RL28 - BACSU - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

RL28 - 50S ribosomal protein L28

UniProt:	P37807	Sequences: MARKCVITGKKTTAGNNRSHAMNASKRTWGANLQKVRILVNGKPKKVYVSARALKSGKVERV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	62 (61)
Sequences:	653 (286)
Seq/√Len:	36.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_I	47_V	3.466	1.00
18_R	24_A	2.875	1.00
16_N	26_K	2.650	1.00
8_T	53_A	2.312	0.99
33_L	48_Y	2.311	0.99
50_S	53_A	2.271	0.99
8_T	50_S	2.250	0.99
12_T	28_T	2.197	0.99
52_R	55_K	2.197	0.99
18_R	22_M	2.090	0.99
6_V	48_Y	2.079	0.99
14_A	26_K	1.914	0.98
35_K	46_K	1.548	0.93
4_K	11_K	1.530	0.93
17_N	25_S	1.492	0.92
25_S	34_Q	1.470	0.91
39_L	44_P	1.431	0.90
12_T	30_G	1.379	0.88
6_V	47_V	1.301	0.85
10_K	31_A	1.248	0.82
34_Q	51_A	1.169	0.78
49_V	54_L	1.149	0.77
16_N	22_M	1.120	0.75
12_T	31_A	1.116	0.75
19_S	23_N	1.108	0.74
23_N	26_K	1.098	0.73
16_N	24_A	1.040	0.69
35_K	48_Y	1.017	0.67
39_L	43_K	0.999	0.66
56_S	59_V	0.996	0.66
40_V	44_P	0.977	0.64
34_Q	46_K	0.958	0.63
40_V	43_K	0.936	0.61
36_V	39_L	0.926	0.60
17_N	23_N	0.918	0.59
19_S	22_M	0.909	0.59
20_H	23_N	0.908	0.59
3_R	30_G	0.897	0.58
11_K	26_K	0.869	0.55
33_L	61_R	0.813	0.50
37_R	46_K	0.803	0.49
9_G	34_Q	0.798	0.49
9_G	51_A	0.797	0.49
6_V	33_L	0.793	0.49
4_K	54_L	0.780	0.47
19_S	25_S	0.753	0.45
38_I	49_V	0.746	0.44
36_V	54_L	0.706	0.41
52_R	56_S	0.686	0.39
39_L	49_V	0.680	0.39
36_V	58_K	0.678	0.39
12_T	60_E	0.671	0.38
37_R	49_V	0.670	0.38
4_K	9_G	0.653	0.37
2_A	48_Y	0.649	0.36
4_K	48_Y	0.648	0.36
7_I	47_V	0.647	0.36
20_H	25_S	0.638	0.35
7_I	10_K	0.633	0.35
7_I	55_K	0.632	0.35
25_S	60_E	0.631	0.35
6_V	38_I	0.625	0.34
17_N	21_A	0.607	0.33
2_A	38_I	0.600	0.32
35_K	44_P	0.599	0.32
34_Q	54_L	0.592	0.32
10_K	53_A	0.588	0.31
1_M	4_K	0.588	0.31
19_S	24_A	0.586	0.31
9_G	14_A	0.585	0.31
27_R	30_G	0.585	0.31
31_A	35_K	0.576	0.31
13_T	25_S	0.575	0.31
54_L	61_R	0.574	0.30
49_V	57_G	0.570	0.30
6_V	31_A	0.568	0.30
8_T	51_A	0.564	0.30
12_T	34_Q	0.561	0.29
17_N	29_W	0.557	0.29
36_V	57_G	0.555	0.29
45_K	58_K	0.554	0.29
35_K	58_K	0.547	0.28
29_W	43_K	0.547	0.28
44_P	56_S	0.544	0.28
7_I	35_K	0.535	0.28
21_A	33_L	0.524	0.27
46_K	60_E	0.523	0.27
3_R	9_G	0.519	0.27
15_G	29_W	0.511	0.26
2_A	47_V	0.510	0.26
2_A	12_T	0.507	0.26
28_T	36_V	0.500	0.25

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
2jz6A	1	1	99.9	0.182	Contact Map
2zjrU	1	0.8871	99.9	0.242	Contact Map
4rb61	1	0.9839	99.9	0.25	Contact Map
3bboY	1	0.9677	99.9	0.287	Contact Map
4tp9X	1	0.9839	99.8	0.306	Contact Map
1vw4S	1	1	99.8	0.361	Contact Map
3j7yX	1	0.9839	99.8	0.368	Contact Map
1w4rA	3	0.6935	46.5	0.88	Contact Map
2orvA	3	0.6935	38.4	0.886	Contact Map
2orwA	3	0.7419	28.2	0.893	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.

Page generated in 0.0047 seconds.