XRE - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

XRE - HTH-type transcriptional regulator Xre

UniProt:	P23789	Sequences: MIGGRLKSLRGKRTQEEIASHIGVSRARYSHYENGRSEPDYDTLQKLADYFQVTTDYLLTGKDKKSDDDMFSDPDLQLAYRDMQDFSPESKQQAIEFINYLKEKEKNRKPKNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	113 (104)
Sequences:	1130 (1000)
Seq/√Len:	98.1

ECOLI - DICA
BACSU - XRE YQAE YOBD YONR ANSR RGHRB SLRR SINR RGHR IMMR YQAF YGZD YAZB
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
18_I	29_Y	3.268	1.00
16_E	20_S	3.088	1.00
49_D	61_G	2.875	1.00
16_E	26_R	2.694	1.00
10_R	33_E	2.559	1.00
25_S	28_R	2.312	1.00
21_H	50_Y	2.286	1.00
24_V	29_Y	2.249	1.00
87_S	90_S	2.130	1.00
27_A	31_H	2.114	1.00
2_I	6_L	2.111	1.00
38_E	41_Y	2.065	1.00
3_G	35_G	2.053	1.00
12_K	65_K	2.048	1.00
55_T	59_L	1.911	1.00
9_L	51_F	1.813	1.00
31_H	36_R	1.713	1.00
18_I	51_F	1.706	1.00
48_A	61_G	1.585	1.00
90_S	105_E	1.580	1.00
97_F	101_L	1.575	1.00
93_Q	100_Y	1.551	1.00
97_F	105_E	1.463	1.00
27_A	30_S	1.430	1.00
28_R	31_H	1.395	0.99
26_R	30_S	1.376	0.99
30_S	34_N	1.371	0.99
56_D	61_G	1.360	0.99
25_S	31_H	1.325	0.99
93_Q	104_K	1.324	0.99
31_H	37_S	1.289	0.99
97_F	100_Y	1.226	0.99
87_S	105_E	1.219	0.99
15_Q	26_R	1.218	0.99
24_V	28_R	1.217	0.99
5_R	57_Y	1.175	0.98
62_K	65_K	1.159	0.98
2_I	41_Y	1.155	0.98
73_D	76_L	1.149	0.98
5_R	63_D	1.148	0.98
41_Y	44_L	1.123	0.98
32_Y	37_S	1.086	0.97
93_Q	101_L	1.083	0.97
32_Y	43_T	1.077	0.97
31_H	34_N	1.074	0.97
26_R	29_Y	1.071	0.97
4_G	35_G	1.069	0.97
6_L	29_Y	1.069	0.97
93_Q	97_F	1.062	0.97
18_I	47_L	1.050	0.96
101_L	104_K	1.045	0.96
40_D	43_T	1.034	0.96
26_R	34_N	1.032	0.96
17_E	20_S	1.013	0.96
44_L	55_T	1.006	0.95
18_I	50_Y	0.979	0.95
39_P	56_D	0.978	0.95
96_E	100_Y	0.968	0.94
15_Q	29_Y	0.964	0.94
23_G	46_K	0.960	0.94
26_R	36_R	0.955	0.94
5_R	60_T	0.944	0.93
90_S	93_Q	0.943	0.93
97_F	104_K	0.943	0.93
86_F	98_I	0.938	0.93
26_R	31_H	0.902	0.92
94_A	98_I	0.898	0.92
78_L	81_R	0.889	0.91
100_Y	103_E	0.886	0.91
17_E	21_H	0.880	0.91
19_A	29_Y	0.872	0.90
22_I	47_L	0.861	0.90
38_E	43_T	0.860	0.90
24_V	27_A	0.856	0.90
100_Y	104_K	0.837	0.89
95_I	98_I	0.825	0.88
80_Y	83_M	0.803	0.86
101_L	105_E	0.798	0.86
