RS9 - BACSU - GREMLIN Contacts

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RS9 - 30S ribosomal protein S9

UniProt:	P21470	Sequences: MAQVQYYGTGRRKSSVARVRLVPGEGRIVVNNREISEHIPSAALIEDIKQPLTLTETAGTYDVLVNVHGGGLSGQAGAIRHGIARALLEADPEYRTTLKRAGLLTRDARMKERKKYGLKGARRAPQFSKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	130 (126)
Sequences:	2850 (1237)
Seq/√Len:	110.2

ECOLI - RS9
BACSU - RS9
HALSA - RS9
SULSO - RS9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_L	124_A	4.611	1.00
65_V	79_I	2.992	1.00
84_A	104_L	2.878	1.00
19_V	82_G	2.759	1.00
88_L	104_L	2.506	1.00
111_K	120_G	2.432	1.00
118_L	125_P	2.417	1.00
119_K	125_P	2.253	1.00
120_G	123_R	2.182	1.00
61_Y	90_A	2.084	1.00
36_S	45_I	2.078	1.00
50_Q	103_L	2.014	1.00
96_T	100_R	1.978	1.00
7_Y	20_R	1.973	1.00
42_A	45_I	1.942	1.00
5_Q	20_R	1.858	1.00
14_S	110_M	1.826	1.00
26_G	62_D	1.819	1.00
95_R	99_K	1.814	1.00
50_Q	80_R	1.811	1.00
11_R	85_R	1.780	1.00
27_R	62_D	1.747	1.00
52_L	63_V	1.729	1.00
35_I	45_I	1.727	1.00
88_L	95_R	1.686	1.00
22_V	64_L	1.669	1.00
27_R	34_E	1.641	1.00
119_K	123_R	1.637	1.00
53_T	58_A	1.607	1.00
40_P	45_I	1.547	1.00
5_Q	22_V	1.536	1.00
54_L	101_A	1.516	1.00
39_I	79_I	1.450	1.00
55_T	94_Y	1.443	1.00
24_G	62_D	1.437	1.00
33_R	37_E	1.430	1.00
67_V	79_I	1.398	1.00
57_T	94_Y	1.395	1.00
35_I	48_I	1.371	1.00
47_D	50_Q	1.359	1.00
25_E	62_D	1.321	0.99
34_E	37_E	1.262	0.99
73_S	77_G	1.258	0.99
77_G	80_R	1.252	0.99
111_K	114_K	1.189	0.99
57_T	60_T	1.180	0.99
8_G	86_A	1.167	0.99
57_T	61_Y	1.140	0.99
23_P	60_T	1.117	0.98
119_K	124_A	1.112	0.98
11_R	16_V	1.095	0.98
29_V	64_L	1.070	0.98
112_E	115_K	1.066	0.98
82_G	106_R	1.055	0.98
49_K	58_A	1.053	0.97
44_L	72_L	1.038	0.97
12_R	77_G	1.032	0.97
21_L	86_A	1.015	0.97
120_G	125_P	1.015	0.97
44_L	73_S	1.007	0.97
55_T	98_L	1.005	0.97
80_R	103_L	0.983	0.96
47_D	77_G	0.971	0.96
11_R	110_M	0.953	0.95
22_V	62_D	0.948	0.95
70_G	74_G	0.947	0.95
74_G	77_G	0.925	0.95
11_R	81_H	0.922	0.95
48_I	51_P	0.921	0.95
40_P	72_L	0.914	0.94
120_G	124_A	0.911	0.94
9_T	82_G	0.903	0.94
32_N	66_N	0.897	0.94
41_S	72_L	0.890	0.94
46_E	50_Q	0.880	0.93
21_L	63_V	0.876	0.93
116_Y	127_F	0.874	0.93
6_Y	90_A	0.872	0.93
49_K	52_L	0.870	0.93
90_A	94_Y	0.867	0.93
84_A	88_L	0.865	0.93
18_R	66_N	0.859	0.92
15_S	74_G	0.846	0.92
47_D	76_A	0.837	0.91
20_R	66_N	0.828	0.91
91_D	94_Y	0.825	0.91
99_K	105_T	0.823	0.91
114_K	120_G	0.819	0.90
54_L	103_L	0.817	0.90
25_E	46_E	0.809	0.90
114_K	119_K	0.800	0.89
88_L	94_Y	0.794	0.89
97_T	101_A	0.791	0.89
105_T	108_A	0.789	0.89
7_Y	66_N	0.789	0.89
