RL7 - ECOLI - GREMLIN Contacts

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RL7 - 50S ribosomal protein L7/L12

UniProt:	P0A7K2	Sequences: MSITKDQIIEAVAAMSVMDVVELISAMEEKFGVSAAAAVAVAAGPVEAAEEKTEFDVILKAAGANKVAVIKAVRGATGLGLKEAKDLVESAPAALKEGVSKDDAEALKKALEEAGAEVEVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10873
Length:	121 (117)
Sequences:	2664 (1070)
Seq/√Len:	98.9

ECOLI - RL7
BACSU - RL7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_A	30_K	3.078	1.00
82_K	86_D	2.968	1.00
108_K	112_E	2.900	1.00
7_Q	11_A	2.780	1.00
76_A	107_L	2.739	1.00
111_L	116_A	2.717	1.00
106_A	110_A	2.496	1.00
60_K	119_E	2.496	1.00
60_K	117_E	2.474	1.00
65_N	68_A	2.420	1.00
61_A	117_E	2.311	1.00
58_I	94_A	2.266	1.00
72_A	75_G	2.191	1.00
109_K	113_E	2.135	1.00
75_G	110_A	2.128	1.00
5_K	15_M	1.753	1.00
62_A	89_E	1.688	1.00
56_D	98_G	1.562	1.00
86_D	90_S	1.532	1.00
51_E	101_K	1.523	1.00
8_I	11_A	1.505	1.00
100_S	103_D	1.490	1.00
108_K	118_V	1.487	1.00
21_V	25_S	1.467	1.00
10_E	14_A	1.456	1.00
9_I	27_M	1.451	1.00
13_A	31_F	1.445	1.00
73_V	88_V	1.394	0.99
10_E	13_A	1.393	0.99
17_V	20_V	1.389	0.99
103_D	106_A	1.362	0.99
68_A	114_A	1.353	0.99
61_A	64_A	1.350	0.99
105_E	109_K	1.338	0.99
106_A	109_K	1.311	0.99
96_K	103_D	1.272	0.99
6_D	10_E	1.266	0.99
52_K	55_F	1.231	0.99
7_Q	10_E	1.198	0.98
25_S	28_E	1.179	0.98
5_K	26_A	1.175	0.98
96_K	107_L	1.174	0.98
11_A	14_A	1.162	0.98
6_D	26_A	1.160	0.98
72_A	113_E	1.148	0.98
12_V	31_F	1.137	0.98
38_A	41_V	1.114	0.98
112_E	117_E	1.061	0.97
109_K	112_E	1.054	0.97
54_E	98_G	1.035	0.96
5_K	11_A	1.034	0.96
99_V	120_V	1.031	0.96
58_I	119_E	1.029	0.96
73_V	95_L	1.025	0.96
52_K	56_D	1.020	0.96
11_A	15_M	1.020	0.96
55_F	101_K	1.017	0.96
8_I	23_L	1.011	0.96
90_S	93_A	1.008	0.95
102_D	106_A	1.006	0.95
9_I	13_A	0.988	0.95
65_N	114_A	0.974	0.95
66_K	88_V	0.969	0.94
18_M	21_V	0.965	0.94
103_D	107_L	0.964	0.94
72_A	110_A	0.959	0.94
9_I	26_A	0.959	0.94
12_V	27_M	0.953	0.94
101_K	105_E	0.944	0.94
59_L	91_A	0.943	0.94
67_V	74_R	0.937	0.93
83_E	86_D	0.935	0.93
108_K	120_V	0.924	0.93
56_D	94_A	0.915	0.93
86_D	93_A	0.911	0.92
9_I	31_F	0.906	0.92
20_V	27_M	0.902	0.92
5_K	9_I	0.892	0.92
99_V	107_L	0.878	0.91
16_S	19_D	0.877	0.91
102_D	105_E	0.872	0.91
28_E	35_A	0.858	0.90
57_V	104_A	0.856	0.90
76_A	110_A	0.834	0.89
87_L	93_A	0.815	0.87
99_V	103_D	0.806	0.87
88_V	91_A	0.800	0.86
8_I	26_A	0.800	0.86
