RS21 - BACSU - GREMLIN Contacts

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RS21 - 30S ribosomal protein S21

UniProt:	P21478	Sequences: MSKTVVRKNESLEDALRRFKRSVSKTGTLQEARKREFYEKPSVKRKKKSEAARKRKF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	57 (55)
Sequences:	328 (106)
Seq/√Len:	14.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_E	35_R	4.435	1.00
33_R	36_E	3.244	0.98
43_V	47_K	2.730	0.96
12_L	24_S	2.137	0.85
5_V	23_V	1.894	0.77
17_R	50_E	1.867	0.76
20_K	25_K	1.810	0.74
49_S	53_R	1.680	0.68
34_K	37_F	1.575	0.63
17_R	25_K	1.560	0.62
39_E	47_K	1.560	0.62
13_E	22_S	1.551	0.62
42_S	46_K	1.390	0.53
29_L	32_A	1.370	0.52
48_K	52_A	1.368	0.52
34_K	47_K	1.361	0.51
23_V	28_T	1.306	0.48
12_L	50_E	1.247	0.45
35_R	54_K	1.195	0.42
2_S	22_S	1.157	0.40
6_V	45_R	1.130	0.39
45_R	48_K	1.106	0.38
34_K	54_K	1.092	0.37
22_S	25_K	1.068	0.36
4_T	26_T	1.066	0.36
37_F	42_S	1.033	0.34
38_Y	43_V	1.028	0.34
44_K	53_R	1.027	0.34
6_V	23_V	1.004	0.33
5_V	49_S	0.969	0.31
4_T	28_T	0.953	0.30
39_E	55_R	0.952	0.30
20_K	54_K	0.929	0.29
7_R	11_S	0.858	0.26
30_Q	33_R	0.849	0.26
32_A	55_R	0.841	0.25
20_K	29_L	0.831	0.25
52_A	55_R	0.826	0.25
21_R	42_S	0.804	0.24
14_D	33_R	0.775	0.23
22_S	26_T	0.759	0.22
7_R	14_D	0.757	0.22
26_T	30_Q	0.756	0.22
4_T	23_V	0.753	0.22
25_K	51_A	0.746	0.22
48_K	51_A	0.741	0.21
9_N	13_E	0.735	0.21
33_R	53_R	0.734	0.21
25_K	52_A	0.727	0.21
3_K	28_T	0.690	0.20
23_V	36_E	0.685	0.19
22_S	45_R	0.679	0.19
10_E	18_R	0.663	0.19
24_S	35_R	0.661	0.19
31_E	34_K	0.660	0.19
7_R	10_E	0.660	0.19
9_N	21_R	0.653	0.18
11_S	28_T	0.650	0.18
9_N	49_S	0.648	0.18
11_S	14_D	0.636	0.18
5_V	33_R	0.634	0.18
2_S	52_A	0.631	0.18
3_K	7_R	0.629	0.18
27_G	51_A	0.605	0.17
4_T	24_S	0.598	0.17
24_S	50_E	0.585	0.16
28_T	34_K	0.584	0.16
17_R	46_K	0.581	0.16
40_K	46_K	0.578	0.16
18_R	49_S	0.565	0.16
6_V	25_K	0.559	0.15
8_K	25_K	0.558	0.15
14_D	24_S	0.553	0.15
24_S	32_A	0.551	0.15
2_S	44_K	0.548	0.15
8_K	21_R	0.546	0.15
6_V	30_Q	0.538	0.15
20_K	52_A	0.535	0.15
14_D	28_T	0.531	0.15
13_E	38_Y	0.515	0.14
4_T	8_K	0.507	0.14
44_K	47_K	0.500	0.14

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
3bbnU	1	0.9298	99.8	0.219	Contact Map
4kiyU	1	0.8947	99.8	0.245	Contact Map
4tp8U	1	0.8947	99.7	0.302	Contact Map
5aj3U	1	0.9825	99.7	0.306	Contact Map
2qpvA	2	0.4386	7.1	0.906	Contact Map
1w3iA	3	0.5439	4.7	0.913	Contact Map
4lurA	1	0.5965	4.4	0.915	Contact Map
2y4tA	1	0.5965	4.1	0.916	Contact Map
2ia0A	2	0.4912	3.2	0.92	Contact Map
4ykeA	2	0	3	0.921	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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