GBSR - BACSU - GREMLIN Contacts

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GBSR - HTH-type transcriptional repressor GbsR

UniProt:	P71015	Sequences: MDENPEFAAIEQARDLVIDSIAETMDLYGITRSVGILYGTMYMRDEMTLDEMREELQMSKPSMSTGVKKLQDLNVVKKTFHRGIRKHTFVAEKDFFKFFTNFFPPKWEREVQVNVTAIEEAQADLQKVLCKEDLDEDIKNEALQLYDQLESSKAYYDWLKRLAESVQTGEIFKFIPVETK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	180 (154)
Sequences:	644 (441)
Seq/√Len:	35.6

BACSU - GBSR OPCR YVAV

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_S	58_M	4.645	1.00
48_T	88_T	3.942	1.00
84_I	88_T	3.576	1.00
35_G	38_Y	3.518	1.00
46_E	81_H	2.989	1.00
37_L	52_M	2.760	1.00
58_M	87_H	2.519	1.00
137_D	140_N	2.399	1.00
21_I	38_Y	2.149	0.99
59_S	65_T	2.103	0.99
46_E	51_E	2.070	0.99
49_L	63_M	2.054	0.99
140_N	143_L	2.000	0.98
81_H	88_T	1.939	0.98
72_D	142_A	1.885	0.98
79_T	88_T	1.882	0.98
157_D	161_R	1.868	0.97
99_F	156_Y	1.830	0.97
52_M	63_M	1.743	0.96
21_I	35_G	1.729	0.96
111_V	161_R	1.725	0.96
13_A	117_A	1.721	0.96
49_L	60_K	1.693	0.95
50_D	86_K	1.639	0.94
56_L	70_L	1.630	0.94
139_K	143_L	1.582	0.93
71_Q	89_F	1.549	0.93
136_E	140_N	1.533	0.92
97_K	101_N	1.526	0.92
82_R	99_F	1.489	0.91
119_E	150_E	1.452	0.90
75_V	98_F	1.443	0.90
36_I	84_I	1.432	0.89
32_R	36_I	1.398	0.88
110_E	113_V	1.368	0.87
59_S	82_R	1.361	0.87
103_F	149_L	1.353	0.86
116_T	119_E	1.330	0.85
115_V	119_E	1.293	0.84
30_I	86_K	1.289	0.83
24_T	96_F	1.256	0.82
35_G	39_G	1.252	0.82
94_D	108_E	1.248	0.81
122_Q	137_D	1.225	0.80
30_I	34_V	1.224	0.80
11_E	136_E	1.219	0.80
41_M	81_H	1.214	0.79
127_K	136_E	1.213	0.79
126_Q	139_K	1.212	0.79
102_F	149_L	1.210	0.79
39_G	103_F	1.204	0.79
95_F	99_F	1.184	0.78
61_P	65_T	1.179	0.77
31_T	111_V	1.170	0.77
111_V	122_Q	1.156	0.76
63_M	114_N	1.155	0.76
40_T	47_M	1.149	0.76
16_L	120_E	1.148	0.76
33_S	99_F	1.143	0.75
124_D	127_K	1.140	0.75
58_M	99_F	1.139	0.75
9_A	76_V	1.133	0.75
140_N	144_Q	1.114	0.73
20_S	23_E	1.097	0.72
156_Y	160_K	1.093	0.72
22_A	32_R	1.092	0.72
49_L	64_S	1.083	0.71
47_M	126_Q	1.077	0.71
79_T	90_V	1.075	0.71
54_E	157_D	1.075	0.71
136_E	143_L	1.067	0.70
36_I	87_H	1.064	0.70
51_E	125_L	1.058	0.69
86_K	148_Q	1.041	0.68
74_N	112_Q	1.025	0.67
40_T	52_M	1.019	0.66
103_F	159_L	1.008	0.66
30_I	57_Q	1.003	0.65
105_P	117_A	1.002	0.65
13_A	83_G	1.001	0.65
24_T	95_F	0.991	0.64
31_T	56_L	0.984	0.64
38_Y	75_V	0.982	0.63
24_T	49_L	0.974	0.63
14_R	141_E	0.968	0.62
9_A	130_C	0.961	0.62
10_I	44_R	0.959	0.62
54_E	140_N	0.951	0.61
129_L	136_E	0.944	0.60
53_R	67_V	0.935	0.60
105_P	108_E	0.929	0.59
14_R	55_E	0.928	0.59
125_L	142_A	0.925	0.59
17_V	91_A	0.921	0.58
49_L	114_N	0.920	0.58
46_E	88_T	0.914	0.58
68_K	78_K	0.913	0.58
56_L	66_G	0.907	0.57
17_V	106_K	0.902	0.57
19_D	57_Q	0.901	0.57
130_C	134_L	0.890	0.56
119_E	123_A	0.885	0.55
135_D	138_I	0.883	0.55
22_A	40_T	0.881	0.55
33_S	62_S	0.879	0.55
41_M	44_R	0.879	0.55
65_T	88_T	0.868	0.54
12_Q	124_D	0.866	0.54
140_N	154_A	0.857	0.53
30_I	42_Y	0.852	0.53
14_R	145_L	0.850	0.52
71_Q	87_H	0.849	0.52
22_A	28_Y	0.847	0.52
17_V	30_I	0.845	0.52
71_Q	76_V	0.835	0.51
