RIMP - ECOLI - GREMLIN Contacts

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RIMP - Ribosome maturation factor RimP

UniProt:	P0A8A8	Sequences: MSTLEQKLTEMITAPVEALGFELVGIEFIRGRTSTLRIYIDSEDGINVDDCADVSHQVSAVLDVEDPITVAYNLEVSSPGLDRPLFTAEHYARFVGEEVTLVLRMAVQNRRKWQGVIKAVDGEMITVTVEGKDEVFALSNIQKANLVPHF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11179
Length:	150 (143)
Sequences:	3224 (2274)
Seq/√Len:	190.2

ECOLI - RIMP
BACSU - RIMP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_K	128_T	2.826	1.00
16_V	54_V	2.758	1.00
13_T	17_E	2.590	1.00
124_M	135_V	2.412	1.00
103_L	113_W	2.396	1.00
88_A	138_L	2.337	1.00
137_A	140_N	2.167	1.00
28_F	36_L	2.158	1.00
25_G	86_F	2.109	1.00
40_I	54_V	1.990	1.00
38_I	58_V	1.952	1.00
126_T	135_V	1.926	1.00
98_E	116_V	1.904	1.00
120_V	138_L	1.877	1.00
12_I	58_V	1.818	1.00
9_T	13_T	1.813	1.00
24_V	90_H	1.807	1.00
95_V	119_A	1.665	1.00
121_D	124_M	1.656	1.00
47_N	50_D	1.646	1.00
61_V	64_V	1.601	1.00
119_A	126_T	1.597	1.00
129_V	132_K	1.580	1.00
87_T	90_H	1.571	1.00
16_V	23_L	1.565	1.00
39_Y	77_S	1.562	1.00
116_V	128_T	1.541	1.00
89_E	92_A	1.535	1.00
22_E	93_R	1.499	1.00
19_L	57_Q	1.495	1.00
128_T	131_G	1.481	1.00
42_S	50_D	1.470	1.00
27_E	37_R	1.435	1.00
52_A	56_H	1.431	1.00
88_A	120_V	1.430	1.00
49_D	52_A	1.428	1.00
121_D	135_V	1.418	1.00
18_A	57_Q	1.414	1.00
24_V	84_P	1.414	1.00
115_G	127_V	1.410	1.00
125_I	141_I	1.399	1.00
7_K	10_E	1.390	1.00
41_D	46_I	1.377	1.00
91_Y	144_A	1.367	1.00
21_F	46_I	1.362	1.00
40_I	46_I	1.357	1.00
99_V	117_I	1.331	1.00
94_F	146_L	1.321	1.00
104_R	142_Q	1.311	1.00
118_K	126_T	1.311	1.00
9_T	87_T	1.295	1.00
105_M	140_N	1.280	1.00
22_E	89_E	1.267	1.00
141_I	144_A	1.267	1.00
60_A	64_V	1.266	1.00
6_Q	10_E	1.242	1.00
99_V	144_A	1.231	1.00
37_R	75_E	1.202	1.00
51_C	55_S	1.194	1.00
11_M	61_V	1.193	1.00
88_A	92_A	1.188	1.00
46_I	78_S	1.186	1.00
19_L	54_V	1.151	1.00
61_V	65_E	1.150	1.00
114_Q	147_V	1.137	1.00
28_F	70_V	1.120	1.00
130_E	133_D	1.115	1.00
12_I	38_I	1.110	1.00
102_V	112_K	1.104	1.00
9_T	23_L	1.088	1.00
81_L	148_P	1.086	1.00
95_V	120_V	1.085	1.00
21_F	50_D	1.081	1.00
30_R	34_S	1.058	1.00
100_T	112_K	1.057	1.00
19_L	53_D	1.055	1.00
105_M	111_R	1.043	1.00
33_T	73_N	1.036	1.00
28_F	34_S	1.035	1.00
103_L	107_V	1.030	1.00
99_V	127_V	1.024	1.00
94_F	97_E	1.022	1.00
8_L	12_I	1.017	1.00
118_K	133_D	1.011	1.00
24_V	94_F	1.010	1.00
121_D	126_T	1.006	1.00
79_P	83_R	0.999	0.99
91_Y	138_L	0.995	0.99
48_V	51_C	0.985	0.99
85_L	90_H	0.980	0.99
98_E	147_V	0.964	0.99
12_I	16_V	0.964	0.99
51_C	78_S	0.963	0.99
15_P	61_V	0.954	0.99
55_S	59_S	0.950	0.99
7_K	65_E	0.949	0.99
100_T	147_V	0.945	0.99
107_V	140_N	0.944	0.99
59_S	63_D	0.927	0.99
58_V	74_L	0.925	0.99
6_Q	9_T	0.921	0.99
27_E	39_Y	0.919	0.99
103_L	136_F	0.907	0.99
34_S	70_V	0.903	0.99
88_A	123_E	0.894	0.99
102_V	143_K	0.893	0.99
100_T	114_Q	0.883	0.99
90_H	93_R	0.881	0.99