52_K	98_G	0.794	0.86
5_K	8_I	0.788	0.86
110_A	113_E	0.786	0.85
8_I	12_V	0.786	0.85
56_D	97_E	0.784	0.85
45_P	49_A	0.782	0.85
43_A	47_E	0.782	0.85
63_G	69_V	0.781	0.85
38_A	42_A	0.779	0.85
94_A	97_E	0.776	0.85
57_V	107_L	0.771	0.84
80_G	83_E	0.768	0.84
63_G	116_A	0.762	0.84
56_D	121_K	0.759	0.83
21_V	27_M	0.755	0.83
44_G	47_E	0.741	0.82
60_K	121_K	0.739	0.82
28_E	34_S	0.736	0.82
60_K	92_P	0.734	0.81
112_E	120_V	0.729	0.81
51_E	55_F	0.715	0.80
78_G	96_K	0.709	0.79
112_E	118_V	0.705	0.79
37_A	42_A	0.702	0.78
74_R	77_T	0.697	0.78
26_A	30_K	0.697	0.78
70_I	74_R	0.697	0.78
74_R	79_L	0.696	0.78
74_R	80_G	0.690	0.77
8_I	27_M	0.690	0.77
15_M	27_M	0.683	0.76
15_M	31_F	0.676	0.76
76_A	111_L	0.674	0.76
12_V	34_S	0.673	0.75
87_L	95_L	0.668	0.75
12_V	23_L	0.659	0.74
9_I	30_K	0.657	0.74
55_F	120_V	0.648	0.73
67_V	70_I	0.634	0.71
23_L	27_M	0.632	0.71
53_T	120_V	0.627	0.70
24_I	31_F	0.626	0.70
44_G	49_A	0.625	0.70
60_K	91_A	0.622	0.70
45_P	48_A	0.610	0.68
90_S	94_A	0.607	0.68
12_V	17_V	0.606	0.68
52_K	101_K	0.604	0.67
79_L	87_L	0.600	0.67
52_K	100_S	0.600	0.67
39_V	42_A	0.595	0.66
77_T	80_G	0.594	0.66
88_V	92_P	0.592	0.66
77_T	96_K	0.589	0.65
105_E	120_V	0.588	0.65
19_D	22_E	0.585	0.65
59_L	66_K	0.579	0.64
77_T	95_L	0.578	0.64
21_V	24_I	0.576	0.64
111_L	118_V	0.575	0.64
46_V	49_A	0.575	0.64
111_L	114_A	0.574	0.63
13_A	27_M	0.570	0.63
7_Q	15_M	0.562	0.62
99_V	104_A	0.558	0.61
25_S	29_E	0.556	0.61
37_A	41_V	0.549	0.60
27_M	31_F	0.547	0.60
28_E	33_V	0.542	0.59
54_E	100_S	0.540	0.59
6_D	30_K	0.540	0.59
59_L	116_A	0.538	0.59
12_V	15_M	0.533	0.58
20_V	23_L	0.530	0.57
72_A	111_L	0.527	0.57
59_L	62_A	0.517	0.56
5_K	20_V	0.513	0.55
67_V	89_E	0.512	0.55
28_E	31_F	0.512	0.55
72_A	76_A	0.510	0.55
25_S	32_G	0.510	0.55
5_K	30_K	0.507	0.54
87_L	94_A	0.507	0.54
20_V	24_I	0.506	0.54
95_L	111_L	0.505	0.54
34_S	37_A	0.503	0.54
66_K	89_E	0.500	0.53
68_A	72_A	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
4kix6	1	0.2479	100	0.046	Contact Map
2zjq5	1	0.5868	100	0.08	Contact Map
1dd3A	6	0.9835	100	0.086	Contact Map
2ftcE	2	0.9835	100	0.115	Contact Map
1ctfA	2	0.562	99.9	0.338	Contact Map
4qs1e	1	0.595	99.9	0.378	Contact Map
4kcze	1	0.595	99.9	0.381	Contact Map
1dd4C	7	0.3306	98.4	0.749	Contact Map
1zavU	5	0.2479	97.1	0.811	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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