RBFA - BACSU - GREMLIN Contacts

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RBFA - Ribosome-binding factor A

UniProt:	P32731	Sequences: MSMRANRVGEQMKKELGDIISRKLKDPRIGFLTVTDVRVSGDLQIAKVYISVLGDEKKREEALKGLAKAKGFIRSEIGSRIRLRKTPEIEFEFDESIDYGNRIETLIHELHSEKPSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	117 (108)
Sequences:	2932 (1769)
Seq/√Len:	170.2

ECOLI - RBFA
BACSU - RBFA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_I	63_L	3.163	1.00
44_Q	85_K	2.779	1.00
47_K	92_E	2.691	1.00
67_A	70_K	2.532	1.00
105_T	109_E	2.421	1.00
15_E	80_R	2.384	1.00
10_E	13_K	2.171	1.00
16_L	48_V	2.101	1.00
40_S	45_I	2.043	1.00
45_I	90_E	1.970	1.00
8_V	83_L	1.945	1.00
75_S	79_S	1.859	1.00
74_R	88_E	1.804	1.00
73_I	89_I	1.783	1.00
103_I	107_I	1.646	1.00
19_I	73_I	1.646	1.00
78_G	86_T	1.626	1.00
63_L	67_A	1.601	1.00
104_E	108_H	1.587	1.00
76_E	79_S	1.535	1.00
47_K	90_E	1.524	1.00
34_V	50_I	1.510	1.00
70_K	88_E	1.503	1.00
9_G	39_V	1.496	1.00
57_K	61_E	1.495	1.00
107_I	111_H	1.427	1.00
18_D	80_R	1.407	1.00
101_N	105_T	1.401	1.00
76_E	80_R	1.401	1.00
16_L	73_I	1.376	1.00
11_Q	14_K	1.348	1.00
96_S	100_G	1.346	1.00
29_I	65_G	1.342	1.00
37_V	46_A	1.336	1.00
5_A	9_G	1.329	1.00
41_G	44_Q	1.319	1.00
102_R	105_T	1.312	1.00
50_I	66_L	1.309	1.00
65_G	68_K	1.288	1.00
19_I	77_I	1.286	1.00
52_V	62_A	1.282	1.00
59_R	93_F	1.279	1.00
59_R	95_E	1.259	1.00
99_Y	102_R	1.251	1.00
74_R	86_T	1.240	1.00
107_I	110_L	1.219	1.00
102_R	106_L	1.184	1.00
60_E	64_K	1.182	1.00
11_Q	15_E	1.174	1.00
77_I	86_T	1.142	1.00
18_D	22_R	1.134	1.00
95_E	99_Y	1.128	1.00
45_I	88_E	1.124	1.00
105_T	108_H	1.079	1.00
96_S	99_Y	1.076	1.00
106_L	110_L	1.068	1.00
59_R	98_D	1.062	1.00
18_D	21_S	1.051	0.99
12_M	16_L	1.050	0.99
26_D	65_G	1.022	0.99
30_G	62_A	0.982	0.99
72_F	76_E	0.971	0.99
109_E	112_S	0.968	0.99
50_I	93_F	0.963	0.99
15_E	18_D	0.962	0.99
23_K	72_F	0.960	0.99
33_T	51_S	0.956	0.99
28_R	69_A	0.933	0.99
15_E	81_I	0.929	0.99
63_L	93_F	0.921	0.99
23_K	76_E	0.917	0.99
65_G	69_A	0.910	0.98
12_M	77_I	0.902	0.98
61_E	64_K	0.902	0.98
99_Y	103_I	0.876	0.98
8_V	39_V	0.873	0.98
23_K	80_R	0.852	0.98
27_P	69_A	0.848	0.98
4_R	8_V	0.841	0.97
28_R	68_K	0.841	0.97
15_E	19_I	0.839	0.97
71_G	75_S	0.837	0.97
16_L	89_I	0.818	0.97
