RRF - BACSU - GREMLIN Contacts

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RRF - Ribosome-recycling factor

UniProt:	P81101	Sequences: MSKEVLTQTKEKMEKAIAAYQRELATVRAGRANPSLLDKVTVEYYGAQTPLNQLSSINVPEARMLVITPYDKTAIGDIEKAILKADLGLTPTSDGNMIRIAIPALTEERRKELVKVVKKYAEEAKVAVRNVRRDANDDLKKLEKNGDITEDELRASTEDVQKLTDEYVSKIDSVTKDKEKEIMEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	185 (181)
Sequences:	3567 (2024)
Seq/√Len:	150.4

ECOLI - RRF
BACSU - RRF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_K	96_N	3.045	1.00
121_A	175_T	2.971	1.00
10_K	166_E	2.935	1.00
161_Q	165_D	2.678	1.00
139_L	153_L	2.540	1.00
20_Y	124_A	2.510	1.00
170_K	173_S	2.447	1.00
61_E	64_M	2.347	1.00
169_S	173_S	2.267	1.00
20_Y	24_L	2.230	1.00
158_E	162_K	2.134	1.00
166_E	170_K	2.106	1.00
107_E	111_K	1.980	1.00
83_L	90_T	1.977	1.00
143_E	153_L	1.953	1.00
69_P	78_I	1.929	1.00
121_A	171_I	1.904	1.00
128_V	171_I	1.873	1.00
75_I	93_S	1.872	1.00
9_T	135_A	1.853	1.00
176_K	180_K	1.846	1.00
36_L	102_I	1.839	1.00
173_S	177_D	1.808	1.00
180_K	184_E	1.786	1.00
7_T	10_K	1.772	1.00
66_V	97_M	1.740	1.00
14_E	170_K	1.714	1.00
109_R	112_E	1.711	1.00
136_N	160_V	1.674	1.00
27_V	117_V	1.667	1.00
10_K	14_E	1.665	1.00
54_L	74_A	1.658	1.00
41_T	48_Q	1.647	1.00
155_A	159_D	1.590	1.00
74_A	77_D	1.589	1.00
58_N	66_V	1.577	1.00
14_E	167_Y	1.565	1.00
64_M	101_A	1.553	1.00
44_Y	49_T	1.550	1.00
11_E	15_K	1.542	1.00
139_L	160_V	1.534	1.00
133_R	137_D	1.528	1.00
153_L	157_T	1.518	1.00
40_V	85_A	1.489	1.00
162_K	165_D	1.483	1.00
143_E	150_E	1.476	1.00
121_A	125_K	1.469	1.00
79_E	93_S	1.463	1.00
43_E	48_Q	1.441	1.00
17_I	174_V	1.425	1.00
176_K	179_E	1.401	1.00
167_Y	170_K	1.396	1.00
26_T	39_K	1.378	1.00
89_L	102_I	1.368	1.00
107_E	183_M	1.363	1.00
5_V	135_A	1.348	1.00
44_Y	74_A	1.344	1.00
50_P	53_Q	1.344	1.00
10_K	167_Y	1.339	1.00
119_K	123_E	1.328	1.00
21_Q	174_V	1.314	1.00
8_Q	12_K	1.309	1.00
148_I	153_L	1.287	1.00
37_L	65_L	1.287	1.00
173_S	176_K	1.274	1.00
136_N	140_K	1.273	1.00
14_E	18_A	1.254	1.00
113_L	182_I	1.234	1.00
24_L	121_A	1.232	1.00
40_V	81_A	1.226	1.00
12_K	131_V	1.226	1.00
137_D	141_K	1.219	1.00
135_A	160_V	1.219	1.00
18_A	21_Q	1.217	1.00
23_E	120_Y	1.202	1.00
141_K	145_N	1.198	1.00
10_K	163_L	1.189	1.00
24_L	174_V	1.188	1.00
27_V	120_Y	1.182	1.00
152_E	155_A	1.166	1.00
114_V	179_E	1.141	1.00
117_V	175_T	1.122	0.99
136_N	157_T	1.117	0.99
