SLRR - BACSU - GREMLIN Contacts

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SLRR - HTH-type transcriptional regulator SlrR

UniProt:	P71049	Sequences: MIGRIIRLYRKRKGYSINQLAVESGVSKSYLSKIERGVHTNPSVQFLKKVSATLEVELTELFDAETMMYEKISGGEEEWRVHLVQAVQAGMEKEELFTFTNRLKKEQPETASYRNRKLTESNIEEWKALMAEAREIGLSVHEVKSFLKTKGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	152 (121)
Sequences:	450 (408)
Seq/√Len:	37.1

ECOLI - DICA
BACSU - SLRR YQAE SINR ANSR YONR YOBD RGHRB RGHR IMMR XRE YQAF YGZD
HALSA - O51961 Q9HRZ8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_L	31_L	4.132	1.00
3_G	37_G	3.119	1.00
2_I	6_I	2.923	1.00
18_N	22_V	2.567	1.00
15_Y	53_T	2.507	1.00
10_R	35_E	2.409	1.00
26_V	31_L	2.315	1.00
23_E	53_T	2.198	0.99
5_I	63_D	2.163	0.99
119_T	123_I	2.070	0.99
52_A	64_A	2.029	0.99
31_L	34_I	2.003	0.99
27_S	30_Y	1.890	0.98
20_L	54_L	1.822	0.97
59_T	64_A	1.788	0.97
18_N	28_K	1.760	0.97
120_E	123_I	1.759	0.97
9_Y	54_L	1.759	0.97
9_Y	56_V	1.757	0.97
34_I	46_F	1.723	0.96
12_R	68_M	1.668	0.95
102_R	106_E	1.662	0.95
33_K	40_T	1.660	0.95
30_Y	33_K	1.646	0.95
17_I	21_A	1.629	0.95
17_I	28_K	1.621	0.95
17_I	31_L	1.614	0.95
25_G	49_K	1.582	0.94
29_S	33_K	1.568	0.94
118_L	122_N	1.559	0.93
33_K	38_V	1.516	0.93
44_V	47_L	1.495	0.92
2_I	44_V	1.480	0.92
28_K	32_S	1.451	0.91
29_S	32_S	1.437	0.90
24_S	50_V	1.388	0.89
92_E	95_E	1.356	0.88
4_R	37_G	1.331	0.87
32_S	42_P	1.320	0.86
36_R	40_T	1.298	0.85
30_Y	34_I	1.265	0.84
6_I	31_L	1.248	0.83
119_T	122_N	1.248	0.83
43_S	46_F	1.242	0.82
21_A	31_L	1.208	0.81
27_S	32_S	1.200	0.80
5_I	60_E	1.187	0.79
28_K	46_F	1.170	0.78
104_K	108_P	1.136	0.76
65_E	68_M	1.131	0.76
86_A	90_G	1.128	0.76
6_I	54_L	1.122	0.75
58_L	62_F	1.113	0.75
82_H	85_Q	1.100	0.74
34_I	40_T	1.081	0.73
13_K	55_E	1.070	0.72
26_V	33_K	1.065	0.72
60_E	65_E	1.046	0.70
67_M	70_E	1.043	0.70
86_A	89_A	1.029	0.69
5_I	66_T	1.028	0.69
9_Y	60_E	1.023	0.68
79_W	82_H	1.016	0.68
20_L	25_G	1.010	0.67
42_P	47_L	0.996	0.66
95_E	98_T	0.991	0.66
19_Q	22_V	0.989	0.66
38_V	54_L	0.963	0.64
56_V	60_E	0.940	0.62
71_K	75_G	0.927	0.61
24_S	30_Y	0.927	0.61
24_S	53_T	0.918	0.60
47_L	62_F	0.916	0.60
117_K	120_E	0.903	0.59
58_L	64_A	0.900	0.58
34_I	64_A	0.885	0.57
6_I	20_L	0.865	0.55
26_V	30_Y	0.864	0.55
117_K	123_I	0.861	0.55
117_K	122_N	0.861	0.55
18_N	26_V	0.858	0.55
31_L	41_N	0.849	0.54
81_V	85_Q	0.841	0.53
10_R	17_I	0.837	0.53
111_A	115_N	0.832	0.52
77_E	83_L	0.824	0.52
102_R	117_K	0.813	0.51
91_M	116_R	0.807	0.50
6_I	81_V	0.806	0.50
95_E	114_R	0.804	0.50