26_D	29_I	0.817	0.97
19_I	76_E	0.801	0.97
97_I	100_G	0.800	0.97
68_K	72_F	0.799	0.97
77_I	89_I	0.788	0.96
101_N	104_E	0.780	0.96
49_Y	92_E	0.760	0.95
108_H	112_S	0.757	0.95
56_E	59_R	0.753	0.95
12_M	39_V	0.753	0.95
38_R	47_K	0.748	0.95
97_I	101_N	0.736	0.95
24_L	29_I	0.729	0.94
51_S	93_F	0.718	0.94
34_V	48_V	0.714	0.94
16_L	34_V	0.713	0.94
52_V	63_L	0.702	0.93
69_A	72_F	0.700	0.93
36_D	99_Y	0.695	0.93
98_D	101_N	0.693	0.93
39_V	43_L	0.691	0.93
5_A	39_V	0.681	0.92
46_A	89_I	0.680	0.92
13_K	34_V	0.678	0.92
24_L	27_P	0.668	0.91
12_M	81_I	0.666	0.91
73_I	91_F	0.664	0.91
28_R	65_G	0.663	0.91
38_R	49_Y	0.660	0.91
78_G	82_R	0.654	0.90
99_Y	104_E	0.650	0.90
32_L	62_A	0.647	0.90
6_N	53_L	0.641	0.89
52_V	55_D	0.635	0.89
11_Q	82_R	0.629	0.89
13_K	112_S	0.623	0.88
13_K	37_V	0.611	0.87
34_V	63_L	0.608	0.87
44_Q	84_R	0.604	0.86
57_K	60_E	0.599	0.86
40_S	90_E	0.586	0.85
82_R	86_T	0.585	0.85
5_A	41_G	0.580	0.84
103_I	106_L	0.580	0.84
103_I	110_L	0.574	0.84
26_D	69_A	0.573	0.83
26_D	68_K	0.572	0.83
25_K	62_A	0.570	0.83
43_L	84_R	0.567	0.83
67_A	90_E	0.566	0.83
55_D	59_R	0.565	0.83
24_L	28_R	0.565	0.83
14_K	18_D	0.564	0.83
52_V	93_F	0.561	0.82
75_S	78_G	0.560	0.82
40_S	104_E	0.558	0.82
72_F	75_S	0.552	0.81
6_N	9_G	0.546	0.80
81_I	86_T	0.544	0.80
24_L	65_G	0.542	0.80
55_D	98_D	0.538	0.80
4_R	78_G	0.536	0.79
38_R	92_E	0.535	0.79
62_A	65_G	0.535	0.79
50_I	67_A	0.534	0.79
6_N	103_I	0.532	0.79
19_I	80_R	0.529	0.78
32_L	52_V	0.527	0.78
4_R	46_A	0.526	0.78
48_V	89_I	0.525	0.78
36_D	100_G	0.524	0.78
36_D	95_E	0.521	0.77
35_T	51_S	0.516	0.77
28_R	61_E	0.512	0.76
12_M	15_E	0.512	0.76
31_F	62_A	0.511	0.76
104_E	111_H	0.506	0.75
50_I	62_A	0.503	0.75
26_D	72_F	0.500	0.74

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
1pa4A	1	0.8205	100	0.126	Contact Map
1josA	1	0.8376	100	0.127	Contact Map
2e7gA	1	0.9744	100	0.183	Contact Map
2kzfA	1	0.8632	100	0.201	Contact Map
2dyjA	1	0.7863	100	0.242	Contact Map
3lsjA	2	0.9487	16.6	0.923	Contact Map
3ccyA	2	0.906	16	0.924	Contact Map
1vz0A	3	0.6838	13.9	0.926	Contact Map
3fcsB	1	0.9915	13.5	0.926	Contact Map
3odmA	6	0.6581	11.5	0.928	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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