RL332 - BACSU - GREMLIN Contacts

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RL332 - 50S ribosomal protein L33 2

UniProt:	Q06798	Sequences: MRKKITLACKTCGNRNYTTMKSSASAAERLEVKKYCSTCNSHTAHLETK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	49 (49)
Sequences:	240 (90)
Seq/√Len:	12.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_N	38_T	5.165	1.00
33_K	41_S	2.707	0.94
11_T	41_S	2.558	0.92
32_V	35_Y	1.919	0.74
3_K	23_S	1.818	0.70
35_Y	40_N	1.768	0.68
26_A	30_L	1.579	0.59
20_M	25_S	1.536	0.57
3_K	24_A	1.530	0.56
4_K	18_T	1.461	0.53
5_I	30_L	1.457	0.53
13_G	42_H	1.427	0.51
4_K	20_M	1.340	0.47
19_T	30_L	1.314	0.45
24_A	48_T	1.290	0.44
37_S	44_A	1.286	0.44
23_S	49_K	1.228	0.41
2_R	28_E	1.220	0.40
13_G	38_T	1.219	0.40
29_R	46_L	1.187	0.39
8_A	13_G	1.169	0.38
22_S	32_V	1.165	0.38
2_R	8_A	1.142	0.37
19_T	25_S	1.140	0.36
13_G	39_C	1.113	0.35
22_S	30_L	1.073	0.33
39_C	42_H	0.996	0.30
4_K	14_N	0.953	0.28
8_A	35_Y	0.911	0.26
11_T	43_T	0.866	0.24
33_K	44_A	0.863	0.24
18_T	49_K	0.837	0.23
22_S	26_A	0.832	0.23
20_M	49_K	0.830	0.23
6_T	13_G	0.816	0.23
11_T	29_R	0.806	0.22
30_L	40_N	0.798	0.22
10_K	46_L	0.746	0.20
7_L	35_Y	0.745	0.20
4_K	46_L	0.742	0.20
25_S	44_A	0.721	0.19
24_A	27_A	0.707	0.19
6_T	44_A	0.690	0.18
24_A	40_N	0.661	0.17
1_M	23_S	0.657	0.17
30_L	37_S	0.657	0.17
28_E	39_C	0.655	0.17
3_K	18_T	0.643	0.17
26_A	29_R	0.640	0.17
19_T	41_S	0.639	0.17
18_T	26_A	0.636	0.17
14_N	24_A	0.629	0.16
23_S	35_Y	0.627	0.16
5_I	19_T	0.618	0.16
11_T	49_K	0.617	0.16
14_N	39_C	0.609	0.16
14_N	30_L	0.606	0.16
8_A	37_S	0.602	0.16
21_K	26_A	0.595	0.16
18_T	33_K	0.595	0.16
26_A	32_V	0.594	0.16
4_K	29_R	0.576	0.15
2_R	10_K	0.575	0.15
1_M	46_L	0.573	0.15
32_V	46_L	0.563	0.15
10_K	24_A	0.561	0.15
18_T	30_L	0.549	0.14
33_K	48_T	0.543	0.14
11_T	28_E	0.534	0.14
40_N	46_L	0.528	0.14
6_T	32_V	0.523	0.14
6_T	35_Y	0.513	0.13
6_T	20_M	0.510	0.13
8_A	14_N	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
1nkw1	1	1	99.8	0.193	Contact Map
4rb66	1	1	99.8	0.201	Contact Map
4tp91	1	1	99.8	0.205	Contact Map
3bbo3	1	1	99.8	0.211	Contact Map
2zjr1	1	1	99.8	0.212	Contact Map
3j7y1	1	0.9592	99.7	0.269	Contact Map
1vw4X	1	0.9592	99.7	0.282	Contact Map
3j21j	1	0.4898	83.6	0.816	Contact Map
1vq83	1	0.4898	83.2	0.817	Contact Map
3j39o	1	0.5102	77	0.828	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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