43_S	52_A	0.799	0.50
65_E	70_E	0.797	0.49
26_V	50_V	0.792	0.49
5_I	8_L	0.790	0.49
41_N	44_V	0.787	0.48
115_N	120_E	0.775	0.47
6_I	15_Y	0.771	0.47
51_S	64_A	0.769	0.47
29_S	40_T	0.750	0.45
95_E	103_L	0.744	0.45
18_N	30_Y	0.741	0.44
42_P	59_T	0.739	0.44
28_K	38_V	0.734	0.44
34_I	43_S	0.733	0.44
87_V	91_M	0.726	0.43
116_R	119_T	0.726	0.43
32_S	40_T	0.721	0.43
97_F	101_N	0.713	0.42
72_I	75_G	0.705	0.41
101_N	105_K	0.701	0.41
45_Q	74_G	0.693	0.40
15_Y	20_L	0.691	0.40
9_Y	53_T	0.689	0.40
7_R	18_N	0.688	0.40
101_N	107_Q	0.687	0.40
95_E	110_T	0.681	0.39
53_T	56_V	0.670	0.38
101_N	106_E	0.670	0.38
20_L	53_T	0.667	0.38
24_S	54_L	0.665	0.38
3_G	6_I	0.664	0.38
96_L	108_P	0.664	0.38
22_V	28_K	0.663	0.38
79_W	89_A	0.646	0.36
71_K	74_G	0.639	0.36
102_R	105_K	0.637	0.36
47_L	59_T	0.636	0.36
103_L	108_P	0.629	0.35
27_S	34_I	0.628	0.35
30_Y	41_N	0.626	0.35
2_I	43_S	0.624	0.35
98_T	103_L	0.617	0.34
102_R	114_R	0.617	0.34
29_S	43_S	0.613	0.34
98_T	106_E	0.609	0.33
18_N	32_S	0.605	0.33
21_A	28_K	0.603	0.33
51_S	58_L	0.599	0.33
91_M	105_K	0.596	0.32
87_V	100_T	0.594	0.32
91_M	99_F	0.592	0.32
101_N	108_P	0.588	0.32
88_Q	102_R	0.585	0.32
27_S	42_P	0.584	0.31
7_R	11_K	0.582	0.31
48_K	59_T	0.577	0.31
14_G	29_S	0.570	0.30
32_S	36_R	0.566	0.30
29_S	34_I	0.562	0.30
57_E	60_E	0.561	0.30
21_A	36_R	0.560	0.30
60_E	68_M	0.560	0.30
92_E	98_T	0.560	0.30
71_K	79_W	0.560	0.30
25_G	51_S	0.558	0.30
33_K	36_R	0.558	0.30
78_E	86_A	0.557	0.29
11_K	24_S	0.554	0.29
100_T	114_R	0.553	0.29
20_L	50_V	0.550	0.29
99_F	106_E	0.546	0.29
77_E	82_H	0.542	0.28
34_I	42_P	0.541	0.28
3_G	14_G	0.541	0.28
5_I	58_L	0.539	0.28
16_S	54_L	0.537	0.28
92_E	104_K	0.536	0.28
98_T	102_R	0.531	0.28
89_A	101_N	0.530	0.28
82_H	109_E	0.522	0.27
33_K	44_V	0.522	0.27
77_E	85_Q	0.518	0.27
79_W	85_Q	0.517	0.27
19_Q	23_E	0.517	0.27
77_E	114_R	0.514	0.26
87_V	90_G	0.510	0.26
30_Y	40_T	0.505	0.26
17_I	50_V	0.503	0.26
43_S	54_L	0.503	0.26
89_A	98_T	0.502	0.26
114_R	119_T	0.502	0.26
3_G	115_N	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
1b0nA	2	0.6711	99.8	0.472	Contact Map
4ndwA	2	0.7237	99.7	0.493	Contact Map
3r1fA	2	0.7237	99.7	0.504	Contact Map
4o8bA	2	0.6382	99.7	0.508	Contact Map
3op9A	4	0.6842	99.7	0.511	Contact Map
4jcyA	2	0.5789	99.7	0.514	Contact Map
3qwgA	2	0.4868	99.7	0.515	Contact Map
2ebyA	2	0.6447	99.6	0.541	Contact Map
3ivpA	2	0.6974	99.6	0.543	Contact Map
3u3wA	2	0.9408	99.6	0.543	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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