OPENSEQ.org - RIMM - ECOLI GREMLIN

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RIMM - Ribosome maturation factor RimM

UniProt:	P0A7X6	Sequence MSKQLTAQAPVDPIVLGKMGSSYGIRGWLRVFSSTEDAESIFDYQPWFIQKAGQWQQVQLESWKHHNQDMIIKLKGVDDRDAANLLTNCEIVVDSSQLPQLEEGDYYWKDLMGCQVVTTEGYDLGKVVDMMETGSNDVLVIKANLKDAFGIKERLVPFLDGQVIKKVDLTTRSIEVDWDPGF	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11153
Length:	182 (172)
Sequences:	1627
Seq/Len:	9.46

RIMM
Paralog alert: 0.00 [within 20: 0.00] - ratio of genomes with paralogs

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
168_D	171_T	4.07	1.00
59_Q	75_K	3.086	1.00
114_C	172_R	2.992	1.00
61_E	73_K	2.895	1.00
115_Q	123_D	2.816	1.00
79_D	82_A	2.802	1.00
127_V	174_I	2.704	1.00
59_Q	76_G	2.575	1.00
117_V	173_S	2.549	1.00
81_D	84_N	2.536	1.00
22_S	80_R	2.301	1.00
140_V	153_E	2.258	1.00
114_C	169_L	2.233	1.00
118_T	122_Y	2.232	1.00
139_L	158_F	2.179	1.00
77_V	83_A	2.137	1.00
128_V	142_K	2.109	1.00
22_S	84_N	2.083	1.00
73_K	78_D	1.966	1.00
19_M	29_L	1.883	1.00
108_W	130_M	1.831	1.00
23_Y	71_I	1.83	1.00
119_T	177_D	1.76	1.00
95_S	109_K	1.75	1.00
159_L	163_V	1.706	1.00
127_V	139_L	1.705	1.00
58_V	74_L	1.677	1.00
117_V	123_D	1.653	1.00
80_R	84_N	1.629	1.00
115_Q	126_K	1.604	1.00
28_W	64_K	1.581	1.00
116_V	176_V	1.572	1.00
61_E	75_K	1.564	1.00
166_K	175_E	1.561	1.00
29_L	74_L	1.554	1.00
15_V	92_V	1.541	1.00
37_D	40_S	1.519	1.00
115_Q	173_S	1.514	1.00
29_L	72_I	1.493	1.00
179_D	182_F	1.468	1.00
95_S	110_D	1.455	1.00
46_P	57_Q	1.428	0.99
168_D	173_S	1.412	0.99
78_D	82_A	1.377	0.99
18_K	90_E	1.369	0.99
127_V	158_F	1.36	0.99
110_D	169_L	1.35	0.99
21_S	87_T	1.321	0.99
84_N	87_T	1.311	0.99
98_L	107_Y	1.305	0.99
165_K	177_D	1.305	0.99
44_Y	47_W	1.3	0.99
116_V	141_I	1.292	0.99
108_W	132_E	1.288	0.99
143_A	154_R	1.262	0.98
20_G	87_T	1.255	0.98
14_I	98_L	1.246	0.98
139_L	174_I	1.245	0.98
28_W	73_K	1.229	0.98
118_T	178_W	1.223	0.98
25_I	81_D	1.219	0.98
141_I	156_V	1.2	0.98
104_G	161_G	1.191	0.98
117_V	175_E	1.19	0.98
94_D	97_Q	1.155	0.97
15_V	90_E	1.154	0.97
133_T	138_V	1.148	0.97
144_N	150_G	1.143	0.97
23_Y	30_R	1.14	0.97
18_K	32_F	1.126	0.96
33_S	41_I	1.108	0.96
82_A	85_L	1.102	0.96
31_V	72_I	1.098	0.95
17_G	31_V	1.094	0.95
132_E	137_D	1.081	0.95
22_S	87_T	1.076	0.95
98_L	109_K	1.067	0.95
99_P	107_Y	1.051	0.94
133_T	136_N	1.031	0.93
66_H	71_I	1.027	0.93
83_A	86_L	1.015	0.92
126_K	142_K	1.008	0.92
29_L	83_A	1.007	0.92
20_G	88_N	1.007	0.92
159_L	179_D	1.006	0.92

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
2qggA	1	0.978	100	0.06	Contact Map	0.755
2f1lA	1	0.9835	100	0.062	Contact Map	0.802
3h9nA	1	0.9396	100	0.072	Contact Map	0.759
2dyiA	1	0.8736	100	0.152	Contact Map	0.747
3htrA	2	0.467	95.7	0.871	Contact Map	0.612
1pm3A	2	0.489	83	0.906	Contact Map	0.573
1eysH	1	0.8462	56.7	0.923	Contact Map	0.656
3j21c	1	0.4725	36.4	0.932	Contact Map	0.545
1rzhH	1	0.8681	29.9	0.935	Contact Map	0.656
3izcj	1	0.2967	24	0.938	Contact Map	0.44

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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