RS13 - HALSA - GREMLIN Contacts

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RS13 - 30S ribosomal protein S13

UniProt:	Q9V2W4	Sequences: MSSEEQEDVDEDIQYFVRIGQTDLDGTKTVERALAELGGVGRRVARIVADEAGVDRTATMGGLEDDAIESVTDAVDSFTEHAPAWLANRQNDFYTGENQHITGTDVELTRDQDINRMRMIRSYKGIRHERGQKVRGQRTKSTGRTEGTIGVNVEAIKEEQAEDDAADGGEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	171 (145)
Sequences:	384 (245)
Seq/√Len:	20.3

ECOLI - RS13
BACSU - RS13
HALSA - RS13
SULSO - RS13

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
133_K	143_G	4.053	1.00
58_A	67_A	4.047	1.00
117_M	124_K	3.479	1.00
117_M	122_S	3.283	1.00
30_V	54_V	3.219	1.00
89_R	92_D	2.844	0.99
125_G	128_H	2.494	0.97
64_E	67_A	2.466	0.97
31_E	46_R	2.436	0.97
48_V	74_A	2.349	0.96
19_I	68_I	2.249	0.95
44_V	78_F	2.086	0.93
46_R	50_D	2.075	0.93
121_R	129_E	1.952	0.90
33_A	60_M	1.909	0.89
13_I	103_G	1.862	0.88
14_Q	65_D	1.819	0.87
77_S	122_S	1.756	0.85
90_Q	98_N	1.748	0.84
58_A	64_E	1.706	0.83
49_A	54_V	1.693	0.82
113_D	128_H	1.693	0.82
18_R	144_R	1.666	0.81
15_Y	78_F	1.620	0.79
88_N	92_D	1.571	0.77
78_F	82_A	1.558	0.76
113_D	117_M	1.482	0.73
146_E	151_V	1.481	0.73
24_L	36_E	1.478	0.73
49_A	86_L	1.463	0.72
11_E	64_E	1.446	0.71
96_G	100_H	1.416	0.69
30_V	49_A	1.406	0.69
85_W	92_D	1.399	0.68
117_M	123_Y	1.389	0.68
17_V	60_M	1.387	0.68
72_T	76_D	1.347	0.65
31_E	45_A	1.347	0.65
146_E	150_G	1.333	0.64
145_T	148_T	1.322	0.64
36_E	71_V	1.312	0.63
85_W	88_N	1.300	0.62
41_G	111_D	1.294	0.62
38_G	107_E	1.271	0.61
113_D	125_G	1.271	0.61
15_Y	44_V	1.271	0.61
85_W	89_R	1.267	0.60
110_R	114_I	1.251	0.59
116_R	124_K	1.235	0.58
101_I	138_R	1.215	0.57
93_F	116_R	1.213	0.57
115_N	118_R	1.203	0.56
12_D	24_L	1.193	0.56
65_D	72_T	1.189	0.55
28_K	32_R	1.186	0.55
16_F	20_G	1.182	0.55
123_Y	141_S	1.180	0.55
32_R	141_S	1.176	0.54
22_T	54_V	1.170	0.54
79_T	84_A	1.167	0.54
13_I	59_T	1.164	0.54
20_G	147_G	1.160	0.53
16_F	140_K	1.144	0.52
24_L	68_I	1.136	0.52
26_G	61_G	1.126	0.51
36_E	94_Y	1.124	0.51
12_D	149_I	1.109	0.50
63_L	106_V	1.105	0.50
58_A	62_G	1.085	0.49
103_G	133_K	1.055	0.47
29_T	58_A	1.052	0.46
126_I	130_R	1.046	0.46
12_D	32_R	1.037	0.45
115_N	129_E	1.011	0.44
88_N	144_R	0.989	0.42
26_G	88_N	0.984	0.42
69_E	145_T	0.980	0.42
68_I	91_N	0.974	0.41
52_A	74_A	0.971	0.41
55_D	58_A	0.970	0.41
146_E	154_E	0.965	0.41
17_V	24_L	0.956	0.40
109_T	120_I	0.952	0.40
68_I	112_Q	0.938	0.39
24_L	30_V	0.932	0.39
101_I	106_V	0.930	0.39
26_G	92_D	0.927	0.38
38_G	145_T	0.917	0.38
123_Y	133_K	0.909	0.37
127_R	144_R	0.890	0.36
148_T	152_N	0.884	0.36
40_V	79_T	0.883	0.36
13_I	24_L	0.875	0.35
53_G	98_N	0.873	0.35
85_W	96_G	0.871	0.35
71_V	74_A	0.870	0.35
33_A	121_R	0.859	0.34
24_L	49_A	0.858	0.34
64_E	70_S	0.853	0.34
15_Y	111_D	0.827	0.32
27_T	103_G	0.824	0.32
133_K	142_T	0.824	0.32
70_S	119_M	0.812	0.32
142_T	149_I	0.803	0.31
89_R	113_D	0.797	0.31
140_K	145_T	0.796	0.31
148_T	155_A	0.791	0.30
104_T	111_D	0.786	0.30
56_R	107_E	0.782	0.30
