RL12 - HALSA - GREMLIN Contacts

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RL12 - 50S ribosomal protein L12

UniProt:	P05768	Sequences: MEYVYAALILNEADEELTEDNITGVLEAAGVDVEESRAKALVAALEDVDIEEAVEEAAAAPAAAPAASGSDDEAAADDGDDDEEADADEAAEAEDAGDDDDEEPSGEGLGDLFG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	114 (103)
Sequences:	190 (140)
Seq/√Len:	13.7

HALSA - RL12
SULSO - RL12

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_T	21_N	5.389	1.00
33_V	38_A	2.599	0.93
76_A	80_D	2.588	0.93
26_L	37_R	2.316	0.89
26_L	29_A	2.224	0.86
74_A	78_D	2.158	0.85
77_D	81_D	2.147	0.84
16_E	35_E	2.016	0.80
13_A	31_V	1.896	0.76
57_A	61_P	1.865	0.75
49_D	97_G	1.804	0.72
23_T	27_E	1.718	0.68
49_D	52_E	1.705	0.68
17_L	67_A	1.645	0.65
36_S	44_A	1.617	0.63
9_I	25_V	1.614	0.63
24_G	27_E	1.581	0.62
64_A	68_S	1.552	0.60
75_A	79_G	1.490	0.57
12_E	34_E	1.479	0.56
65_P	69_G	1.464	0.55
7_A	41_L	1.410	0.53
101_D	104_P	1.390	0.52
9_I	57_A	1.349	0.49
76_A	81_D	1.314	0.47
77_D	82_D	1.312	0.47
6_A	44_A	1.302	0.47
1_M	5_Y	1.291	0.46
42_V	57_A	1.290	0.46
8_L	12_E	1.268	0.45
49_D	55_E	1.263	0.45
14_D	100_D	1.251	0.44
60_A	63_A	1.244	0.44
99_D	110_G	1.223	0.43
23_T	78_D	1.217	0.42
17_L	43_A	1.202	0.42
37_R	110_G	1.184	0.41
66_A	75_A	1.167	0.40
51_E	106_G	1.152	0.39
16_E	55_E	1.127	0.38
6_A	28_A	1.123	0.37
47_D	56_E	1.117	0.37
68_S	71_D	1.115	0.37
37_R	40_A	1.111	0.37
71_D	74_A	1.105	0.37
70_S	73_E	1.104	0.37
54_V	98_D	1.096	0.36
41_L	107_E	1.092	0.36
67_A	73_E	1.090	0.36
48_V	105_S	1.078	0.35
23_T	38_A	1.064	0.35
8_L	106_G	1.062	0.34
6_A	18_T	1.050	0.34
2_E	5_Y	1.035	0.33
41_L	111_D	1.011	0.32
100_D	103_E	0.992	0.31
11_N	51_E	0.971	0.30
95_D	103_E	0.968	0.30
51_E	54_V	0.967	0.30
4_V	61_P	0.967	0.30
41_L	53_A	0.949	0.29
22_I	53_A	0.947	0.29
65_P	70_S	0.942	0.29
102_E	111_D	0.933	0.28
68_S	81_D	0.903	0.27
47_D	78_D	0.903	0.27
108_G	114_G	0.897	0.27
4_V	78_D	0.897	0.27
32_D	59_A	0.893	0.27
36_S	107_E	0.887	0.27
101_D	106_G	0.884	0.26
25_V	33_V	0.880	0.26
66_A	71_D	0.865	0.26
100_D	105_S	0.865	0.26
60_A	64_A	0.844	0.25
4_V	107_E	0.841	0.25
42_V	61_P	0.839	0.25
32_D	56_E	0.829	0.24
51_E	56_E	0.822	0.24
4_V	60_A	0.821	0.24
53_A	60_A	0.820	0.24
9_I	111_D	0.818	0.24
101_D	105_S	0.817	0.24
68_S	73_E	0.812	0.23
98_D	101_D	0.807	0.23
49_D	110_G	0.806	0.23
26_L	43_A	0.804	0.23
25_V	73_E	0.803	0.23
37_R	44_A	0.800	0.23
23_T	34_E	0.798	0.23
26_L	100_D	0.797	0.23
14_D	104_P	0.781	0.22
44_A	55_E	0.777	0.22
5_Y	50_I	0.776	0.22
15_E	24_G	0.767	0.22
4_V	49_D	0.763	0.22
28_A	45_L	0.758	0.21
73_E	77_D	0.755	0.21
79_G	82_D	0.742	0.21
107_E	111_D	0.732	0.21
46_E	111_D	0.730	0.20
103_E	111_D	0.730	0.20
29_A	40_A	0.730	0.20
52_E	56_E	0.727	0.20
5_Y	9_I	0.720	0.20
40_A	44_A	0.707	0.20
68_S	77_D	0.700	0.19
1_M	50_I	0.698	0.19
98_D	104_P	0.695	0.19
3_Y	112_L	0.693	0.19
54_V	58_A	0.692	0.19
64_A	78_D	0.685	0.19
31_V	37_R	0.674	0.19
78_D	82_D	0.672	0.19
48_V	94_E	0.659	0.18
43_A	100_D	0.652	0.18
99_D	106_G	0.652	0.18
41_L	60_A	0.649	0.18
95_D	104_P	0.630	0.17
21_N	43_A	0.630	0.17
100_D	104_P	0.629	0.17
8_L	51_E	0.626	0.17
54_V	110_G	0.611	0.17
53_A	58_A	0.611	0.17
28_A	43_A	0.602	0.16
82_D	94_E	0.600	0.16
17_L	48_V	0.597	0.16
72_D	77_D	0.596	0.16
17_L	26_L	0.593	0.16
70_S	95_D	0.591	0.16
28_A	70_S	0.586	0.16
53_A	110_G	0.581	0.16
12_E	106_G	0.578	0.16
59_A	111_D	0.571	0.15
53_A	59_A	0.567	0.15
23_T	55_E	0.565	0.15
21_N	102_E	0.559	0.15
37_R	100_D	0.557	0.15
6_A	35_E	0.551	0.15
16_E	49_D	0.538	0.15
4_V	19_E	0.537	0.15
71_D	75_A	0.535	0.14
21_N	81_D	0.535	0.14
22_I	104_P	0.532	0.14
27_E	44_A	0.522	0.14
17_L	22_I	0.521	0.14
34_E	106_G	0.519	0.14
13_A	66_A	0.517	0.14
67_A	81_D	0.512	0.14
35_E	79_G	0.510	0.14
35_E	74_A	0.507	0.14
56_E	110_G	0.506	0.14
11_N	15_E	0.504	0.14
69_G	72_D	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
3izsv	1	0.5	99.7	0.535	Contact Map
3j3bs	1	0.5	99.7	0.536	Contact Map
3j3bu	1	0.4825	99.7	0.54	Contact Map
3j61s	1	0.4912	99.7	0.548	Contact Map
3izst	1	0.4912	99.7	0.566	Contact Map
3j61u	2	0.5088	99.6	0.581	Contact Map
3a1yA	3	0.5088	99.5	0.606	Contact Map
1vq8G	1	0.0088	99.3	0.645	Contact Map
3j21k	1	0	97.6	0.794	Contact Map
3wy9C	1	0.2281	96.9	0.816	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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