ISCR - ECOLI - GREMLIN Contacts

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ISCR - HTH-type transcriptional regulator IscR

UniProt:	P0AGK8	Sequences: MRLTSKGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDASSIAVGEVISAVDESVDATRCQGKGGCQGGDKCLTHALWRDLSDRLTGFLNNITLGELVNNQEVLDVSGRQHTHDAPRTRTQDAIDVKLRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13397
Length:	162 (134)
Sequences:	5916 (4045)
Seq/√Len:	349.5

ECOLI - ISCR NSRR
BACSU - NSRR YWGB CYMR YWNA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_G	122_N	3.870	1.00
72_S	127_G	3.010	1.00
92_C	104_C	2.984	1.00
16_D	34_R	2.803	1.00
56_S	66_L	2.770	1.00
10_A	83_V	2.755	1.00
127_G	131_N	2.606	1.00
14_M	54_L	2.599	1.00
112_D	120_F	2.407	1.00
52_N	82_A	2.399	1.00
69_K	78_E	2.383	1.00
81_S	122_N	2.299	1.00
14_M	126_L	2.284	1.00
92_C	98_C	2.137	1.00
77_G	81_S	2.068	1.00
13_A	46_F	2.057	1.00
25_P	66_L	2.051	1.00
17_V	55_V	1.949	1.00
18_A	130_V	1.910	1.00
116_R	120_F	1.880	1.00
98_C	104_C	1.808	1.00
29_A	39_L	1.803	1.00
116_R	119_G	1.707	1.00
16_D	26_V	1.628	1.00
70_D	73_S	1.581	1.00
112_D	124_I	1.580	1.00
58_V	66_L	1.576	1.00
50_R	57_S	1.550	1.00
29_A	33_E	1.548	1.00
69_K	73_S	1.547	1.00
113_L	117_L	1.495	1.00
7_G	80_I	1.484	1.00
47_S	51_K	1.452	1.00
75_A	125_T	1.452	1.00
37_I	42_L	1.451	1.00
120_F	123_N	1.364	1.00
13_A	42_L	1.343	1.00
20_N	24_G	1.340	1.00
21_S	71_A	1.306	1.00
28_L	46_F	1.282	1.00
75_A	78_E	1.252	1.00
114_S	118_T	1.245	1.00
69_K	74_I	1.231	1.00
118_T	122_N	1.215	1.00
109_L	124_I	1.213	1.00
81_S	118_T	1.196	1.00
13_A	31_I	1.181	1.00
112_D	132_N	1.149	1.00
7_G	84_D	1.133	1.00
16_D	35_Q	1.130	1.00
16_D	20_N	1.128	1.00
47_S	50_R	1.116	1.00
115_D	119_G	1.115	1.00
27_P	30_D	1.110	1.00
56_S	68_G	1.099	1.00
25_P	58_V	1.076	1.00
6_K	44_Q	1.055	1.00
54_L	74_I	1.054	1.00
33_E	39_L	1.043	1.00
20_N	26_V	1.043	1.00
113_L	121_L	1.036	1.00
119_G	123_N	1.028	1.00
46_F	65_Y	1.010	1.00
108_A	132_N	1.010	1.00
80_I	121_L	1.004	1.00
14_M	79_V	0.990	1.00
9_Y	37_I	0.989	1.00
78_E	122_N	0.969	1.00
54_L	82_A	0.964	1.00
40_S	43_E	0.950	1.00
111_R	115_D	0.949	1.00
11_V	76_V	0.943	1.00
8_R	12_T	0.932	1.00
30_D	34_R	0.911	1.00
14_M	49_L	0.909	1.00
113_L	116_R	0.908	1.00
5_S	41_Y	0.897	1.00
15_L	130_V	0.886	1.00
46_F	55_V	0.878	1.00
28_L	43_E	0.874	1.00
19_L	130_V	0.870	1.00
70_D	127_G	0.863	1.00
89_A	114_S	0.861	1.00
76_V	109_L	0.855	1.00
17_V	26_V	0.851	1.00
6_K	48_R	0.850	1.00
47_S	57_S	0.844	1.00
24_G	30_D	0.838	1.00
47_S	65_Y	0.834	1.00
48_R	52_N	0.834	1.00
30_D	33_E	0.830	1.00
77_G	118_T	0.827	1.00
6_K	41_Y	0.824	1.00
67_L	71_A	0.822	1.00
112_D	116_R	0.808	1.00
107_H	111_R	0.800	1.00
120_F	124_I	0.800	1.00
43_E	65_Y	0.799	1.00
6_K	10_A	0.796	1.00
128_E	131_N	0.793	1.00
