RIMM - BACSU - GREMLIN Contacts

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RIMM - Ribosome maturation factor RimM

UniProt:	O31740	Sequences: MTKRWFNVGKIVNTHGIKGEVRVISKTDFAEERYKPGNTLYLFMDGRNEPVEVTVNTHRLHKQFHLLQFKERQNLNEVEELKNAIIKVPEEELGELNEGEFYFHEIIGCEVFTEEGELIGKVKEILTPGANDVWVIGRKGKKDALIPYIESVVKHIDVREKKIEIELMEGLIDE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	174 (163)
Sequences:	3819 (2870)
Seq/√Len:	224.8

ECOLI - RIMM
BACSU - RIMM

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
110_E	118_L	3.516	1.00
157_D	160_E	3.493	1.00
112_F	162_K	2.789	1.00
56_N	68_Q	2.637	1.00
54_T	70_K	2.558	1.00
114_E	166_E	2.467	1.00
74_N	77_E	2.417	1.00
123_K	137_G	2.364	1.00
109_C	161_K	2.275	1.00
112_F	118_L	2.235	1.00
72_R	78_V	2.126	1.00
39_T	52_E	2.092	1.00
155_H	164_E	2.064	1.00
109_C	158_V	2.048	1.00
135_V	143_D	2.023	1.00
14_T	75_L	1.966	1.00
113_T	117_E	1.936	1.00
54_T	71_E	1.861	1.00
68_Q	73_Q	1.851	1.00
122_V	163_I	1.846	1.00
110_E	121_K	1.758	1.00
56_N	70_K	1.746	1.00
76_N	79_E	1.743	1.00
20_E	59_R	1.741	1.00
110_E	162_K	1.690	1.00
7_N	85_I	1.654	1.00
7_N	87_K	1.642	1.00
53_V	69_F	1.624	1.00
134_W	148_Y	1.617	1.00
154_K	166_E	1.613	1.00
138_R	144_A	1.601	1.00
20_E	68_Q	1.582	1.00
75_L	79_E	1.542	1.00
29_F	32_E	1.509	1.00
103_F	125_I	1.487	1.00
111_V	136_I	1.486	1.00
21_V	69_F	1.480	1.00
13_N	82_K	1.470	1.00
11_I	21_V	1.439	1.00
90_E	104_H	1.383	1.00
43_F	85_I	1.374	1.00
10_K	85_I	1.373	1.00
89_P	92_E	1.347	1.00
23_V	67_L	1.344	1.00
103_F	127_T	1.335	1.00
14_T	79_E	1.331	1.00
79_E	82_K	1.331	1.00
149_I	152_V	1.315	1.00
112_F	164_E	1.296	1.00
43_F	87_K	1.280	1.00
77_E	80_E	1.270	1.00
127_T	132_D	1.265	1.00
111_V	165_I	1.255	1.00
15_H	66_L	1.254	1.00
10_K	24_I	1.234	1.00
73_Q	77_E	1.217	1.00
107_I	124_E	1.205	1.00
109_C	163_I	1.198	1.00
97_N	100_E	1.191	1.00
14_T	82_K	1.183	1.00
157_D	162_K	1.181	1.00
118_L	139_K	1.159	1.00
146_I	165_I	1.158	1.00
43_F	84_A	1.155	1.00
99_G	150_E	1.148	1.00
42_L	84_A	1.142	1.00
41_Y	52_E	1.137	1.00
105_E	158_V	1.129	1.00
21_V	67_L	1.128	1.00
114_E	154_K	1.125	1.00
72_R	81_L	1.122	1.00
126_L	135_V	1.117	1.00
124_E	135_V	1.109	1.00
94_G	102_Y	1.104	1.00
61_H	66_L	1.101	1.00
50_P	87_K	1.090	1.00
22_R	64_F	1.078	1.00
44_M	84_A	1.077	1.00
134_W	163_I	1.073	1.00
113_T	167_L	1.067	1.00
17_I	76_N	1.059	1.00
17_I	75_L	1.054	1.00
40_L	55_V	1.049	1.00
122_V	134_W	1.049	1.00
21_V	78_V	1.032	1.00
138_R	143_D	1.030	1.00
118_L	121_K	1.028	1.00
12_V	24_I	1.026	1.00
5_W	89_P	1.019	1.00
128_P	131_N	1.011	1.00
13_N	22_R	1.005	1.00
121_K	137_G	0.997	1.00
42_L	53_V	0.989	1.00
137_G	143_D	0.984	1.00
5_W	41_Y	0.984	1.00
27_T	33_R	0.984	1.00
39_T	54_T	0.983	1.00
12_V	82_K	0.969	1.00
20_E	57_T	0.964	1.00
93_L	102_Y	0.951	1.00
93_L	104_H	0.949	1.00
9_G	23_V	0.939	1.00
126_L	133_V	0.925	1.00
43_F	50_P	0.924	1.00
29_F	33_R	0.912	0.99
90_E	105_E	0.905	0.99
42_L	86_I	0.903	0.99
57_T	68_Q	0.895	0.99
136_I	146_I	0.888	0.99
6_F	90_E	0.886	0.99
128_P	133_V	0.886	0.99
106_I	122_V	0.883	0.99
44_M	51_V	0.875	0.99
131_N	149_I	0.874	0.99
122_V	148_Y	0.871	0.99
10_K	26_K	0.865	0.99
106_I	134_W	0.863	0.99
58_H	65_H	0.863	0.99
12_V	22_R	0.860	0.99
25_S	65_H	0.854	0.99
149_I	168_M	0.843	0.99
96_L	100_E	0.837	0.99