59_V	65_L	1.101	0.99
89_L	100_I	1.096	0.99
44_Y	71_D	1.095	0.99
13_M	164_T	1.090	0.99
128_V	164_T	1.088	0.99
124_A	171_I	1.087	0.99
34_P	57_I	1.070	0.99
54_L	71_D	1.058	0.99
24_L	175_T	1.057	0.99
21_Q	170_K	1.049	0.99
71_D	74_A	1.047	0.99
165_D	169_S	1.030	0.99
105_L	113_L	1.024	0.99
143_E	146_G	1.000	0.99
6_L	159_D	0.997	0.99
16_A	131_V	0.994	0.99
149_T	153_L	0.981	0.99
92_T	101_A	0.981	0.99
118_K	179_E	0.980	0.99
120_Y	123_E	0.980	0.99
37_L	67_I	0.975	0.99
63_R	104_A	0.966	0.98
177_D	180_K	0.962	0.98
5_V	142_L	0.960	0.98
43_E	77_D	0.947	0.98
5_V	9_T	0.940	0.98
139_L	156_S	0.931	0.98
16_A	127_A	0.928	0.98
19_A	23_E	0.920	0.98
87_L	100_I	0.919	0.98
60_P	66_V	0.913	0.98
20_Y	175_T	0.910	0.98
55_S	69_P	0.907	0.98
94_D	99_R	0.903	0.98
142_L	148_I	0.874	0.97
111_K	183_M	0.874	0.97
15_K	131_V	0.872	0.97
130_N	133_R	0.871	0.97
146_G	149_T	0.870	0.97
138_D	141_K	0.861	0.97
117_V	182_I	0.855	0.97
22_R	25_A	0.853	0.97
128_V	168_V	0.852	0.97
118_K	175_T	0.845	0.96
19_A	22_R	0.842	0.96
163_L	167_Y	0.835	0.96
9_T	13_M	0.834	0.96
49_T	54_L	0.833	0.96
164_T	168_V	0.832	0.96
127_A	131_V	0.832	0.96
140_K	157_T	0.827	0.96
137_D	140_K	0.823	0.96
113_L	116_V	0.822	0.96
34_P	65_L	0.817	0.96
6_L	163_L	0.816	0.96
9_T	163_L	0.810	0.95
114_V	183_M	0.809	0.95
37_L	100_I	0.808	0.95
34_P	59_V	0.807	0.95
79_E	83_L	0.801	0.95
142_L	145_N	0.800	0.95
109_R	113_L	0.794	0.95
82_I	89_L	0.792	0.95
125_K	172_D	0.789	0.95
7_T	11_E	0.783	0.95
43_E	46_G	0.783	0.95
12_K	134_D	0.783	0.95
20_Y	117_V	0.777	0.94
59_V	62_A	0.772	0.94
18_A	22_R	0.771	0.94
59_V	64_M	0.771	0.94
8_Q	11_E	0.769	0.94
124_A	127_A	0.767	0.94
42_V	54_L	0.760	0.94
165_D	168_V	0.755	0.93
68_T	96_N	0.752	0.93
166_E	169_S	0.752	0.93
142_L	147_D	0.751	0.93
17_I	170_K	0.749	0.93
13_M	167_Y	0.747	0.93
54_L	70_Y	0.747	0.93
6_L	160_V	0.744	0.93
169_S	172_D	0.739	0.93
105_L	109_R	0.738	0.93
77_D	80_K	0.733	0.92
21_Q	25_A	0.723	0.92
142_L	156_S	0.722	0.92
6_L	156_S	0.718	0.92
26_T	38_D	0.716	0.91
76_G	84_K	0.714	0.91
16_A	128_V	0.712	0.91
116_V	120_Y	0.712	0.91
6_L	10_K	0.708	0.91
162_K	166_E	0.705	0.91
17_I	128_V	0.702	0.91
26_T	120_Y	0.701	0.91
60_P	64_M	0.693	0.90
87_L	90_T	0.679	0.89
76_G	79_E	0.668	0.88
23_E	123_E	0.666	0.88
56_S	70_Y	0.665	0.88
154_R	157_T	0.665	0.88
49_T	53_Q	0.665	0.88
77_D	84_K	0.657	0.88
20_Y	174_V	0.656	0.87
24_L	117_V	0.651	0.87
