RL30 - BACSU - GREMLIN Contacts

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RL30 - 50S ribosomal protein L30

UniProt:	P19947	Sequences: MAKLEITLKRSVIGRPEDQRVTVRTLGLKKTNQTVVHEDNAAIRGMINKVSHLVSVKEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	59 (57)
Sequences:	1485 (700)
Seq/√Len:	92.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_D	44_R	3.208	1.00
12_V	23_V	2.580	1.00
48_N	51_S	2.509	1.00
7_T	34_T	2.234	1.00
17_E	21_V	2.160	1.00
18_D	49_K	2.125	1.00
19_Q	52_H	2.112	1.00
8_L	23_V	2.049	1.00
5_E	57_K	2.037	1.00
29_K	33_Q	2.015	1.00
23_V	50_V	1.666	1.00
9_K	55_S	1.653	1.00
37_H	43_I	1.573	1.00
3_K	36_V	1.568	1.00
5_E	36_V	1.525	1.00
6_I	37_H	1.351	0.99
7_T	57_K	1.320	0.99
21_V	25_T	1.282	0.99
7_T	55_S	1.254	0.99
3_K	38_E	1.247	0.99
4_L	47_I	1.201	0.98
21_V	24_R	1.188	0.98
30_K	33_Q	1.150	0.97
12_V	24_R	1.147	0.97
22_T	46_M	1.084	0.96
16_P	19_Q	1.082	0.96
43_I	46_M	1.040	0.95
4_L	39_D	1.039	0.95
25_T	46_M	1.023	0.95
4_L	44_R	1.022	0.95
8_L	12_V	0.993	0.94
25_T	42_A	0.988	0.94
22_T	49_K	0.952	0.93
38_E	43_I	0.911	0.91
39_D	47_I	0.910	0.91
19_Q	49_K	0.902	0.91
25_T	37_H	0.900	0.91
8_L	33_Q	0.884	0.90
12_V	20_R	0.871	0.89
10_R	15_R	0.800	0.85
16_P	20_R	0.765	0.82
17_E	20_R	0.752	0.81
15_R	19_Q	0.749	0.81
20_R	24_R	0.737	0.79
4_L	58_E	0.734	0.79
17_E	24_R	0.734	0.79
8_L	31_T	0.710	0.77
5_E	34_T	0.695	0.75
24_R	29_K	0.693	0.75
16_P	52_H	0.691	0.75
16_P	22_T	0.688	0.75
40_N	43_I	0.686	0.74
28_L	31_T	0.683	0.74
4_L	36_V	0.683	0.74
16_P	49_K	0.671	0.73
6_I	35_V	0.663	0.72
37_H	46_M	0.653	0.71
22_T	37_H	0.650	0.70
10_R	29_K	0.648	0.70
2_A	39_D	0.645	0.70
38_E	42_A	0.645	0.70
10_R	16_P	0.643	0.70
47_I	54_V	0.641	0.69
18_D	22_T	0.636	0.69
6_I	43_I	0.629	0.68
34_T	57_K	0.620	0.67
15_R	53_L	0.609	0.65
15_R	51_S	0.602	0.65
2_A	38_E	0.597	0.64
22_T	25_T	0.586	0.62
3_K	34_T	0.549	0.58
23_V	28_L	0.547	0.57
12_V	15_R	0.545	0.57
2_A	42_A	0.536	0.56
15_R	20_R	0.526	0.54
4_L	57_K	0.518	0.53
23_V	33_Q	0.516	0.53
12_V	33_Q	0.516	0.53
41_A	54_V	0.514	0.53
35_V	43_I	0.511	0.52
23_V	29_K	0.511	0.52
10_R	14_G	0.506	0.52
44_R	47_I	0.505	0.51
26_L	37_H	0.504	0.51
22_T	43_I	0.503	0.51
42_A	54_V	0.500	0.51

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
1vw4U	1	0.9831	99.9	0.181	Contact Map
4tp9Z	1	0.0339	99.9	0.196	Contact Map
1bxyA	1	1	99.8	0.209	Contact Map
3j7yZ	1	1	99.8	0.228	Contact Map
3j3vY	1	0.9492	99.8	0.24	Contact Map
2zjrW	1	0.9322	99.8	0.25	Contact Map
3j21Y	1	1	99.8	0.288	Contact Map
1vq8W	1	0.9661	99.7	0.34	Contact Map
1vx75	1	1	99.6	0.361	Contact Map
4w20F	1	1	99.6	0.363	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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