RIMP - BACSU - GREMLIN Contacts

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RIMP - Ribosome maturation factor RimP

UniProt:	P32726	Sequences: MSKKVTDTVQEMAQPIVDSLQLELVDIEFVKEGQSWFLRVFIDSDDGVDIEECAKVSEALSEKLDEADPISQNYFLEVSSPGAERPLKKKADFEKSLGKNVYIKTYEPIDGVKVFEGELAEFDGQTVTVEITIKTRKKRINIPYEKIANARLAVTF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	156 (145)
Sequences:	3271 (2334)
Seq/√Len:	193.8

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
120_A	130_E	2.944	1.00
17_V	56_V	2.755	1.00
14_Q	18_D	2.499	1.00
126_T	141_N	2.459	1.00
105_T	115_F	2.396	1.00
90_K	144_Y	2.307	1.00
143_P	146_K	2.177	1.00
26_D	88_K	2.114	1.00
29_F	38_L	2.067	1.00
40_V	60_L	1.996	1.00
42_I	56_V	1.927	1.00
100_N	118_E	1.889	1.00
122_F	144_Y	1.863	1.00
10_Q	14_Q	1.848	1.00
128_T	141_N	1.824	1.00
25_V	92_D	1.811	1.00
13_A	60_L	1.792	1.00
123_D	126_T	1.685	1.00
41_F	79_S	1.673	1.00
49_D	52_E	1.658	1.00
97_L	121_E	1.629	1.00
121_E	128_T	1.622	1.00
63_K	66_E	1.611	1.00
120_A	139_R	1.582	1.00
23_E	95_K	1.544	1.00
20_L	59_A	1.544	1.00
89_K	92_D	1.531	1.00
118_E	130_E	1.528	1.00
17_V	24_L	1.510	1.00
93_F	150_A	1.488	1.00
91_A	94_E	1.481	1.00
130_E	139_R	1.453	1.00
147_I	150_A	1.443	1.00
43_D	48_V	1.433	1.00
90_K	122_F	1.422	1.00
19_S	59_A	1.419	1.00
107_E	146_K	1.417	1.00
28_E	39_R	1.416	1.00
25_V	86_P	1.407	1.00
8_T	11_E	1.402	1.00
44_S	52_E	1.393	1.00
131_I	138_K	1.392	1.00
54_A	58_E	1.389	1.00
128_T	139_R	1.387	1.00
63_K	67_A	1.385	1.00
117_G	129_V	1.375	1.00
51_E	54_A	1.369	1.00
101_V	119_L	1.367	1.00
96_S	152_L	1.355	1.00
42_I	48_V	1.326	1.00
22_L	48_V	1.300	1.00
10_Q	89_K	1.292	1.00
123_D	141_N	1.283	1.00
23_E	91_A	1.270	1.00
106_Y	148_A	1.247	1.00
101_V	150_A	1.247	1.00
39_R	77_E	1.240	1.00
7_D	11_E	1.232	1.00
127_V	147_I	1.225	1.00
53_C	57_S	1.213	1.00
12_M	63_K	1.206	1.00
48_V	80_S	1.205	1.00
120_A	128_T	1.186	1.00
90_K	94_E	1.184	1.00
62_E	66_E	1.174	1.00
20_L	55_K	1.174	1.00
130_E	137_K	1.130	1.00
116_E	153_A	1.127	1.00
132_T	137_K	1.120	1.00
104_K	114_V	1.101	1.00
81_P	85_R	1.099	1.00
97_L	122_F	1.093	1.00
35_S	75_F	1.092	1.00
93_F	144_Y	1.092	1.00
29_F	72_Q	1.087	1.00
102_Y	114_V	1.083	1.00
20_L	56_V	1.080	1.00
96_S	99_K	1.070	1.00
8_T	67_A	1.044	1.00
105_T	109_I	1.029	1.00
29_F	36_W	1.023	1.00
22_L	52_E	1.020	1.00
10_Q	24_L	1.012	1.00
50_I	53_C	1.009	1.00
13_A	40_V	1.005	1.00
57_S	61_S	1.001	1.00
101_V	129_V	1.001	1.00
9_V	13_A	1.000	1.00
83_A	154_V	0.991	1.00
102_Y	153_A	0.989	0.99
16_I	63_K	0.985	0.99
123_D	128_T	0.977	0.99
100_N	153_A	0.973	0.99
25_V	96_S	0.972	0.99
53_C	80_S	0.965	0.99
30_V	39_R	0.961	0.99
28_E	41_F	0.940	0.99
32_E	36_W	0.940	0.99
61_S	65_D	0.936	0.99
7_D	10_Q	0.930	0.99
15_P	18_D	0.928	0.99
