RS9 - SULSO - GREMLIN Contacts

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RS9 - 30S ribosomal protein S9

UniProt:	P95992	Sequences: MSEEQKLVISSARRKTARATCYIYAGKGRVFVNNVPIELIPIEMVRLKIMEPLLLAGNDIRSKIDAKIITYGGGIMGQADAARMALARALVKFTGSKELEKIYRAYDRTMLAGDPRQTESEKWMRYSARRWRQKSYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	137 (125)
Sequences:	2840 (1297)
Seq/√Len:	116.0

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
125_R	131_W	4.429	1.00
56_A	60_I	4.150	1.00
87_A	111_L	2.829	1.00
68_I	82_A	2.825	1.00
21_C	85_A	2.571	1.00
91_V	111_L	2.408	1.00
118_T	127_S	2.344	1.00
125_R	132_R	2.318	1.00
94_T	98_E	2.244	1.00
126_Y	132_R	2.136	1.00
127_S	130_R	2.131	1.00
64_I	93_F	2.057	1.00
9_I	22_Y	1.930	1.00
101_K	105_A	1.886	1.00
51_E	110_M	1.864	1.00
51_E	83_R	1.812	1.00
43_E	46_R	1.794	1.00
7_L	22_Y	1.777	1.00
28_G	65_D	1.777	1.00
16_T	117_Q	1.736	1.00
37_I	46_R	1.728	1.00
41_P	46_R	1.713	1.00
100_E	104_R	1.698	1.00
29_R	36_P	1.694	1.00
13_R	88_R	1.635	1.00
29_R	65_D	1.625	1.00
53_L	66_A	1.608	1.00
91_V	100_E	1.583	1.00
126_Y	130_R	1.575	1.00
26_G	65_D	1.500	1.00
24_Y	67_K	1.480	1.00
60_I	99_L	1.475	1.00
54_L	61_R	1.475	1.00
55_L	108_R	1.462	1.00
57_G	61_R	1.436	1.00
40_I	82_A	1.385	1.00
70_T	82_A	1.346	1.00
56_A	99_L	1.332	1.00
105_A	108_R	1.312	1.00
48_K	51_E	1.302	1.00
35_V	38_E	1.257	0.99
7_L	24_Y	1.241	0.99
80_D	83_R	1.238	0.99
37_I	49_I	1.224	0.99
60_I	63_K	1.208	0.99
76_M	80_D	1.191	0.99
27_K	65_D	1.148	0.99
118_T	121_E	1.141	0.99
60_I	64_I	1.092	0.98
126_Y	131_W	1.088	0.98
10_S	89_A	1.068	0.98
25_A	63_K	1.056	0.98
14_R	80_D	1.046	0.98
50_M	61_R	1.039	0.98
13_R	18_R	1.036	0.98
119_E	122_K	1.031	0.98
127_S	132_R	1.025	0.97
31_F	67_K	1.011	0.97
85_A	113_G	0.952	0.96
94_T	99_L	0.950	0.96
48_K	80_D	0.944	0.96
45_V	75_I	0.942	0.96
83_R	110_M	0.941	0.96
127_S	131_W	0.939	0.96
49_I	52_P	0.936	0.96
93_F	99_L	0.933	0.96
56_A	103_Y	0.928	0.95
13_R	84_M	0.925	0.95
23_I	89_A	0.920	0.95
13_R	117_Q	0.916	0.95
73_G	77_G	0.915	0.95
45_V	76_M	0.897	0.95
24_Y	65_D	0.895	0.95
47_L	51_E	0.893	0.94
11_S	85_A	0.891	0.94
77_G	80_D	0.888	0.94
104_R	112_A	0.861	0.93
17_A	77_G	0.853	0.93
102_I	108_R	0.850	0.93
60_I	94_T	0.846	0.93
55_L	110_M	0.845	0.93
50_M	53_L	0.840	0.92
22_Y	69_I	0.830	0.92
123_W	134_K	0.825	0.92
41_P	75_I	0.822	0.92
34_N	69_I	0.817	0.91
8_V	93_F	0.813	0.91
84_M	113_G	0.813	0.91
23_I	66_A	0.811	0.91
87_A	91_V	0.808	0.91
48_K	79_A	0.806	0.91
44_M	47_L	0.806	0.91
55_L	102_I	0.804	0.91
31_F	36_P	0.800	0.90
112_A	115_P	0.799	0.90
20_T	69_I	0.796	0.90