21_F	53_D	0.875	0.99
11_M	14_A	0.853	0.98
14_A	17_E	0.848	0.98
123_E	139_S	0.836	0.98
124_M	138_L	0.836	0.98
41_D	93_R	0.828	0.98
16_V	19_L	0.825	0.98
128_T	134_E	0.812	0.98
7_K	67_P	0.803	0.98
91_Y	125_I	0.790	0.97
90_H	146_L	0.776	0.97
54_V	58_V	0.771	0.97
82_D	148_P	0.768	0.97
8_L	26_I	0.760	0.97
42_S	45_G	0.758	0.97
39_Y	86_F	0.755	0.97
43_E	93_R	0.753	0.97
36_L	62_L	0.751	0.96
122_G	138_L	0.736	0.96
130_E	134_E	0.735	0.96
90_H	94_F	0.729	0.96
104_R	111_R	0.728	0.96
11_M	65_E	0.727	0.96
82_D	146_L	0.723	0.96
15_P	57_Q	0.720	0.95
84_P	94_F	0.717	0.95
59_S	74_L	0.704	0.95
129_V	134_E	0.699	0.95
87_T	91_Y	0.699	0.95
101_L	141_I	0.695	0.95
126_T	133_D	0.694	0.95
82_D	147_V	0.688	0.94
23_L	26_I	0.686	0.94
81_L	145_N	0.685	0.94
37_R	77_S	0.685	0.94
50_D	53_D	0.682	0.94
13_T	87_T	0.675	0.94
113_W	136_F	0.674	0.94
5_E	9_T	0.669	0.93
24_V	48_V	0.668	0.93
131_G	134_E	0.668	0.93
92_A	122_G	0.660	0.93
35_T	73_N	0.657	0.93
85_L	146_L	0.655	0.93
84_P	90_H	0.653	0.93
15_P	54_V	0.642	0.92
102_V	142_Q	0.642	0.92
28_F	68_I	0.634	0.91
101_L	127_V	0.630	0.91
91_Y	117_I	0.628	0.91
29_I	35_T	0.627	0.91
30_R	70_V	0.621	0.91
42_S	46_I	0.618	0.90
92_A	119_A	0.617	0.90
145_N	148_P	0.612	0.90
49_D	53_D	0.608	0.90
29_I	37_R	0.605	0.89
71_A	77_S	0.604	0.89
123_E	137_A	0.604	0.89
62_L	72_Y	0.603	0.89
15_P	19_L	0.600	0.89
59_S	66_D	0.600	0.89
86_F	90_H	0.598	0.89
31_G	34_S	0.597	0.89
138_L	144_A	0.594	0.89
85_L	91_Y	0.593	0.88
84_P	144_A	0.586	0.88
88_A	122_G	0.581	0.87
57_Q	60_A	0.580	0.87
81_L	94_F	0.580	0.87
101_L	136_F	0.580	0.87
25_G	39_Y	0.577	0.87
48_V	52_A	0.573	0.87
10_E	14_A	0.570	0.86
91_Y	141_I	0.568	0.86
92_A	95_V	0.564	0.86
115_G	136_F	0.564	0.86
101_L	144_A	0.560	0.85
51_C	146_L	0.558	0.85
32_R	70_V	0.556	0.85
52_A	55_S	0.555	0.85
16_V	20_G	0.552	0.85
62_L	67_P	0.552	0.85
22_E	41_D	0.552	0.85
120_V	125_I	0.550	0.84
129_V	133_D	0.544	0.84
98_E	114_Q	0.540	0.83
89_E	94_F	0.535	0.83
48_V	78_S	0.535	0.83
12_I	54_V	0.535	0.83
33_T	59_S	0.534	0.83
14_A	62_L	0.529	0.82
72_Y	142_Q	0.529	0.82
9_T	16_V	0.528	0.82
22_E	43_E	0.525	0.82
103_L	111_R	0.522	0.81
36_L	72_Y	0.521	0.81
136_F	140_N	0.518	0.81
45_G	51_C	0.516	0.81
82_D	94_F	0.514	0.80
57_Q	61_V	0.514	0.80
117_I	127_V	0.512	0.80
48_V	61_V	0.505	0.79
63_D	67_P	0.505	0.79
22_E	87_T	0.504	0.79
95_V	118_K	0.500	0.78

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
1ib8A	1	0.9933	100	0.069	Contact Map
3pgwB	1	0.3933	70.3	0.907	Contact Map
1y96A	1	0.4467	55.4	0.916	Contact Map
4c92A	1	0.3867	53.9	0.916	Contact Map
3fb9A	1	0.52	52.9	0.917	Contact Map
1m5qA	8	0.3933	41.9	0.922	Contact Map
4m7dA	1	0.36	39.6	0.923	Contact Map
4a53A	1	0.4133	39.4	0.923	Contact Map
4m77A	1	0.3733	39.4	0.923	Contact Map
4f7uG	1	0.3667	38.9	0.924	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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