41_Y	45_L	0.790	1.00
68_G	74_I	0.785	1.00
50_R	55_V	0.785	1.00
125_T	128_E	0.781	1.00
21_S	70_D	0.779	1.00
78_E	81_S	0.777	1.00
87_V	118_T	0.765	1.00
76_V	129_L	0.761	1.00
96_G	101_G	0.761	1.00
57_S	65_Y	0.758	1.00
54_L	78_E	0.757	1.00
21_S	24_G	0.755	1.00
28_L	39_L	0.750	1.00
111_R	114_S	0.742	1.00
10_A	45_L	0.736	1.00
43_E	50_R	0.734	1.00
7_G	83_V	0.727	0.99
3_L	110_W	0.725	0.99
3_L	80_I	0.718	0.99
78_E	82_A	0.717	0.99
9_Y	45_L	0.712	0.99
112_D	123_N	0.697	0.99
16_D	30_D	0.696	0.99
39_L	43_E	0.691	0.99
16_D	31_I	0.688	0.99
38_S	41_Y	0.686	0.99
131_N	134_E	0.682	0.99
81_S	86_S	0.679	0.99
98_C	107_H	0.678	0.99
9_Y	41_Y	0.661	0.99
40_S	44_Q	0.660	0.99
75_A	122_N	0.657	0.99
53_G	68_G	0.654	0.99
74_I	79_V	0.654	0.99
119_G	122_N	0.645	0.99
109_L	112_D	0.645	0.99
59_R	110_W	0.639	0.99
31_I	46_F	0.639	0.99
80_I	84_D	0.638	0.99
44_Q	47_S	0.638	0.99
32_S	37_I	0.633	0.99
71_A	130_V	0.631	0.99
27_P	62_G	0.630	0.98
100_G	103_K	0.630	0.98
15_L	129_L	0.630	0.98
92_C	107_H	0.630	0.98
75_A	123_N	0.627	0.98
91_R	94_G	0.627	0.98
110_W	117_L	0.626	0.98
54_L	69_K	0.625	0.98
88_D	94_G	0.620	0.98
3_L	7_G	0.613	0.98
71_A	126_L	0.612	0.98
4_T	84_D	0.612	0.98
8_R	106_T	0.602	0.98
79_V	126_L	0.599	0.98
48_R	51_K	0.595	0.98
17_V	46_F	0.585	0.98
71_A	74_I	0.584	0.98
20_N	34_R	0.583	0.98
52_N	78_E	0.582	0.97
41_Y	59_R	0.581	0.97
4_T	7_G	0.578	0.97
19_L	34_R	0.578	0.97
55_V	59_R	0.578	0.97
104_C	107_H	0.577	0.97
79_V	82_A	0.576	0.97
127_G	130_V	0.575	0.97
93_Q	96_G	0.575	0.97
5_S	91_R	0.575	0.97
4_T	41_Y	0.574	0.97
113_L	120_F	0.567	0.97
72_S	131_N	0.565	0.97
68_G	71_A	0.564	0.97
106_T	110_W	0.563	0.97
5_S	36_G	0.562	0.97
50_R	65_Y	0.560	0.97
74_I	126_L	0.559	0.97
52_N	69_K	0.559	0.97
112_D	115_D	0.553	0.97
101_G	107_H	0.550	0.96
19_L	105_L	0.550	0.96
12_T	35_Q	0.540	0.96
72_S	128_E	0.540	0.96
116_R	121_L	0.535	0.96
99_Q	102_D	0.531	0.96
76_V	124_I	0.527	0.96
69_K	72_S	0.526	0.95
53_G	56_S	0.522	0.95
109_L	120_F	0.521	0.95
9_Y	117_L	0.519	0.95
20_N	30_D	0.517	0.95
9_Y	35_Q	0.512	0.95
40_S	65_Y	0.510	0.95
6_K	9_Y	0.508	0.95
27_P	59_R	0.506	0.94
5_S	43_E	0.504	0.94
27_P	50_R	0.503	0.94
8_R	89_A	0.501	0.94
44_Q	48_R	0.500	0.94
108_A	111_R	0.500	0.94

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
4hf1A	2	0.8765	100	0.205	Contact Map
1xd7A	2	0.7037	100	0.297	Contact Map
4hf0A	3	0.7531	100	0.299	Contact Map
1ylfA	5	0.7407	100	0.342	Contact Map
3k69A	2	0.8704	100	0.343	Contact Map
3lwfA	5	0.8642	100	0.347	Contact Map
4cicA	2	0.8272	100	0.349	Contact Map
3t8rA	2	0.7469	100	0.386	Contact Map
2y75A	5	0.7901	99.9	0.415	Contact Map
2jscA	2	0.5556	98.5	0.766	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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