84_A	98_N	0.781	0.30
33_A	112_Q	0.772	0.29
48_V	77_S	0.770	0.29
75_V	102_T	0.770	0.29
23_D	88_N	0.768	0.29
37_L	81_H	0.768	0.29
31_E	149_I	0.758	0.29
20_G	76_D	0.748	0.28
58_A	117_M	0.746	0.28
65_D	73_D	0.741	0.28
12_D	19_I	0.733	0.27
48_V	81_H	0.732	0.27
71_V	152_N	0.727	0.27
57_T	131_G	0.723	0.27
146_E	155_A	0.718	0.27
41_G	61_G	0.717	0.27
40_V	44_V	0.717	0.27
12_D	30_V	0.714	0.26
104_T	130_R	0.714	0.26
16_F	99_Q	0.711	0.26
103_G	143_G	0.709	0.26
34_L	71_V	0.709	0.26
61_G	89_R	0.708	0.26
42_R	82_A	0.697	0.26
123_Y	128_H	0.697	0.26
132_Q	149_I	0.692	0.25
110_R	147_G	0.686	0.25
83_P	88_N	0.684	0.25
85_W	151_V	0.683	0.25
53_G	82_A	0.683	0.25
128_H	142_T	0.681	0.25
87_A	101_I	0.677	0.25
26_G	150_G	0.668	0.24
25_D	106_V	0.666	0.24
48_V	117_M	0.664	0.24
79_T	98_N	0.663	0.24
21_Q	43_R	0.663	0.24
48_V	53_G	0.661	0.24
61_G	88_N	0.661	0.24
88_N	96_G	0.660	0.24
29_T	57_T	0.657	0.24
146_E	149_I	0.654	0.23
115_N	133_K	0.650	0.23
26_G	96_G	0.645	0.23
61_G	92_D	0.640	0.23
102_T	122_S	0.632	0.22
85_W	113_D	0.632	0.22
27_T	71_V	0.632	0.22
13_I	112_Q	0.625	0.22
59_T	155_A	0.618	0.22
87_A	153_V	0.616	0.22
15_Y	114_I	0.608	0.21
45_A	140_K	0.605	0.21
33_A	132_Q	0.605	0.21
123_Y	138_R	0.603	0.21
26_G	100_H	0.601	0.21
43_R	141_S	0.599	0.21
43_R	103_G	0.599	0.21
57_T	104_T	0.598	0.21
47_I	95_T	0.593	0.21
28_K	138_R	0.593	0.21
13_I	27_T	0.590	0.21
12_D	81_H	0.590	0.21
142_T	147_G	0.589	0.21
72_T	123_Y	0.588	0.20
109_T	113_D	0.584	0.20
12_D	115_N	0.582	0.20
150_G	155_A	0.576	0.20
50_D	149_I	0.573	0.20
77_S	80_E	0.573	0.20
96_G	150_G	0.573	0.20
61_G	124_K	0.573	0.20
35_A	42_R	0.572	0.20
64_E	132_Q	0.572	0.20
37_L	153_V	0.571	0.20
82_A	86_L	0.569	0.20
56_R	71_V	0.568	0.20
115_N	131_G	0.567	0.20
102_T	117_M	0.564	0.19
43_R	130_R	0.562	0.19
130_R	138_R	0.559	0.19
24_L	116_R	0.555	0.19
12_D	53_G	0.553	0.19
14_Q	33_A	0.550	0.19
47_I	101_I	0.547	0.19
73_D	76_D	0.547	0.19
146_E	153_V	0.547	0.19
34_L	133_K	0.539	0.18
54_V	83_P	0.537	0.18
86_L	96_G	0.534	0.18
60_M	121_R	0.531	0.18
96_G	144_R	0.530	0.18
45_A	86_L	0.529	0.18
62_G	69_E	0.528	0.18
61_G	144_R	0.527	0.18
91_N	149_I	0.524	0.18
78_F	130_R	0.524	0.18
129_E	138_R	0.523	0.18
108_L	114_I	0.522	0.18
81_H	154_E	0.522	0.18
34_L	127_R	0.521	0.18
92_D	96_G	0.519	0.18
51_E	62_G	0.519	0.18
45_A	122_S	0.514	0.18
57_T	84_A	0.514	0.18
115_N	121_R	0.510	0.17
112_Q	129_E	0.507	0.17
65_D	74_A	0.506	0.17
117_M	128_H	0.500	0.17

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
3j20O	1	0.8596	100	0.168	Contact Map
3j7aS	1	0.7427	100	0.169	Contact Map
4bpeM	1	0.8889	100	0.17	Contact Map
3j60S	1	0.883	100	0.175	Contact Map
3j38S	1	0.7953	100	0.176	Contact Map
3zeyM	1	0.8889	100	0.176	Contact Map
4ujpT	1	0.8421	100	0.222	Contact Map
4rb5M	1	0.6959	100	0.403	Contact Map
4tp8M	1	0.6667	100	0.448	Contact Map
3bbnM	1	0.5789	100	0.473	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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