	1.068	0.70
129_L	136_P	1.064	0.70
49_L	64_S	1.063	0.70
74_N	112_S	1.055	0.70
156_Y	160_S	1.053	0.69
21_A	35_R	1.044	0.69
65_Q	88_L	1.034	0.68
13_E	55_A	1.027	0.67
13_E	141_K	1.026	0.67
40_I	76_A	1.017	0.67
68_R	77_E	0.998	0.65
86_K	148_E	0.994	0.65
49_L	114_N	0.987	0.64
30_P	56_T	0.985	0.64
16_L	106_N	0.984	0.64
103_F	159_L	0.981	0.64
16_L	91_V	0.980	0.64
56_T	66_V	0.975	0.63
126_S	139_E	0.974	0.63
122_N	137_E	0.968	0.63
36_V	66_V	0.967	0.63
56_T	81_E	0.966	0.63
19_K	114_N	0.961	0.62
54_E	140_E	0.957	0.62
140_E	154_H	0.944	0.61
122_N	154_H	0.941	0.61
102_L	106_N	0.938	0.60
21_A	84_V	0.936	0.60
140_E	150_K	0.930	0.60
39_I	56_T	0.925	0.59
81_E	122_N	0.920	0.59
100_I	103_F	0.917	0.59
35_R	87_D	0.916	0.58
30_P	35_R	0.902	0.57
29_M	33_V	0.902	0.57
21_A	27_F	0.900	0.57
127_D	136_P	0.899	0.57
54_E	157_D	0.899	0.57
124_E	127_D	0.899	0.57
10_E	136_P	0.896	0.57
137_E	147_N	0.894	0.57
37_L	66_V	0.891	0.56
19_K	22_E	0.886	0.56
138_A	143_N	0.885	0.56
48_T	156_Y	0.874	0.55
29_M	57_G	0.873	0.55
38_G	91_V	0.867	0.54
53_S	67_V	0.859	0.54
29_M	41_Y	0.844	0.52
16_L	29_M	0.839	0.52
23_N	95_Y	0.835	0.51
58_M	61_T	0.833	0.51
89_Y	152_W	0.833	0.51
17_I	45_K	0.830	0.51
47_M	126_S	0.830	0.51
76_A	139_E	0.830	0.51
31_S	109_K	0.824	0.51
11_H	51_E	0.823	0.50
123_R	130_Q	0.793	0.48
16_L	25_H	0.787	0.47
31_S	96_Y	0.785	0.47
26_T	63_M	0.779	0.47
105_A	108_T	0.778	0.47
34_G	103_F	0.777	0.46
30_P	73_A	0.777	0.46
12_A	51_E	0.776	0.46
142_V	157_D	0.763	0.45
89_Y	98_T	0.762	0.45
18_E	57_G	0.759	0.45
77_E	96_Y	0.759	0.45
8_I	120_K	0.758	0.45
22_E	40_I	0.750	0.44
71_I	89_Y	0.749	0.44
50_S	53_S	0.748	0.44
20_I	27_F	0.743	0.44
32_T	42_M	0.734	0.43
8_I	130_Q	0.733	0.43
74_N	156_Y	0.732	0.43
25_H	142_V	0.731	0.43
72_D	81_E	0.723	0.42
58_M	66_V	0.723	0.42
42_M	148_E	0.721	0.42
20_I	24_M	0.702	0.40
63_M	114_N	0.701	0.40
8_I	44_R	0.698	0.40
9_I	150_K	0.696	0.40
30_P	65_Q	0.696	0.40
9_I	43_N	0.686	0.39
71_I	76_A	0.684	0.39
27_F	60_K	0.681	0.38
57_G	78_K	0.674	0.38
32_T	62_R	0.673	0.38
13_E	145_L	0.670	0.37
71_I	87_D	0.669	0.37
79_V	87_D	0.666	0.37
13_E	43_N	0.662	0.37
62_R	114_N	0.662	0.37
126_S	150_K	0.660	0.37
89_Y	97_Q	0.658	0.36
23_N	114_N	0.656	0.36
8_I	76_A	0.652	0.36
49_L	96_Y	0.649	0.36
46_P	88_L	0.646	0.35
65_Q	82_K	0.643	0.35
128_L	131_R	0.636	0.35
42_M	74_N	0.633	0.34
89_Y	93_Q	0.632	0.34
115_K	123_R	0.628	0.34
47_M	117_L	0.627	0.34
109_K	113_K	0.626	0.34
39_I	98_T	0.622	0.34
89_Y	148_E	0.621	0.34
50_S	97_Q	0.620	0.33
62_R	70_M	0.616	0.33
36_V	75_I	0.613	0.33
58_M	103_F	0.602	0.32
55_A	118_Y	0.600	0.32
11_H	116_V	0.598	0.32
16_L	42_M	0.597	0.32
73_A	105_A	0.597	0.32
147_N	161_R	0.590	0.31
14_E	57_G	0.588	0.31
60_K	113_K	0.578	0.30
77_E	87_D	0.576	0.30
147_N	164_E	0.573	0.30
50_S	156_Y	0.573	0.30
25_H	110_V	0.568	0.30
81_E	154_H	0.564	0.29
126_S	157_D	0.562	0.29
26_T	32_T	0.556	0.29
24_M	102_L	0.555	0.29
135_T	139_E	0.552	0.28
49_L	107_W	0.552	0.28
39_I	105_A	0.551	0.28
24_M	158_W	0.550	0.28
62_R	106_N	0.546	0.28
36_V	48_T	0.545	0.28
33_V	66_V	0.545	0.28
14_E	137_E	0.541	0.28
143_N	147_N	0.541	0.28
92_E	158_W	0.539	0.27
20_I	38_G	0.537	0.27
39_I	113_K	0.535	0.27
27_F	113_K	0.535	0.27
37_L	102_L	0.535	0.27
51_E	154_H	0.532	0.27
68_R	97_Q	0.532	0.27
86_K	141_K	0.528	0.27
102_L	148_E	0.527	0.27
10_E	93_Q	0.525	0.27
99_F	149_L	0.525	0.27
129_L	139_E	0.521	0.26
16_L	24_M	0.520	0.26
81_E	84_V	0.518	0.26
12_A	93_Q	0.515	0.26
76_A	91_V	0.514	0.26
50_S	62_R	0.513	0.26
8_I	140_E	0.512	0.26
52_L	76_A	0.511	0.26
41_Y	95_Y	0.509	0.25
22_E	110_V	0.507	0.25
48_T	58_M	0.504	0.25
42_M	145_L	0.502	0.25
102_L	131_R	0.500	0.25

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
4nb5A	4	0.8	99.5	0.734	Contact Map
1ku9A	2	0.8162	99.3	0.765	Contact Map
3qphA	2	0.8378	98.8	0.805	Contact Map
3kp7A	2	0.7243	98.7	0.81	Contact Map
3g3zA	2	0.7676	98.7	0.811	Contact Map
3deuA	2	0.7135	98.7	0.811	Contact Map
4l9nA	2	0.7459	98.7	0.811	Contact Map
1lj9A	2	0.7784	98.7	0.812	Contact Map
3fm5A	4	0.7514	98.7	0.813	Contact Map
2fbhA	2	0.7189	98.7	0.814	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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