37_I	41_P	0.793	0.90
42_I	75_I	0.790	0.90
10_S	21_C	0.787	0.90
50_M	54_L	0.787	0.90
91_V	99_L	0.781	0.89
49_I	79_A	0.779	0.89
121_E	126_Y	0.775	0.89
100_E	111_L	0.772	0.89
130_R	134_K	0.770	0.89
23_I	64_I	0.758	0.88
10_S	92_K	0.741	0.87
118_T	130_R	0.739	0.87
9_I	69_I	0.732	0.86
121_E	127_S	0.731	0.86
53_L	60_I	0.721	0.85
30_V	37_I	0.720	0.85
123_W	132_R	0.712	0.85
27_K	47_L	0.711	0.84
53_L	62_S	0.709	0.84
19_A	70_T	0.705	0.84
17_A	73_G	0.705	0.84
47_L	50_M	0.702	0.84
31_F	34_N	0.696	0.83
35_V	41_P	0.693	0.83
8_V	91_V	0.692	0.83
104_R	111_L	0.691	0.83
42_I	45_V	0.682	0.82
9_I	20_T	0.677	0.82
102_I	105_A	0.674	0.81
97_K	101_K	0.663	0.80
46_R	49_I	0.661	0.80
43_E	47_L	0.660	0.80
47_L	54_L	0.656	0.79
48_K	110_M	0.651	0.79
53_L	86_L	0.651	0.79
53_L	64_I	0.650	0.79
94_T	97_K	0.649	0.79
48_K	83_R	0.638	0.78
57_G	60_I	0.637	0.77
97_K	102_I	0.637	0.77
12_A	18_R	0.630	0.77
118_T	126_Y	0.630	0.77
41_P	45_V	0.626	0.76
21_C	130_R	0.624	0.76
32_V	36_P	0.623	0.76
18_R	123_W	0.623	0.76
8_V	23_I	0.621	0.76
24_Y	93_F	0.619	0.75
40_I	49_I	0.612	0.75
56_A	61_R	0.610	0.74
20_T	70_T	0.607	0.74
22_Y	118_T	0.605	0.74
17_A	81_A	0.604	0.74
126_Y	134_K	0.601	0.73
129_R	137_R	0.592	0.72
30_V	49_I	0.589	0.72
31_F	69_I	0.586	0.71
12_A	19_A	0.584	0.71
88_R	113_G	0.574	0.70
40_I	120_S	0.571	0.69
121_E	124_M	0.564	0.69
51_E	134_K	0.563	0.68
19_A	32_V	0.559	0.68
91_V	104_R	0.555	0.67
35_V	117_Q	0.554	0.67
12_A	84_M	0.553	0.67
125_R	130_R	0.548	0.66
126_Y	133_Q	0.548	0.66
10_S	23_I	0.546	0.66
121_E	125_R	0.545	0.66
22_Y	77_G	0.540	0.65
84_M	88_R	0.532	0.64
115_P	133_Q	0.531	0.64
7_L	67_K	0.529	0.64
126_Y	135_S	0.529	0.64
23_I	86_L	0.527	0.63
35_V	77_G	0.527	0.63
41_P	82_A	0.525	0.63
118_T	123_W	0.523	0.63
11_S	103_Y	0.521	0.62
40_I	76_M	0.518	0.62
32_V	40_I	0.517	0.62
63_K	71_Y	0.516	0.62
113_G	117_Q	0.510	0.61
45_V	48_K	0.509	0.61
18_R	71_Y	0.508	0.61
70_T	75_I	0.507	0.60
120_S	136_Y	0.506	0.60
103_Y	113_G	0.505	0.60
121_E	128_A	0.502	0.60
36_P	92_K	0.502	0.60
41_P	49_I	0.500	0.59

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
3j20K	1	0.9708	100	0.061	Contact Map
3j7aM	1	0.9562	100	0.07	Contact Map
3j60Q	1	0.8686	100	0.074	Contact Map
4ujpR	1	0.9781	100	0.076	Contact Map
4bpeI	1	0.9854	100	0.079	Contact Map
4w23Q	1	0.9708	100	0.082	Contact Map
4tp8I	1	0.9197	100	0.084	Contact Map
4rb5I	1	0.9197	100	0.085	Contact Map
3bbnI	1	0.9124	100	0.087	Contact Map
5aj3I	1	0.927	100	0.087	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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