RIMM - ECOLI - GREMLIN Contacts

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RIMM - Ribosome maturation factor RimM

UniProt:	P0A7X6	Sequences: MSKQLTAQAPVDPIVLGKMGSSYGIRGWLRVFSSTEDAESIFDYQPWFIQKAGQWQQVQLESWKHHNQDMIIKLKGVDDRDAANLLTNCEIVVDSSQLPQLEEGDYYWKDLMGCQVVTTEGYDLGKVVDMMETGSNDVLVIKANLKDAFGIKERLVPFLDGQVIKKVDLTTRSIEVDWDPGF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11153
Length:	182 (163)
Sequences:	3751 (2838)
Seq/√Len:	222.3

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
115_Q	123_D	3.546	1.00
168_D	171_T	3.479	1.00
117_V	173_S	2.863	1.00
59_Q	75_K	2.692	1.00
61_E	73_K	2.606	1.00
119_T	177_D	2.552	1.00
128_V	142_K	2.421	1.00
79_D	82_A	2.417	1.00
114_C	172_R	2.255	1.00
117_V	123_D	2.142	1.00
166_K	175_E	2.112	1.00
77_V	83_A	2.102	1.00
118_T	122_Y	2.059	1.00
140_V	153_E	2.052	1.00
114_C	169_L	2.027	1.00
22_S	80_R	1.990	1.00
59_Q	76_G	1.895	1.00
73_K	78_D	1.878	1.00
61_E	75_K	1.833	1.00
127_V	174_I	1.824	1.00
115_Q	173_S	1.816	1.00
81_D	84_N	1.800	1.00
28_W	64_K	1.769	1.00
115_Q	126_K	1.767	1.00
15_V	92_V	1.683	1.00
143_A	154_R	1.670	1.00
165_K	177_D	1.631	1.00
15_V	90_E	1.623	1.00
139_L	158_F	1.609	1.00
58_V	74_L	1.603	1.00
80_R	84_N	1.590	1.00
116_V	141_I	1.586	1.00
28_W	73_K	1.547	1.00
108_W	130_M	1.534	1.00
46_P	57_Q	1.532	1.00
21_S	87_T	1.517	1.00
29_L	74_L	1.448	1.00
19_M	29_L	1.435	1.00
108_W	132_E	1.420	1.00
159_L	163_V	1.418	1.00
22_S	84_N	1.403	1.00
18_K	90_E	1.395	1.00
94_D	97_Q	1.376	1.00
95_S	109_K	1.376	1.00
143_A	150_G	1.355	1.00
78_D	82_A	1.347	1.00
84_N	87_T	1.347	1.00
31_V	72_I	1.318	1.00
132_E	137_D	1.278	1.00
23_Y	71_I	1.273	1.00
50_Q	90_E	1.272	1.00
117_V	175_E	1.272	1.00
159_L	162_Q	1.272	1.00
18_K	32_F	1.260	1.00
82_A	85_L	1.252	1.00
50_Q	89_C	1.249	1.00
37_D	40_S	1.246	1.00
112_M	129_D	1.240	1.00
110_D	169_L	1.233	1.00
102_E	105_D	1.229	1.00
114_C	174_I	1.221	1.00
29_L	72_I	1.219	1.00
168_D	173_S	1.210	1.00
116_V	176_V	1.202	1.00
22_S	87_T	1.164	1.00
77_V	86_L	1.153	1.00
123_D	144_N	1.149	1.00
129_D	140_V	1.149	1.00
131_M	140_V	1.148	1.00
118_T	178_W	1.116	1.00
13_P	94_D	1.115	1.00
123_D	126_K	1.101	1.00
29_L	83_A	1.099	1.00
55_W	92_V	1.096	1.00
25_I	80_R	1.095	1.00
127_V	139_L	1.091	1.00
156_V	176_V	1.088	1.00
126_K	142_K	1.086	1.00
30_R	69_D	1.077	1.00
142_K	153_E	1.073	1.00
104_G	160_D	1.063	1.00
21_S	30_R	1.052	1.00
139_L	174_I	1.042	1.00
66_H	71_I	1.034	1.00
144_N	150_G	1.024	1.00
98_L	109_K	1.019	1.00
98_L	107_Y	1.002	1.00
95_S	110_D	0.999	1.00
143_A	152_K	0.996	1.00
20_G	32_F	0.990	1.00
25_I	81_D	0.984	1.00
14_I	95_S	0.984	1.00
133_T	136_N	0.971	1.00
20_G	87_T	0.968	1.00
119_T	165_K	0.962	1.00
62_S	73_K	0.959	1.00
99_P	107_Y	0.939	1.00
131_M	138_V	0.935	1.00
28_W	62_S	0.934	1.00
111_L	139_L	0.931	1.00
63_W	70_M	0.928	1.00
136_N	159_L	0.913	0.99
18_K	34_S	0.906	0.99
127_V	158_F	0.906	0.99
17_G	31_V	0.906	0.99
41_I	44_Y	0.900	0.99
50_Q	92_V	0.898	0.99
51_K	89_C	0.898	0.99
133_T	138_V	0.896	0.99
13_P	48_F	0.890	0.99
141_I	156_V	0.885	0.99
143_A	153_E	0.882	0.99
113_G	126_K	0.878	0.99
23_Y	28_W	0.872	0.99
116_V	156_V	0.871	0.99
58_V	91_I	0.863	0.99
65_H	70_M	0.859	0.99
111_L	127_V	0.858	0.99
95_S	98_L	0.856	0.99
23_Y	30_R	0.856	0.99
169_L	172_R	0.848	0.99
20_G	30_R	0.847	0.99
