RS12 - BACSU - GREMLIN Contacts

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RS12 - 30S ribosomal protein S12

UniProt:	P21472	Sequences: MPTINQLIRKGRVSKVENSKSPALNKGYNSFKKEHTNVSSPQKRGVCTRVGTMTPKKPNSALRKYARVRLTNGIEVTAYIPGIGHNLQEHSVVLIRGGRVKDLPGVRYHIVRGALDTAGVENRAQGRSKYGTKKPKAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	138 (123)
Sequences:	1273 (360)
Seq/√Len:	32.5

ECOLI - RS12
BACSU - RS12
HALSA - RS12
SULSO - RS12

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_R	77_T	6.038	1.00
54_T	62_L	3.912	1.00
51_G	65_Y	3.775	1.00
42_Q	111_V	3.448	1.00
52_T	62_L	3.140	1.00
51_G	77_T	2.792	1.00
100_V	109_H	2.694	1.00
56_K	99_R	2.663	1.00
79_Y	109_H	2.397	0.99
110_I	117_T	2.379	0.99
76_V	95_I	2.271	0.99
40_S	43_K	2.077	0.98
109_H	129_K	2.072	0.98
56_K	100_V	1.819	0.96
90_H	120_V	1.787	0.95
43_K	72_N	1.683	0.94
2_P	7_L	1.649	0.93
10_K	72_N	1.614	0.92
43_K	71_T	1.609	0.92
12_R	23_A	1.607	0.92
4_I	7_L	1.602	0.92
45_G	70_L	1.532	0.90
56_K	104_P	1.501	0.89
44_R	115_L	1.475	0.88
49_R	74_I	1.469	0.88
124_A	135_P	1.404	0.86
9_R	114_A	1.390	0.85
10_K	14_S	1.381	0.85
7_L	10_K	1.367	0.84
21_S	24_L	1.364	0.84
53_M	77_T	1.341	0.83
78_A	110_I	1.282	0.80
47_C	136_K	1.273	0.79
96_R	99_R	1.262	0.79
64_K	79_Y	1.235	0.77
120_V	123_R	1.226	0.77
96_R	109_H	1.213	0.76
43_K	95_I	1.184	0.74
49_R	81_P	1.174	0.74
119_G	134_K	1.167	0.73
46_V	83_I	1.145	0.72
61_A	103_L	1.144	0.72
125_Q	129_K	1.138	0.71
40_S	115_L	1.109	0.69
14_S	124_A	1.106	0.69
85_H	103_L	1.101	0.69
73_G	135_P	1.079	0.67
17_E	20_K	1.076	0.67
59_N	102_D	1.051	0.65
15_K	19_S	1.051	0.65
15_K	18_N	1.044	0.65
86_N	118_A	1.024	0.63
44_R	75_E	1.005	0.62
67_R	84_G	1.004	0.61
39_S	44_R	1.003	0.61
78_A	81_P	0.995	0.61
47_C	51_G	0.979	0.59
73_G	107_R	0.978	0.59
75_E	90_H	0.970	0.59
54_T	124_A	0.954	0.57
125_Q	132_T	0.945	0.57
125_Q	135_P	0.944	0.57
65_Y	77_T	0.929	0.55
8_I	11_G	0.927	0.55
95_I	110_I	0.924	0.55
19_S	22_P	0.922	0.55
2_P	69_R	0.918	0.55
5_N	8_I	0.912	0.54
117_T	122_N	0.904	0.53
41_P	98_G	0.903	0.53
55_P	103_L	0.874	0.51
1_M	7_L	0.874	0.51
12_R	24_L	0.871	0.51
84_G	112_R	0.848	0.49
61_A	102_D	0.844	0.48
54_T	101_K	0.840	0.48
63_R	102_D	0.840	0.48
56_K	59_N	0.834	0.48
96_R	129_K	0.826	0.47
7_L	11_G	0.826	0.47
84_G	113_G	0.826	0.47
74_I	118_A	0.822	0.47
82_G	108_Y	0.816	0.46
82_G	98_G	0.808	0.45
20_K	103_L	0.792	0.44
82_G	120_V	0.787	0.44
69_R	75_E	0.784	0.44
7_L	54_T	0.777	0.43
86_N	91_S	0.776	0.43
53_M	107_R	0.772	0.43
44_R	118_A	0.770	0.42
50_V	124_A	0.769	0.42
92_V	101_K	0.763	0.42
