ISCU - ECOLI - GREMLIN Contacts

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ISCU - Iron-sulfur cluster assembly scaffold protein IscU

UniProt:	P0ACD4	Sequences: MAYSEKVIDHYENPRNVGSFDNNDENVGSGMVGAPACGDVMKLQIKVNDEGIIEDARFKTYGCGSAIASSSLVTEWVKGKSLDEAQAIKNTDIAEELELPPVKIHCSILAEDAIKAAIADYKSKREAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13395
Length:	128 (116)
Sequences:	2489 (1196)
Seq/√Len:	111.1

ECOLI - ISCU
BACSU - SUFU
HALSA - Q9HMM5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_N	54_E	4.859	1.00
15_R	75_E	3.510	1.00
16_N	78_K	2.742	1.00
20_F	57_R	2.632	1.00
81_S	84_E	2.619	1.00
80_K	84_E	2.577	1.00
72_L	94_A	2.500	1.00
55_D	78_K	2.440	1.00
31_M	42_K	2.350	1.00
19_S	59_K	2.251	1.00
56_A	77_V	2.202	1.00
16_N	74_T	2.173	1.00
9_D	15_R	2.103	1.00
18_G	57_R	1.896	1.00
46_K	55_D	1.880	1.00
53_I	85_A	1.831	1.00
24_D	46_K	1.812	1.00
46_K	54_E	1.795	1.00
72_L	96_E	1.669	1.00
32_V	113_A	1.662	1.00
52_I	81_S	1.654	1.00
94_A	104_I	1.639	1.00
70_S	110_A	1.634	1.00
77_V	114_I	1.591	1.00
44_Q	57_R	1.586	1.00
29_S	44_Q	1.578	1.00
22_N	46_K	1.565	1.00
58_F	74_T	1.550	1.00
10_H	71_S	1.538	1.00
10_H	15_R	1.538	1.00
19_S	44_Q	1.535	1.00
73_V	114_I	1.519	1.00
71_S	74_T	1.454	1.00
15_R	71_S	1.381	1.00
16_N	71_S	1.366	1.00
56_A	74_T	1.365	1.00
28_G	117_A	1.305	0.99
51_G	83_D	1.295	0.99
82_L	118_I	1.294	0.99
47_V	82_L	1.288	0.99
84_E	87_A	1.286	0.99
20_F	44_Q	1.285	0.99
7_V	65_S	1.256	0.99
31_M	40_V	1.253	0.99
24_D	28_G	1.235	0.99
4_S	8_I	1.203	0.99
72_L	76_W	1.189	0.99
86_Q	115_K	1.144	0.99
86_Q	122_K	1.097	0.98
40_V	61_Y	1.090	0.98
17_V	67_I	1.039	0.97
114_I	118_I	0.976	0.96
48_N	51_G	0.965	0.96
115_K	119_A	0.952	0.96
43_L	73_V	0.945	0.95
29_S	42_K	0.939	0.95
69_S	111_E	0.918	0.95
86_Q	119_A	0.914	0.94
119_A	122_K	0.907	0.94
97_L	100_P	0.903	0.94
73_V	111_E	0.901	0.94
10_H	75_E	0.901	0.94
83_D	86_Q	0.900	0.94
48_N	52_I	0.895	0.94
30_G	113_A	0.883	0.93
19_S	57_R	0.879	0.93
82_L	86_Q	0.870	0.93
20_F	24_D	0.858	0.92
6_K	93_I	0.856	0.92
108_I	112_D	0.855	0.92
17_V	60_T	0.846	0.92
34_A	101_P	0.845	0.92
105_H	109_L	0.844	0.92
28_G	120_D	0.843	0.92
16_N	75_E	0.834	0.91
45_I	56_A	0.822	0.91
28_G	45_I	0.816	0.90
15_R	74_T	0.814	0.90
104_I	108_I	0.796	0.89
41_M	60_T	0.786	0.89
17_V	59_K	0.786	0.89
76_W	80_K	0.773	0.88
53_I	114_I	0.773	0.88
47_V	51_G	0.768	0.87
65_S	69_S	0.764	0.87
30_G	43_L	0.759	0.87
72_L	93_I	0.758	0.87