27_V	113_L	0.644	0.86
150_E	154_R	0.642	0.86
90_T	101_A	0.640	0.86
167_Y	176_K	0.639	0.86
7_T	14_E	0.638	0.86
52_N	70_Y	0.634	0.86
17_I	21_Q	0.634	0.86
58_N	68_T	0.632	0.85
38_D	52_N	0.631	0.85
138_D	142_L	0.626	0.85
149_T	152_E	0.626	0.85
75_I	94_D	0.622	0.85
40_V	51_L	0.622	0.85
114_V	175_T	0.621	0.84
19_A	127_A	0.614	0.84
80_K	84_K	0.612	0.84
113_L	117_V	0.612	0.84
17_I	167_Y	0.611	0.84
170_K	174_V	0.610	0.83
66_V	99_R	0.609	0.83
70_Y	74_A	0.608	0.83
163_L	166_E	0.608	0.83
17_I	171_I	0.606	0.83
125_K	168_V	0.605	0.83
154_R	158_E	0.601	0.83
159_D	163_L	0.601	0.83
16_A	124_A	0.598	0.82
90_T	100_I	0.591	0.81
16_A	19_A	0.591	0.81
9_T	131_V	0.591	0.81
159_D	162_K	0.590	0.81
35_S	65_L	0.583	0.81
67_I	83_L	0.578	0.80
73_T	76_G	0.578	0.80
42_V	74_A	0.577	0.80
11_E	14_E	0.576	0.80
116_V	119_K	0.575	0.80
101_A	104_A	0.574	0.80
63_R	184_E	0.568	0.79
94_D	97_M	0.565	0.78
14_E	17_I	0.565	0.78
52_N	71_D	0.565	0.78
170_K	177_D	0.565	0.78
20_Y	171_I	0.563	0.78
67_I	78_I	0.561	0.78
133_R	136_N	0.560	0.78
19_A	37_L	0.559	0.78
21_Q	177_D	0.557	0.78
89_L	101_A	0.551	0.77
49_T	71_D	0.549	0.77
114_V	182_I	0.545	0.76
29_A	33_N	0.545	0.76
14_E	163_L	0.542	0.76
25_A	90_T	0.539	0.75
73_T	77_D	0.539	0.75
158_E	161_Q	0.538	0.75
38_D	70_Y	0.535	0.75
76_G	92_T	0.533	0.74
148_I	156_S	0.533	0.74
121_A	172_D	0.532	0.74
37_L	40_V	0.532	0.74
136_N	139_L	0.531	0.74
36_L	87_L	0.531	0.74
29_A	63_R	0.530	0.74
37_L	87_L	0.528	0.74
55_S	74_A	0.526	0.73
44_Y	48_Q	0.526	0.73
32_A	102_I	0.522	0.73
56_S	74_A	0.522	0.73
8_Q	131_V	0.521	0.73
112_E	116_V	0.521	0.73
119_K	180_K	0.518	0.72
174_V	177_D	0.517	0.72
79_E	92_T	0.515	0.72
112_E	119_K	0.513	0.72
69_P	96_N	0.512	0.71
121_A	124_A	0.510	0.71
118_K	136_N	0.510	0.71
110_R	182_I	0.507	0.71
125_K	175_T	0.505	0.70
156_S	159_D	0.505	0.70
114_V	118_K	0.504	0.70
67_I	101_A	0.500	0.70

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
1is1A	1	1	100	-0.033	Contact Map
1dd5A	1	0.9946	100	-0.033	Contact Map
4kddA	1	0.9946	100	-0.033	Contact Map
1iseA	1	0.9946	100	-0.032	Contact Map
1eh1A	1	0.9946	100	-0.024	Contact Map
4gfqA	1	1	100	-0.02	Contact Map
1ge9A	1	0.9784	100	0.012	Contact Map
3lf9A	1	0.6108	100	0.475	Contact Map
1wihA	1	0.4432	100	0.496	Contact Map
3lhpS	1	0.627	99.9	0.534	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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