RL331 - BACSU - GREMLIN Contacts

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RL331 - 50S ribosomal protein L33 1

UniProt:	P56849	Sequences: MRVNITLACTECGERNYISKKNKRNNPDRVEFKKYCPRDKKSTLHRETK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	49 (49)
Sequences:	407 (122)
Seq/√Len:	17.4

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_E	38_R	5.836	1.00
4_N	18_I	2.544	0.96
12_C	36_C	1.995	0.87
35_Y	40_K	1.875	0.84
33_K	41_K	1.842	0.83
1_M	23_K	1.683	0.76
11_E	41_K	1.673	0.76
13_G	42_S	1.588	0.72
14_E	39_D	1.572	0.71
8_A	15_R	1.549	0.70
26_N	30_V	1.490	0.67
4_N	20_K	1.412	0.63
12_C	39_D	1.384	0.61
3_V	23_K	1.309	0.57
20_K	25_N	1.183	0.49
26_N	29_R	1.169	0.48
39_D	42_S	1.114	0.45
33_K	44_L	1.113	0.45
5_I	32_F	1.074	0.42
26_N	32_F	1.069	0.42
29_R	46_R	1.044	0.41
8_A	37_P	1.029	0.40
10_T	31_E	1.010	0.39
1_M	4_N	0.978	0.37
5_I	19_S	0.973	0.37
13_G	38_R	0.947	0.35
36_C	39_D	0.937	0.35
13_G	39_D	0.922	0.34
32_F	35_Y	0.901	0.33
25_N	30_V	0.880	0.32
24_R	27_P	0.871	0.31
41_K	49_K	0.867	0.31
15_R	48_T	0.866	0.31
8_A	27_P	0.864	0.31
2_R	6_T	0.859	0.30
2_R	8_A	0.849	0.30
32_F	46_R	0.843	0.30
3_V	49_K	0.825	0.29
11_E	44_L	0.820	0.28
21_K	47_E	0.805	0.28
22_N	30_V	0.796	0.27
3_V	18_I	0.785	0.27
35_Y	43_T	0.779	0.26
5_I	30_V	0.778	0.26
24_R	48_T	0.765	0.26
19_S	48_T	0.715	0.24
7_L	28_D	0.713	0.24
4_N	46_R	0.711	0.23
25_N	32_F	0.710	0.23
19_S	30_V	0.695	0.23
6_T	48_T	0.688	0.22
1_M	24_R	0.666	0.22
6_T	18_I	0.652	0.21
10_T	46_R	0.652	0.21
22_N	32_F	0.647	0.21
11_E	40_K	0.641	0.21
29_R	37_P	0.641	0.21
22_N	26_N	0.609	0.19
10_T	44_L	0.599	0.19
20_K	26_N	0.599	0.19
13_G	43_T	0.598	0.19
2_R	28_D	0.590	0.19
15_R	29_R	0.574	0.18
14_E	42_S	0.567	0.18
8_A	35_Y	0.550	0.17
15_R	31_E	0.537	0.17
38_R	42_S	0.536	0.17
4_N	14_E	0.531	0.17
38_R	49_K	0.530	0.16
6_T	44_L	0.528	0.16
33_K	39_D	0.525	0.16
33_K	46_R	0.519	0.16
4_N	28_D	0.511	0.16
16_N	39_D	0.500	0.16

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	0.184	Contact Map
4rb66	1	1	99.8	0.192	Contact Map
3bbo3	1	1	99.8	0.197	Contact Map
4tp91	1	1	99.8	0.198	Contact Map
2zjr1	1	1	99.8	0.203	Contact Map
3j7y1	1	0.9592	99.8	0.263	Contact Map
1vw4X	1	0.9592	99.7	0.275	Contact Map
3j21j	1	0.4898	82.8	0.819	Contact Map
1vq83	1	0.4898	82.5	0.82	Contact Map
4a18C	1	0.4898	76.5	0.83	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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