42_A	46_E	0.786	0.88
15_S	70_G	0.780	0.88
48_I	76_A	0.778	0.88
57_T	91_D	0.778	0.88
111_K	123_R	0.776	0.88
52_L	59_G	0.773	0.88
33_R	40_P	0.768	0.87
8_G	89_E	0.767	0.87
36_S	49_K	0.764	0.87
43_A	46_E	0.763	0.87
17_A	67_V	0.758	0.87
95_R	104_L	0.755	0.86
8_G	19_V	0.754	0.86
81_H	106_R	0.753	0.86
6_Y	88_L	0.752	0.86
6_Y	21_L	0.746	0.86
28_I	35_I	0.746	0.86
29_V	34_E	0.742	0.85
54_L	97_T	0.735	0.85
7_Y	18_R	0.724	0.84
29_V	32_N	0.723	0.84
88_L	99_K	0.715	0.83
49_K	53_T	0.713	0.83
21_L	61_Y	0.709	0.83
116_Y	125_P	0.704	0.82
123_R	127_F	0.703	0.82
18_R	67_V	0.703	0.82
47_D	103_L	0.696	0.82
22_V	90_A	0.687	0.81
41_S	44_L	0.684	0.80
35_I	40_P	0.671	0.79
10_G	16_V	0.652	0.77
29_V	66_N	0.648	0.77
19_V	123_R	0.644	0.76
30_V	39_I	0.643	0.76
52_L	57_T	0.643	0.76
46_E	49_K	0.642	0.76
85_R	106_R	0.639	0.76
55_T	58_A	0.638	0.76
28_I	48_I	0.634	0.75
111_K	119_K	0.633	0.75
92_P	97_T	0.630	0.75
46_E	53_T	0.622	0.74
97_T	100_R	0.614	0.73
39_I	48_I	0.613	0.73
10_G	17_A	0.612	0.73
45_I	48_I	0.605	0.72
119_K	127_F	0.598	0.71
114_K	117_G	0.594	0.70
39_I	113_R	0.591	0.70
52_L	83_I	0.587	0.70
52_L	61_Y	0.585	0.69
47_D	80_R	0.583	0.69
114_K	118_L	0.581	0.69
122_R	130_R	0.580	0.69
8_G	21_L	0.575	0.68
119_K	126_Q	0.571	0.67
44_L	47_D	0.571	0.67
15_S	78_A	0.564	0.66
39_I	73_S	0.564	0.66
5_Q	64_L	0.563	0.66
10_G	81_H	0.561	0.66
9_T	98_L	0.560	0.66
90_A	96_T	0.554	0.65
40_P	44_L	0.553	0.65
81_H	85_R	0.550	0.65
17_A	79_I	0.550	0.65
38_H	113_R	0.545	0.64
40_P	79_I	0.544	0.64
20_R	64_L	0.543	0.64
30_V	34_E	0.539	0.63
67_V	72_L	0.537	0.63
20_R	111_K	0.535	0.62
26_G	31_N	0.534	0.62
21_L	83_I	0.534	0.62
114_K	121_A	0.532	0.62
16_V	116_Y	0.529	0.62
92_P	99_K	0.528	0.61
118_L	123_R	0.526	0.61
33_R	110_M	0.525	0.61
10_G	78_A	0.525	0.61
111_K	116_Y	0.524	0.61
119_K	128_S	0.523	0.61
83_I	98_L	0.522	0.61
33_R	74_G	0.521	0.60
28_I	49_K	0.520	0.60
99_K	104_L	0.516	0.60
60_T	68_H	0.511	0.59
32_N	37_E	0.510	0.59
8_G	87_L	0.510	0.59
20_R	74_G	0.509	0.59
15_S	110_M	0.507	0.58
16_V	68_H	0.505	0.58
50_Q	127_F	0.500	0.57

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
4rb5I	1	0.9769	100	0.037	Contact Map
3bbnI	1	0.9692	100	0.041	Contact Map
4tp8I	1	0.9769	100	0.042	Contact Map
5aj3I	1	0.9923	100	0.054	Contact Map
4bpeI	1	0.9923	100	0.071	Contact Map
3j60Q	1	0.8692	100	0.073	Contact Map
3j7aM	1	0.9615	100	0.075	Contact Map
4ujpR	1	0.9846	100	0.078	Contact Map
4w23Q	1	0.9846	100	0.079	Contact Map
3zeyK	1	0.9923	100	0.086	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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