106_Y	158_F	0.842	0.99
12_D	95_S	0.840	0.99
33_S	70_M	0.831	0.99
156_V	163_V	0.828	0.99
44_Y	47_W	0.824	0.99
140_V	155_L	0.819	0.99
138_V	155_L	0.815	0.99
48_F	57_Q	0.813	0.99
118_T	124_L	0.813	0.99
46_P	97_Q	0.802	0.99
100_Q	103_E	0.793	0.98
166_K	173_S	0.793	0.98
25_I	79_D	0.791	0.98
32_F	69_D	0.787	0.98
20_G	88_N	0.783	0.98
42_F	65_H	0.774	0.98
128_V	153_E	0.770	0.98
128_V	140_V	0.769	0.98
111_L	114_C	0.759	0.98
143_A	151_I	0.758	0.98
64_K	71_I	0.753	0.98
164_I	176_V	0.744	0.98
117_V	121_G	0.743	0.98
81_D	85_L	0.741	0.98
141_I	163_V	0.739	0.98
138_V	163_V	0.724	0.97
121_G	175_E	0.724	0.97
49_I	58_V	0.720	0.97
124_L	178_W	0.719	0.97
14_I	98_L	0.715	0.97
136_N	163_V	0.714	0.97
47_W	91_I	0.713	0.97
115_Q	172_R	0.707	0.97
19_M	74_L	0.706	0.97
34_S	90_E	0.706	0.97
23_Y	64_K	0.701	0.97
35_T	41_I	0.698	0.97
14_I	107_Y	0.681	0.96
43_D	103_E	0.681	0.96
49_I	91_I	0.680	0.96
46_P	59_Q	0.678	0.96
16_L	41_I	0.668	0.96
167_V	174_I	0.664	0.95
82_A	86_L	0.663	0.95
42_F	63_W	0.656	0.95
51_K	54_Q	0.653	0.95
12_D	94_D	0.652	0.95
50_Q	55_W	0.652	0.95
31_V	91_I	0.649	0.95
33_S	41_I	0.638	0.94
150_G	153_E	0.637	0.94
13_P	92_V	0.637	0.94
19_M	31_V	0.635	0.94
40_S	44_Y	0.633	0.94
118_T	176_V	0.633	0.94
106_Y	169_L	0.630	0.94
163_V	178_W	0.628	0.94
158_F	164_I	0.623	0.94
58_V	77_V	0.623	0.94
43_D	100_Q	0.618	0.93
142_K	151_I	0.614	0.93
158_F	174_I	0.614	0.93
28_W	71_I	0.609	0.93
33_S	40_S	0.608	0.93
60_L	63_W	0.607	0.93
17_G	41_I	0.604	0.93
138_V	159_L	0.600	0.92
18_K	88_N	0.597	0.92
36_E	41_I	0.592	0.92
98_L	110_D	0.592	0.92
156_V	164_I	0.589	0.92
51_K	55_W	0.583	0.91
40_S	43_D	0.583	0.91
162_Q	177_D	0.582	0.91
83_A	86_L	0.579	0.91
130_M	139_L	0.577	0.91
131_M	155_L	0.577	0.91
14_I	109_K	0.576	0.91
104_G	110_D	0.575	0.91
29_L	86_L	0.570	0.90
20_G	69_D	0.570	0.90
122_Y	143_A	0.570	0.90
80_R	83_A	0.568	0.90
17_G	34_S	0.567	0.90
48_F	55_W	0.566	0.90
119_T	175_E	0.563	0.90
118_T	180_P	0.557	0.89
47_W	72_I	0.556	0.89
144_N	151_I	0.555	0.89
53_G	56_Q	0.554	0.89
51_K	56_Q	0.552	0.89
42_F	45_Q	0.550	0.89
60_L	72_I	0.550	0.89
141_I	176_V	0.546	0.88
77_V	82_A	0.544	0.88
41_I	45_Q	0.541	0.88
47_W	58_V	0.540	0.88
135_S	159_L	0.540	0.88
159_L	179_D	0.537	0.88
15_V	34_S	0.536	0.87
127_V	130_M	0.535	0.87
47_W	74_L	0.535	0.87
55_W	89_C	0.532	0.87
108_W	129_D	0.529	0.87
137_D	163_V	0.526	0.86
30_R	66_H	0.526	0.86
21_S	88_N	0.523	0.86
106_Y	167_V	0.523	0.86
35_T	38_A	0.522	0.86
175_E	178_W	0.514	0.85
35_T	93_V	0.513	0.85
158_F	167_V	0.511	0.85
39_E	42_F	0.508	0.85
29_L	87_T	0.507	0.84
162_Q	179_D	0.507	0.84
19_M	49_I	0.507	0.84
130_M	158_F	0.506	0.84
114_C	167_V	0.505	0.84
157_P	163_V	0.504	0.84
47_W	60_L	0.501	0.84
134_G	163_V	0.500	0.84
165_K	175_E	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
2qggA	1	0.9451	100	0.084	Contact Map
3h9nA	3	0.9341	100	0.098	Contact Map
2f1lA	2	0.9011	100	0.098	Contact Map
2dyiA	1	0.8791	100	0.185	Contact Map
3htrA	2	0.4396	95.6	0.873	Contact Map
1pm3A	2	0.3681	83.4	0.906	Contact Map
1eysH	1	0.7857	57.9	0.923	Contact Map
3u28C	1	0.5055	54.9	0.924	Contact Map
3j21c	1	0.4725	54.9	0.924	Contact Map
1rzhH	1	0.8846	53.6	0.925	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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