OPENSEQ.org - RL9 - ECOLI GREMLIN

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RL9 - 50S ribosomal protein L9

UniProt:	P0A7R1	Sequence MQVILLDKVANLGSLGDQVNVKAGYARNFLVPQGKAVPATKKNIEFFEARRAELEAKLAEVLAAANARAEKINALETVTIASKAGDEGKLFGSIGTRDIADAVTAAGVEVAKSEVRLPNGVLRTTGEHEVSFQVHSEVFAKVIVNVVAE	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG10870
Length:	149 (148)
Sequences:	1595
Seq/Len:	10.78

RL9
Paralog alert: 0.01 [within 20: 0.00] - ratio of genomes with paralogs

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
62_L	66_N	3.17	1.00
2_Q	20_N	3.02	1.00
7_D	35_K	2.776	1.00
129_E	141_K	2.584	1.00
104_T	109_E	2.459	1.00
124_T	128_H	2.413	1.00
129_E	143_I	2.341	1.00
127_E	145_N	2.302	1.00
69_A	73_N	2.275	1.00
102_A	105_A	2.235	1.00
59_A	63_A	2.216	1.00
135_H	138_V	2.014	1.00
64_A	67_A	1.967	1.00
79_T	147_V	1.914	1.00
66_N	70_E	1.9	1.00
101_D	105_A	1.883	1.00
67_A	71_K	1.882	1.00
103_V	110_V	1.878	1.00
81_A	147_V	1.842	1.00
79_T	145_N	1.8	1.00
65_A	135_H	1.793	1.00
41_K	45_E	1.785	1.00
70_E	73_N	1.745	1.00
45_E	48_E	1.742	1.00
55_E	59_A	1.708	1.00
5_L	19_V	1.648	1.00
63_A	66_N	1.634	1.00
100_A	115_V	1.619	1.00
48_E	51_R	1.615	1.00
66_N	69_A	1.604	1.00
18_Q	44_I	1.57	1.00
67_A	70_E	1.51	1.00
70_E	74_A	1.499	1.00
82_S	94_I	1.488	1.00
69_A	140_A	1.472	1.00
60_E	64_A	1.442	1.00
9_V	35_K	1.436	1.00
56_A	60_E	1.402	0.99
122_L	144_V	1.4	0.99
30_L	36_A	1.392	0.99
78_V	103_V	1.39	0.99
63_A	67_A	1.381	0.99
99_I	130_V	1.378	0.99
78_V	102_A	1.328	0.99
80_I	102_A	1.25	0.99
2_Q	44_I	1.235	0.98
131_S	139_F	1.223	0.98
26_A	31_V	1.222	0.98
103_V	108_V	1.213	0.98
54_L	58_L	1.212	0.98
131_S	141_K	1.208	0.98
5_L	12_L	1.205	0.98
44_I	48_E	1.193	0.98
82_S	90_L	1.19	0.98
5_L	13_G	1.188	0.98
80_I	94_I	1.185	0.98
73_N	140_A	1.184	0.98
122_L	146_V	1.167	0.97
99_I	117_L	1.164	0.97
133_Q	139_F	1.15	0.97
130_V	144_V	1.149	0.97
51_R	54_L	1.145	0.97
42_K	45_E	1.138	0.97
4_I	43_N	1.137	0.97
62_L	135_H	1.133	0.97
29_F	35_K	1.117	0.96
3_V	26_A	1.111	0.96
4_I	47_F	1.106	0.96
99_I	144_V	1.105	0.96
8_K	14_S	1.097	0.96
96_T	115_V	1.09	0.96
68_R	114_E	1.085	0.96
76_E	106_A	1.075	0.95
31_V	34_G	1.075	0.95
52_A	55_E	1.073	0.95
1_M	26_A	1.065	0.95
2_Q	18_Q	1.061	0.95
6_L	37_V	1.046	0.94
42_K	46_F	1.044	0.94
46_F	50_R	1.043	0.94
74_A	77_T	1.031	0.94
43_N	46_F	1.031	0.94
71_K	76_E	1.027	0.94
12_L	19_V	1.019	0.93
62_L	137_E	1.016	0.93

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
3r8sH	1	0.9933	100	0.036	Contact Map	0.645
1divA	1	0.9866	100	0.041	Contact Map	0.716
3bboJ	1	0.9799	100	0.055	Contact Map	0.491
3v2dI	1	0.9799	100	0.058	Contact Map	0.66
1nkwF	1	0.9732	100	0.065	Contact Map	0.106
2hbaA	2	0.349	99.9	0.555	Contact Map	0.84
4kixH	1	0.3356	99.8	0.565	Contact Map	0.694
3pxgA	6	0.7114	47.3	0.925	Contact Map	0.423
1m55A	2	0.4497	26.5	0.935	Contact Map	0.232
1qzmA	1	0.5168	14.9	0.942	Contact Map	0.182

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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