90_E	93_L	0.834	0.99
44_M	49_E	0.828	0.99
108_G	121_K	0.828	0.99
60_L	65_H	0.826	0.99
101_F	148_Y	0.825	0.99
135_V	145_L	0.825	0.99
111_V	146_I	0.824	0.99
53_V	86_I	0.819	0.99
15_H	22_R	0.818	0.99
158_V	161_K	0.818	0.99
15_H	20_E	0.811	0.99
133_V	145_L	0.806	0.99
40_L	86_I	0.803	0.99
12_V	83_N	0.791	0.99
146_I	152_V	0.791	0.99
139_K	142_K	0.790	0.98
37_G	40_L	0.788	0.98
113_T	119_I	0.783	0.98
17_I	74_N	0.781	0.98
95_E	98_E	0.780	0.98
40_L	53_V	0.775	0.98
116_G	164_E	0.767	0.98
4_R	90_E	0.747	0.98
155_H	162_K	0.740	0.98
123_K	143_D	0.735	0.98
131_N	152_V	0.735	0.98
133_V	152_V	0.732	0.98
23_V	86_I	0.730	0.97
6_F	93_L	0.724	0.97
20_E	66_L	0.721	0.97
156_I	163_I	0.721	0.97
11_I	69_F	0.718	0.97
123_K	135_V	0.715	0.97
28_D	33_R	0.713	0.97
26_K	85_I	0.712	0.97
39_T	92_E	0.703	0.97
24_I	64_F	0.703	0.97
153_V	165_I	0.696	0.97
136_I	152_V	0.690	0.96
138_R	142_K	0.686	0.96
34_Y	37_G	0.684	0.96
112_F	116_G	0.683	0.96
9_G	34_Y	0.678	0.96
6_F	102_Y	0.668	0.96
138_R	141_K	0.666	0.96
77_E	81_L	0.662	0.96
167_L	170_G	0.660	0.95
59_R	66_L	0.653	0.95
152_V	167_L	0.648	0.95
53_V	72_R	0.645	0.95
106_I	109_C	0.645	0.95
110_E	161_K	0.644	0.95
35_K	58_H	0.644	0.95
35_K	60_L	0.643	0.95
40_L	69_F	0.642	0.95
148_Y	163_I	0.640	0.95
76_N	80_E	0.637	0.95
148_Y	153_V	0.633	0.94
114_E	164_E	0.631	0.94
6_F	104_H	0.630	0.94
11_I	23_V	0.629	0.94
36_P	95_E	0.621	0.94
10_K	83_N	0.620	0.94
33_R	36_P	0.618	0.94
15_H	59_R	0.617	0.94
93_L	105_E	0.613	0.93
101_F	158_V	0.613	0.93
41_Y	92_E	0.610	0.93
50_P	84_A	0.605	0.93
151_S	166_E	0.604	0.93
11_I	42_L	0.598	0.92
41_Y	50_P	0.590	0.92
5_W	87_K	0.588	0.92
133_V	149_I	0.588	0.92
99_G	105_E	0.584	0.92
113_T	165_I	0.579	0.91
43_F	48_N	0.572	0.91
146_I	153_V	0.569	0.91
125_I	134_W	0.566	0.90
21_V	81_L	0.565	0.90
55_V	58_H	0.565	0.90
78_V	81_L	0.564	0.90
30_A	34_Y	0.561	0.90
119_I	167_L	0.560	0.90
4_R	89_P	0.560	0.90
148_Y	156_I	0.553	0.89
41_Y	87_K	0.550	0.89
151_S	168_M	0.547	0.89
55_V	67_L	0.546	0.89
27_T	30_A	0.546	0.89
137_G	141_K	0.544	0.88
33_R	37_G	0.541	0.88
144_A	168_M	0.541	0.88
35_K	38_N	0.541	0.88
126_L	145_L	0.538	0.88
101_F	156_I	0.536	0.88
132_D	152_V	0.535	0.88
21_V	82_K	0.534	0.88
8_V	40_L	0.532	0.87
122_V	125_I	0.532	0.87
7_N	10_K	0.531	0.87
23_V	58_H	0.531	0.87
164_E	167_L	0.530	0.87
113_T	116_G	0.528	0.87
130_A	149_I	0.527	0.87
75_L	78_V	0.526	0.87
8_V	33_R	0.525	0.87
36_P	98_E	0.524	0.87
8_V	34_Y	0.524	0.87
72_R	77_E	0.522	0.86
22_R	61_H	0.522	0.86
32_E	35_K	0.521	0.86
152_V	168_M	0.518	0.86
9_G	26_K	0.516	0.86
109_C	156_I	0.515	0.86
102_Y	105_E	0.515	0.86
51_V	72_R	0.514	0.86
154_K	164_E	0.511	0.85
44_M	50_P	0.510	0.85
56_N	73_Q	0.508	0.85
147_P	152_V	0.502	0.84
11_I	84_A	0.500	0.84

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
3h9nA	3	0.9655	100	0.058	Contact Map
2qggA	1	0.9598	100	0.083	Contact Map
2f1lA	2	0.9195	100	0.084	Contact Map
2dyiA	1	0.9023	100	0.138	Contact Map
3htrA	2	0.4598	96.6	0.853	Contact Map
1eysH	1	0.8506	82.9	0.902	Contact Map
1rzhH	1	0.908	80.3	0.904	Contact Map
1vx79	1	0.2529	76.6	0.908	Contact Map
1pm3A	2	0.3851	73.6	0.91	Contact Map
4a18H	1	0.2701	68.1	0.913	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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