137_D	147_D	0.832	0.51
17_V	26_D	0.830	0.51
68_K	77_K	0.824	0.50
40_T	56_L	0.819	0.50
102_F	106_K	0.818	0.50
39_G	91_A	0.816	0.49
79_T	87_H	0.815	0.49
56_L	81_H	0.815	0.49
99_F	149_L	0.814	0.49
115_V	123_A	0.813	0.49
32_R	75_V	0.806	0.49
33_S	43_M	0.787	0.47
38_Y	66_G	0.778	0.46
62_S	65_T	0.774	0.46
145_L	159_L	0.774	0.46
45_D	130_C	0.755	0.44
117_A	121_A	0.750	0.44
58_M	61_P	0.741	0.43
23_E	41_M	0.740	0.43
32_R	109_R	0.734	0.42
140_N	150_E	0.734	0.42
122_Q	153_K	0.734	0.42
12_Q	51_E	0.729	0.42
142_A	157_D	0.729	0.42
28_Y	102_F	0.727	0.42
11_E	93_K	0.727	0.42
55_E	118_I	0.727	0.42
52_M	76_V	0.722	0.41
138_I	143_L	0.721	0.41
9_A	45_D	0.720	0.41
24_T	114_N	0.719	0.41
136_E	139_K	0.714	0.41
126_Q	157_D	0.712	0.41
108_E	123_A	0.710	0.40
126_Q	150_E	0.709	0.40
50_D	156_Y	0.705	0.40
45_D	147_D	0.703	0.40
38_Y	148_Q	0.701	0.40
9_A	135_D	0.696	0.39
122_Q	154_A	0.695	0.39
53_R	87_H	0.693	0.39
22_A	84_I	0.689	0.39
30_I	94_D	0.685	0.38
10_I	150_E	0.672	0.37
74_N	156_Y	0.671	0.37
129_L	134_L	0.670	0.37
11_E	88_T	0.668	0.37
14_R	44_R	0.662	0.36
147_D	165_S	0.662	0.36
48_T	156_Y	0.662	0.36
31_T	36_I	0.658	0.36
100_T	103_F	0.657	0.36
23_E	162_L	0.655	0.36
17_V	43_M	0.655	0.36
15_D	137_D	0.654	0.36
72_D	81_H	0.652	0.36
92_E	101_N	0.652	0.36
37_L	66_G	0.651	0.36
20_S	114_N	0.647	0.35
123_A	130_C	0.647	0.35
96_F	110_E	0.646	0.35
147_D	161_R	0.643	0.35
61_P	109_R	0.639	0.35
31_T	73_L	0.634	0.34
57_Q	78_K	0.633	0.34
17_V	25_M	0.633	0.34
13_A	51_E	0.628	0.34
91_A	164_E	0.626	0.34
77_K	87_H	0.620	0.33
92_E	98_F	0.614	0.33
35_G	103_F	0.608	0.32
37_L	75_V	0.597	0.31
50_D	53_R	0.596	0.31
43_M	145_L	0.589	0.31
28_Y	60_K	0.585	0.31
20_S	68_K	0.585	0.31
94_D	97_K	0.579	0.30
65_T	82_R	0.575	0.30
73_L	105_P	0.572	0.30
35_G	59_S	0.570	0.29
21_I	25_M	0.570	0.29
31_T	65_T	0.569	0.29
11_E	161_R	0.565	0.29
17_V	21_I	0.563	0.29
49_L	96_F	0.563	0.29
21_I	39_G	0.558	0.29
51_E	55_E	0.555	0.28
14_R	43_M	0.553	0.28
43_M	74_N	0.545	0.28
22_A	146_Y	0.544	0.28
23_E	110_E	0.544	0.28
19_D	89_F	0.543	0.28
32_R	96_F	0.541	0.27
34_V	66_G	0.535	0.27
27_L	63_M	0.535	0.27
25_M	102_F	0.533	0.27
143_L	147_D	0.529	0.27
67_V	96_F	0.528	0.27
109_R	113_V	0.526	0.26
81_H	84_I	0.525	0.26
21_I	28_Y	0.520	0.26
129_L	139_K	0.512	0.25
92_E	158_W	0.511	0.25
25_M	158_W	0.510	0.25
22_A	36_I	0.510	0.25
81_H	90_V	0.510	0.25
48_T	58_M	0.510	0.25
155_Y	158_W	0.509	0.25
32_R	56_L	0.508	0.25
49_L	107_W	0.508	0.25
42_Y	95_F	0.506	0.25
43_M	148_Q	0.505	0.25
45_D	137_D	0.505	0.25
62_S	70_L	0.503	0.25
62_S	114_N	0.500	0.25
43_M	95_F	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	0.8167	99.5	0.73	Contact Map
1ku9A	2	0.8333	99.2	0.77	Contact Map
3qphA	2	0.8278	99	0.786	Contact Map
3bjaA	2	0.7667	98.8	0.798	Contact Map
2ethA	4	0.7778	98.7	0.807	Contact Map
4yifA	2	0.7722	98.7	0.808	Contact Map
3nqoA	2	0.9	98.7	0.808	Contact Map
2fxaA	4	0.9222	98.7	0.809	Contact Map
3s2wA	3	0.7833	98.7	0.809	Contact Map
3oopA	2	0.7444	98.7	0.809	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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