RS28 - HALSA - GREMLIN Contacts

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RS28 - 30S ribosomal protein S28e

UniProt:	P57710	Sequences: MSAEESEEGATPAEVIEVVGKTGMHGEAMQVKCRIQEGGNQGRIITRNVLGPVRVGDVIQLKETAREADSIGGQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	74 (63)
Sequences:	233 (98)
Seq/√Len:	12.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_H	28_A	4.176	1.00
21_K	28_A	2.623	0.92
33_C	66_R	2.382	0.87
14_E	34_R	2.187	0.82
49_V	59_I	2.109	0.80
37_E	41_Q	1.932	0.73
14_E	46_T	1.908	0.72
17_E	64_T	1.882	0.71
12_P	35_I	1.796	0.67
34_R	45_I	1.781	0.67
47_R	57_D	1.718	0.64
29_M	33_C	1.644	0.60
12_P	44_I	1.577	0.57
31_V	52_P	1.573	0.57
42_G	64_T	1.396	0.48
32_K	40_N	1.357	0.46
43_R	57_D	1.347	0.45
8_E	42_G	1.301	0.43
47_R	66_R	1.276	0.42
29_M	69_D	1.259	0.41
34_R	46_T	1.248	0.40
50_L	65_A	1.207	0.38
24_M	65_A	1.169	0.36
11_T	37_E	1.157	0.36
55_V	62_K	1.154	0.36
49_V	53_V	1.143	0.35
33_C	65_A	1.121	0.34
32_K	65_A	1.043	0.31
57_D	69_D	1.040	0.31
47_R	54_R	1.039	0.31
43_R	47_R	1.037	0.30
24_M	27_E	1.015	0.30
12_P	18_V	0.985	0.28
34_R	44_I	0.978	0.28
23_G	51_G	0.945	0.27
8_E	11_T	0.931	0.26
17_E	46_T	0.900	0.25
31_V	49_V	0.877	0.24
20_G	54_R	0.874	0.24
62_K	71_I	0.874	0.24
15_V	53_V	0.857	0.23
41_Q	44_I	0.856	0.23
23_G	49_V	0.854	0.23
27_E	46_T	0.846	0.23
17_E	45_I	0.843	0.23
30_Q	67_E	0.843	0.23
25_H	68_A	0.829	0.22
47_R	51_G	0.826	0.22
36_Q	60_Q	0.815	0.22
29_M	45_I	0.794	0.21
45_I	48_N	0.793	0.21
27_E	62_K	0.785	0.21
51_G	67_E	0.776	0.20
35_I	60_Q	0.772	0.20
17_E	55_V	0.767	0.20
52_P	57_D	0.753	0.20
48_N	66_R	0.739	0.19
14_E	44_I	0.738	0.19
63_E	71_I	0.717	0.19
28_A	65_A	0.715	0.19
12_P	17_E	0.705	0.18
9_G	36_Q	0.704	0.18
47_R	69_D	0.685	0.18
27_E	64_T	0.679	0.17
19_V	46_T	0.670	0.17
44_I	55_V	0.663	0.17
28_A	45_I	0.645	0.16
60_Q	71_I	0.643	0.16
23_G	50_L	0.641	0.16
48_N	51_G	0.632	0.16
23_G	26_G	0.630	0.16
10_A	60_Q	0.620	0.16
13_A	63_E	0.619	0.16
22_T	54_R	0.605	0.15
33_C	69_D	0.603	0.15
10_A	58_V	0.601	0.15
35_I	59_I	0.589	0.15
47_R	68_A	0.584	0.15
37_E	44_I	0.581	0.15
12_P	34_R	0.576	0.15
33_C	43_R	0.574	0.15
7_E	56_G	0.571	0.15
19_V	37_E	0.563	0.14
29_M	54_R	0.541	0.14
15_V	36_Q	0.538	0.14
19_V	44_I	0.530	0.14
9_G	16_I	0.527	0.13
16_I	69_D	0.523	0.13
16_I	45_I	0.523	0.13
31_V	56_G	0.520	0.13
21_K	40_N	0.516	0.13
35_I	58_V	0.515	0.13
17_E	52_P	0.505	0.13
43_R	58_V	0.500	0.13

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
1ny4A	1	0.9459	100	0.16	Contact Map
1ne3A	1	0.9189	100	0.169	Contact Map
3j20X	1	0.9459	100	0.171	Contact Map
4bpe1	1	0.8919	100	0.177	Contact Map
3zeyZ	1	0.8784	100	0.185	Contact Map
4w23c	1	0.8649	100	0.185	Contact Map
3j7a5	1	0.7838	100	0.188	Contact Map
4ujpd	1	0.8514	100	0.194	Contact Map
2m1lA	2	0.7432	10.2	0.924	Contact Map
3j9tA	1	0.9595	8.4	0.927	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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