9_L	53_V	0.797	0.86
6_L	18_I	0.791	0.86
22_I	50_Y	0.784	0.85
76_L	79_A	0.770	0.84
94_A	101_L	0.766	0.84
15_Q	19_A	0.763	0.84
91_K	102_K	0.761	0.83
93_Q	105_E	0.745	0.82
96_E	104_K	0.742	0.82
81_R	85_D	0.740	0.82
2_I	44_L	0.736	0.81
93_Q	103_E	0.733	0.81
32_Y	40_D	0.733	0.81
92_Q	95_I	0.731	0.81
27_A	34_N	0.729	0.81
72_S	76_L	0.728	0.81
87_S	93_Q	0.727	0.80
19_A	31_H	0.724	0.80
14_T	17_E	0.721	0.80
98_I	101_L	0.716	0.79
80_Y	94_A	0.711	0.79
43_T	46_K	0.702	0.78
52_Q	66_S	0.696	0.78
7_K	33_E	0.688	0.77
92_Q	96_E	0.684	0.76
7_K	10_R	0.680	0.76
93_Q	96_E	0.680	0.76
76_L	83_M	0.664	0.74
34_N	37_S	0.664	0.74
41_Y	45_Q	0.663	0.74
97_F	103_E	0.658	0.74
13_R	21_H	0.654	0.73
83_M	91_K	0.649	0.72
50_Y	53_V	0.638	0.71
2_I	51_F	0.633	0.71
25_S	30_S	0.631	0.70
83_M	87_S	0.627	0.70
79_A	84_Q	0.624	0.70
81_R	103_E	0.619	0.69
37_S	40_D	0.617	0.69
32_Y	39_P	0.615	0.68
74_P	80_Y	0.615	0.68
77_Q	95_I	0.609	0.68
96_E	103_E	0.606	0.67
25_S	37_S	0.602	0.67
19_A	26_R	0.602	0.67
24_V	32_Y	0.602	0.67
44_L	59_L	0.594	0.66
90_S	97_F	0.585	0.65
102_K	105_E	0.577	0.64
25_S	36_R	0.576	0.63
98_I	102_K	0.576	0.63
11_G	25_S	0.572	0.63
30_S	39_P	0.568	0.62
64_K	67_D	0.565	0.62
83_M	96_E	0.556	0.61
77_Q	80_Y	0.554	0.60
5_R	61_G	0.553	0.60
82_D	91_K	0.551	0.60
6_L	43_T	0.549	0.60
82_D	102_K	0.543	0.59
48_A	55_T	0.538	0.58
15_Q	33_E	0.536	0.58
18_I	22_I	0.536	0.58
24_V	47_L	0.531	0.57
79_A	86_F	0.529	0.57
22_I	51_F	0.522	0.56
13_R	50_Y	0.517	0.55
45_Q	61_G	0.516	0.55
8_S	20_S	0.516	0.55
9_L	50_Y	0.515	0.55
94_A	97_F	0.509	0.54
27_A	36_R	0.509	0.54
9_L	57_Y	0.508	0.54
75_D	78_L	0.505	0.54
86_F	94_A	0.501	0.53
82_D	95_I	0.501	0.53
28_R	37_S	0.500	0.53

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
4ndwA	2	0.9558	99.7	0.391	Contact Map
3r1fA	2	0.9558	99.7	0.401	Contact Map
4o8bA	2	0.8407	99.7	0.424	Contact Map
3qwgA	2	0.6372	99.7	0.425	Contact Map
1b0nA	2	0.8673	99.7	0.426	Contact Map
4jcyA	2	0.7611	99.7	0.428	Contact Map
3op9A	4	0.9027	99.7	0.432	Contact Map
3ivpA	2	0.9204	99.6	0.448	Contact Map
2p5tA	2	0.4159	99.5	0.487	Contact Map
2ebyA	2	0.8496	99.5	0.496	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.

Page generated in 0.0062 seconds.