RL9 - BACSU - GREMLIN Contacts

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RL9 - 50S ribosomal protein L9

UniProt:	P37437	Sequences: MKVIFLQDVKGKGKKGEVKNVADGYAHNFLIKKGLAVEANASNISALNGQKQKEKKEAIAELEQAKSLKETLEKLTVELSAKSGEGGRLFGSVTSKQITEQLQKDHNIKVDKRKLELPDGIRALGYTNVPVKLHPEVQAVLKVHVKEEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	149 (145)
Sequences:	3423 (2127)
Seq/√Len:	176.6

ECOLI - RL9
BACSU - RL9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
2_K	20_N	2.909	1.00
62_L	66_K	2.907	1.00
128_N	140_V	2.839	1.00
103_Q	109_K	2.581	1.00
101_Q	104_K	2.299	1.00
126_Y	144_H	2.274	1.00
69_K	73_E	2.261	1.00
7_Q	35_L	2.257	1.00
80_S	146_K	2.239	1.00
128_N	142_K	2.238	1.00
59_I	63_E	2.139	1.00
55_K	59_I	1.909	1.00
100_E	104_K	1.892	1.00
5_F	19_K	1.852	1.00
123_A	127_T	1.848	1.00
70_E	73_E	1.762	1.00
78_E	144_H	1.718	1.00
78_E	146_K	1.717	1.00
66_K	70_E	1.712	1.00
67_S	70_E	1.696	1.00
134_H	137_V	1.691	1.00
67_S	71_T	1.676	1.00
64_Q	67_S	1.676	1.00
63_E	66_K	1.632	1.00
48_N	51_K	1.628	1.00
102_L	110_V	1.582	1.00
76_T	144_H	1.577	1.00
41_A	45_S	1.545	1.00
63_E	67_S	1.509	1.00
65_A	134_H	1.450	1.00
75_L	106_H	1.447	1.00
45_S	48_N	1.444	1.00
9_V	35_L	1.425	1.00
60_A	64_Q	1.415	1.00
121_I	145_V	1.402	1.00
18_V	44_I	1.399	1.00
46_A	50_Q	1.377	1.00
121_I	143_V	1.369	1.00
26_A	31_I	1.353	1.00
130_P	138_Q	1.351	1.00
130_P	140_V	1.339	1.00
76_T	142_K	1.328	1.00
53_K	57_E	1.318	1.00
30_L	36_A	1.313	1.00
81_A	93_V	1.312	1.00
102_L	106_H	1.305	1.00
99_T	115_L	1.305	1.00
126_Y	142_K	1.290	1.00
66_K	69_K	1.288	1.00
129_V	143_V	1.280	1.00
52_Q	55_K	1.272	1.00
81_A	89_L	1.267	1.00
79_L	101_Q	1.265	1.00
69_K	139_A	1.261	1.00
54_E	58_A	1.258	1.00
44_I	48_N	1.251	1.00
132_K	138_Q	1.238	1.00
42_S	46_A	1.227	1.00
5_F	13_G	1.222	1.00
58_A	61_E	1.205	1.00
6_L	37_V	1.198	1.00
77_V	101_Q	1.196	1.00
56_K	60_A	1.194	1.00
2_K	44_I	1.179	1.00
73_E	139_A	1.156	1.00
98_I	117_L	1.156	1.00
2_K	18_V	1.154	1.00
3_V	26_A	1.152	1.00
115_L	131_V	1.136	1.00
116_E	132_K	1.136	1.00
31_I	34_G	1.132	1.00
71_T	75_L	1.123	1.00
53_K	56_K	1.119	1.00
77_V	102_L	1.091	1.00
57_E	61_E	1.075	1.00
8_D	14_K	1.074	1.00
102_L	141_L	1.062	1.00
39_A	44_I	1.057	1.00
5_F	12_K	1.049	1.00
45_S	49_G	1.045	1.00
12_K	19_K	1.043	1.00
18_V	47_L	1.041	1.00
43_N	46_A	1.039	1.00
58_A	62_L	1.035	0.99
29_F	35_L	1.034	0.99
71_T	108_I	1.030	0.99
49_G	52_Q	1.017	0.99
51_K	55_K	1.008	0.99
61_E	64_Q	1.005	0.99
51_K	54_E	0.998	0.99
42_S	45_S	0.997	0.99
70_E	74_K	0.995	0.99
27_H	32_K	0.980	0.99
95_S	115_L	0.976	0.99
4_I	43_N	0.976	0.99
1_M	26_A	0.966	0.99
116_E	130_P	0.943	0.99
83_S	124_L	0.913	0.99
98_I	143_V	0.900	0.99
68_L	114_K	0.887	0.98
98_I	115_L	0.882	0.98
102_L	108_I	0.881	0.98
62_L	136_E	0.871	0.98
47_L	51_K	0.869	0.98
56_K	59_I	0.855	0.98
58_A	134_H	0.855	0.98
79_L	93_V	0.847	0.98
96_K	100_E	0.843	0.98
24_G	29_F	0.834	0.98
49_G	53_K	0.832	0.98