61_A	89_E	0.757	0.41
101_K	107_R	0.753	0.41
3_T	6_Q	0.749	0.41
41_P	82_G	0.747	0.41
44_R	117_T	0.746	0.40
66_A	110_I	0.746	0.40
41_P	44_R	0.746	0.40
9_R	78_A	0.738	0.40
14_S	49_R	0.737	0.40
49_R	53_M	0.736	0.40
48_T	132_T	0.736	0.40
95_I	122_N	0.731	0.39
25_N	74_I	0.730	0.39
22_P	107_R	0.728	0.39
101_K	126_G	0.724	0.39
76_V	105_G	0.723	0.39
53_M	76_V	0.721	0.38
90_H	98_G	0.716	0.38
113_G	120_V	0.716	0.38
4_I	95_I	0.706	0.37
46_V	118_A	0.705	0.37
62_L	115_L	0.696	0.37
19_S	25_N	0.695	0.36
20_K	107_R	0.690	0.36
9_R	17_E	0.690	0.36
64_K	89_E	0.684	0.36
99_R	112_R	0.680	0.35
126_G	130_Y	0.677	0.35
62_L	110_I	0.674	0.35
77_T	117_T	0.673	0.35
75_E	125_Q	0.659	0.34
82_G	90_H	0.651	0.33
2_P	11_G	0.650	0.33
18_N	25_N	0.649	0.33
39_S	93_V	0.641	0.32
74_I	95_I	0.628	0.31
5_N	17_E	0.628	0.31
68_V	113_G	0.623	0.31
67_R	134_K	0.623	0.31
64_K	104_P	0.615	0.31
8_I	40_S	0.613	0.30
73_G	136_K	0.613	0.30
74_I	129_K	0.612	0.30
65_Y	72_N	0.611	0.30
55_P	102_D	0.608	0.30
13_V	122_N	0.608	0.30
64_K	129_K	0.605	0.30
85_H	91_S	0.604	0.30
122_N	125_Q	0.602	0.30
89_E	100_V	0.601	0.30
132_T	135_P	0.600	0.30
53_M	78_A	0.597	0.29
17_E	21_S	0.597	0.29
25_N	71_T	0.596	0.29
47_C	91_S	0.595	0.29
91_S	116_D	0.594	0.29
4_I	22_P	0.588	0.29
1_M	100_V	0.588	0.29
85_H	90_H	0.587	0.29
113_G	119_G	0.583	0.28
44_R	74_I	0.579	0.28
64_K	73_G	0.572	0.28
21_S	40_S	0.571	0.28
50_V	69_R	0.569	0.27
2_P	25_N	0.568	0.27
11_G	14_S	0.567	0.27
55_P	80_I	0.565	0.27
66_A	91_S	0.564	0.27
70_L	105_G	0.562	0.27
80_I	98_G	0.561	0.27
40_S	129_K	0.560	0.27
10_K	126_G	0.560	0.27
16_V	20_K	0.555	0.27
47_C	65_Y	0.554	0.26
12_R	15_K	0.551	0.26
118_A	132_T	0.550	0.26
53_M	67_R	0.548	0.26
114_A	134_K	0.546	0.26
74_I	117_T	0.542	0.26
57_K	91_S	0.539	0.26
2_P	75_E	0.537	0.25
118_A	122_N	0.534	0.25
5_N	135_P	0.532	0.25
111_V	127_R	0.528	0.25
85_H	88_Q	0.518	0.24
25_N	135_P	0.516	0.24
73_G	89_E	0.515	0.24
81_P	117_T	0.515	0.24
99_R	109_H	0.505	0.23
25_N	43_K	0.504	0.23
41_P	45_G	0.500	0.23

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
4ji1L	1	0.8913	100	0.098	Contact Map
4rb5L	1	0.8841	100	0.098	Contact Map
5aj3L	1	0.7899	100	0.196	Contact Map
4bpeL	1	0.9058	100	0.253	Contact Map
3j20N	1	0.9203	100	0.255	Contact Map
4ujpY	1	0.9348	100	0.264	Contact Map
3zeyS	1	0.9348	100	0.264	Contact Map
3wbkC	1	0.0072	7.9	0.957	Contact Map
2jpjA	1	0.1159	7.3	0.958	Contact Map
4kzyn	1	0.5725	7	0.959	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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