10_H	14_P	0.756	0.87
14_P	71_S	0.753	0.86
37_C	105_H	0.752	0.86
83_D	122_K	0.746	0.86
58_F	66_A	0.744	0.86
69_S	110_A	0.739	0.85
24_D	47_V	0.731	0.85
33_G	40_V	0.731	0.85
32_V	116_A	0.729	0.85
65_S	107_S	0.724	0.84
34_A	60_T	0.721	0.84
99_L	115_K	0.709	0.83
34_A	65_S	0.706	0.83
76_W	88_I	0.703	0.82
77_V	85_A	0.703	0.82
62_G	66_A	0.700	0.82
74_T	78_K	0.688	0.81
96_E	100_P	0.687	0.81
19_S	29_S	0.681	0.80
20_F	46_K	0.681	0.80
95_E	98_E	0.680	0.80
72_L	91_T	0.679	0.80
8_I	12_E	0.675	0.80
66_A	103_K	0.663	0.79
86_Q	95_E	0.660	0.78
44_Q	59_K	0.658	0.78
37_C	109_L	0.647	0.77
89_K	115_K	0.639	0.76
53_I	77_V	0.639	0.76
65_S	103_K	0.638	0.76
18_G	55_D	0.636	0.76
96_E	99_L	0.629	0.75
85_A	114_I	0.623	0.74
101_P	105_H	0.622	0.74
6_K	9_D	0.620	0.74
60_T	66_A	0.618	0.74
116_A	119_A	0.618	0.74
73_V	77_V	0.616	0.73
3_Y	38_G	0.613	0.73
42_K	59_K	0.612	0.73
104_I	109_L	0.608	0.72
4_S	12_E	0.601	0.72
24_D	49_D	0.599	0.71
49_D	83_D	0.589	0.70
23_N	81_S	0.580	0.69
20_F	58_F	0.579	0.69
12_E	64_G	0.577	0.69
47_V	117_A	0.574	0.68
4_S	98_E	0.574	0.68
32_V	64_G	0.572	0.68
38_G	62_G	0.572	0.68
51_G	82_L	0.571	0.68
9_D	13_N	0.567	0.67
51_G	54_E	0.564	0.67
64_G	104_I	0.564	0.67
33_G	67_I	0.561	0.66
18_G	59_K	0.560	0.66
108_I	111_E	0.559	0.66
86_Q	118_I	0.559	0.66
91_T	111_E	0.558	0.66
81_S	120_D	0.557	0.66
7_V	68_A	0.556	0.66
49_D	52_I	0.547	0.64
69_S	94_A	0.546	0.64
47_V	54_E	0.546	0.64
35_P	38_G	0.545	0.64
21_D	49_D	0.540	0.63
91_T	98_E	0.537	0.63
83_D	87_A	0.535	0.63
6_K	96_E	0.532	0.62
4_S	100_P	0.531	0.62
48_N	80_K	0.528	0.62
60_T	103_K	0.527	0.62
34_A	111_E	0.527	0.62
47_V	87_A	0.526	0.61
21_D	87_A	0.525	0.61
30_G	120_D	0.524	0.61
55_D	58_F	0.521	0.61
22_N	44_Q	0.520	0.61
73_V	96_E	0.520	0.61
118_I	121_Y	0.519	0.60
10_H	74_T	0.513	0.60
4_S	104_I	0.508	0.59
94_A	111_E	0.508	0.59
111_E	114_I	0.504	0.58
40_V	43_L	0.503	0.58
60_T	105_H	0.500	0.58

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
3lvlA	1	0.9766	100	0.118	Contact Map
2z7eA	5	0.9766	100	0.148	Contact Map
1su0B	1	0.8984	100	0.169	Contact Map
4eb5C	1	0.9531	100	0.173	Contact Map
1xjsA	1	0.9375	100	0.174	Contact Map
2qq4A	5	0.8984	100	0.197	Contact Map
3g0mA	1	0.9297	96.3	0.857	Contact Map
2e5aA	1	0.7891	50.6	0.922	Contact Map
1vqzA	1	0.7734	49.7	0.922	Contact Map
4ce4W	1	0.5	37.9	0.927	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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