98_I	129_V	0.830	0.98
31_I	38_E	0.826	0.97
12_K	25_Y	0.824	0.97
7_Q	15_K	0.823	0.97
76_T	126_Y	0.823	0.97
8_D	15_K	0.822	0.97
83_S	87_G	0.810	0.97
111_D	114_K	0.807	0.97
117_L	120_G	0.804	0.97
4_I	47_L	0.800	0.97
92_S	122_R	0.800	0.97
37_V	43_N	0.798	0.97
100_E	103_Q	0.793	0.97
12_K	22_A	0.786	0.97
54_E	57_E	0.781	0.96
50_Q	54_E	0.756	0.96
40_N	43_N	0.752	0.96
41_A	44_I	0.750	0.96
73_E	140_V	0.745	0.95
84_G	90_F	0.745	0.95
81_A	97_Q	0.744	0.95
57_E	60_A	0.731	0.95
117_L	129_V	0.730	0.95
72_L	139_A	0.729	0.95
84_G	112_K	0.727	0.95
20_N	23_D	0.726	0.95
79_L	146_K	0.726	0.95
118_P	130_P	0.725	0.95
52_Q	56_K	0.724	0.95
16_G	89_L	0.718	0.94
99_T	103_Q	0.713	0.94
29_F	33_K	0.713	0.94
84_G	88_R	0.704	0.94
133_L	137_V	0.686	0.93
6_L	34_G	0.682	0.93
96_K	112_K	0.676	0.92
87_G	124_L	0.674	0.92
62_L	134_H	0.665	0.92
68_L	108_I	0.664	0.92
99_T	110_V	0.663	0.92
120_G	129_V	0.656	0.91
65_A	137_V	0.654	0.91
83_S	89_L	0.652	0.91
31_I	35_L	0.652	0.91
77_V	143_V	0.652	0.91
77_V	106_H	0.647	0.91
26_A	34_G	0.645	0.91
131_V	141_L	0.645	0.91
72_L	75_L	0.644	0.90
97_Q	100_E	0.643	0.90
21_V	30_L	0.640	0.90
16_G	50_Q	0.629	0.89
55_K	58_A	0.627	0.89
75_L	108_I	0.625	0.89
72_L	108_I	0.624	0.89
81_A	86_G	0.615	0.88
46_A	49_G	0.612	0.88
75_L	141_L	0.608	0.88
4_I	39_A	0.605	0.88
59_I	68_L	0.599	0.87
121_I	129_V	0.599	0.87
29_F	32_K	0.592	0.86
60_A	63_E	0.591	0.86
5_F	36_A	0.588	0.86
47_L	50_Q	0.587	0.86
6_L	50_Q	0.580	0.85
121_I	127_T	0.579	0.85
72_L	102_L	0.571	0.84
75_L	102_L	0.571	0.84
127_T	130_P	0.570	0.84
15_K	54_E	0.567	0.84
12_K	32_K	0.559	0.83
38_E	122_R	0.559	0.83
22_A	36_A	0.558	0.83
1_M	23_D	0.557	0.83
8_D	111_D	0.556	0.83
114_K	131_V	0.554	0.83
14_K	17_E	0.552	0.82
101_Q	143_V	0.546	0.82
3_V	31_I	0.545	0.82
127_T	145_V	0.545	0.82
62_L	137_V	0.544	0.81
40_N	44_I	0.540	0.81
15_K	47_L	0.538	0.81
58_A	135_P	0.536	0.81
1_M	4_I	0.535	0.80
103_Q	107_N	0.535	0.80
24_G	36_A	0.533	0.80
37_V	46_A	0.533	0.80
94_T	138_Q	0.532	0.80
71_T	107_N	0.524	0.79
11_G	19_K	0.523	0.79
12_K	27_H	0.522	0.79
102_L	115_L	0.518	0.78
3_V	10_K	0.517	0.78
47_L	54_E	0.516	0.78
115_L	141_L	0.515	0.78
94_T	120_G	0.514	0.78
84_G	91_G	0.511	0.77
82_K	90_F	0.509	0.77
116_E	129_V	0.507	0.77
9_V	12_K	0.507	0.77
30_L	89_L	0.507	0.77
12_K	29_F	0.506	0.77
44_I	132_K	0.504	0.76
60_A	67_S	0.502	0.76
17_E	51_K	0.501	0.76
110_V	139_A	0.500	0.76

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
1divA	2	1	100	0.031	Contact Map
3bboJ	1	0.9866	100	0.041	Contact Map
4tp9H	1	0.9866	100	0.042	Contact Map
4rb6I	1	0.9799	100	0.044	Contact Map
1nkwF	1	0.349	100	0.059	Contact Map
3j7yH	1	0.3624	100	0.13	Contact Map
2hbaA	3	0.349	99.9	0.551	Contact Map
1vw4G	1	0.302	99.8	0.569	Contact Map
4qjty	1	0.8523	99.8	0.573	Contact Map
3pxgA	3	0.6913	57	0.92	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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