13_A	17_V	0.923	0.99
104_K	149_N	0.911	0.99
105_T	142_I	0.900	0.99
17_V	20_L	0.896	0.99
36_W	72_Q	0.896	0.99
87_L	92_D	0.889	0.99
31_K	36_W	0.877	0.99
12_M	67_A	0.855	0.99
102_Y	116_E	0.854	0.99
90_K	125_Q	0.853	0.98
60_L	76_L	0.849	0.98
125_Q	145_E	0.834	0.98
109_I	146_K	0.834	0.98
22_L	55_K	0.830	0.98
92_D	95_K	0.828	0.98
9_V	27_I	0.825	0.98
12_M	15_P	0.823	0.98
84_E	154_V	0.818	0.98
32_E	37_F	0.794	0.98
44_S	47_G	0.792	0.98
43_D	95_K	0.786	0.97
30_V	37_F	0.770	0.97
16_I	59_A	0.767	0.97
24_L	27_I	0.765	0.97
103_I	147_I	0.765	0.97
56_V	60_L	0.763	0.97
45_D	95_K	0.757	0.97
86_P	96_S	0.752	0.97
39_R	79_S	0.750	0.97
106_Y	113_K	0.747	0.97
41_F	88_K	0.744	0.96
38_L	64_L	0.743	0.96
61_S	76_L	0.740	0.96
33_G	36_W	0.735	0.96
89_K	93_F	0.727	0.96
124_G	144_Y	0.725	0.96
92_D	152_L	0.725	0.96
93_F	127_V	0.719	0.96
84_E	153_A	0.711	0.95
8_T	69_P	0.710	0.95
84_E	152_L	0.701	0.95
86_P	92_D	0.700	0.95
126_T	144_Y	0.699	0.95
16_I	56_V	0.695	0.95
93_F	119_L	0.695	0.95
32_E	39_R	0.694	0.95
92_D	96_S	0.691	0.95
110_D	140_I	0.683	0.94
52_E	55_K	0.683	0.94
87_L	152_L	0.679	0.94
23_E	45_D	0.663	0.93
31_K	39_R	0.663	0.93
115_F	142_I	0.660	0.93
83_A	151_R	0.657	0.93
6_T	10_Q	0.654	0.93
93_F	147_I	0.649	0.93
37_F	75_F	0.644	0.92
25_V	50_I	0.641	0.92
104_K	148_A	0.637	0.92
131_I	140_I	0.634	0.92
94_E	124_G	0.631	0.92
87_L	93_F	0.626	0.91
94_E	121_E	0.623	0.91
51_E	55_K	0.623	0.91
14_Q	89_K	0.615	0.91
65_D	74_Y	0.613	0.90
88_K	92_D	0.613	0.90
125_Q	143_P	0.609	0.90
103_I	150_A	0.603	0.90
26_D	41_F	0.601	0.90
59_A	62_E	0.601	0.90
103_I	129_V	0.600	0.89
17_V	21_Q	0.599	0.89
59_A	63_K	0.596	0.89
34_Q	72_Q	0.589	0.89
50_I	54_A	0.589	0.89
13_A	56_V	0.586	0.88
73_N	79_S	0.584	0.88
151_R	154_V	0.582	0.88
64_L	74_Y	0.579	0.88
44_S	48_V	0.577	0.88
105_T	113_K	0.577	0.88
29_F	70_I	0.575	0.87
16_I	20_L	0.573	0.87
42_I	53_C	0.562	0.86
110_D	138_K	0.561	0.86
74_Y	148_A	0.556	0.86
53_C	152_L	0.554	0.85
86_P	150_A	0.553	0.85
144_Y	150_A	0.548	0.85
103_I	142_I	0.544	0.84
100_N	116_E	0.541	0.84
84_E	96_S	0.541	0.84
57_S	64_L	0.537	0.84
90_K	124_G	0.537	0.84
23_E	43_D	0.535	0.83
117_G	142_I	0.535	0.83
83_A	96_S	0.534	0.83
11_E	15_P	0.533	0.83
105_T	140_I	0.533	0.83
61_S	68_D	0.530	0.83
48_V	52_E	0.526	0.82
97_L	120_A	0.523	0.82
12_M	70_I	0.521	0.82
23_E	92_D	0.521	0.82
41_F	48_V	0.520	0.82
94_E	97_L	0.519	0.82
53_C	93_F	0.519	0.82
132_T	138_K	0.517	0.81
50_I	63_K	0.516	0.81
91_A	96_S	0.509	0.80
23_E	89_K	0.508	0.80
34_Q	83_A	0.506	0.80
115_F	129_V	0.503	0.80
87_L	95_K	0.501	0.79
126_T	143_P	0.501	0.79
99_K	118_E	0.500	0.79

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	0.9872	100	0.054	Contact Map
3pgwB	1	0.391	68.7	0.908	Contact Map
1y96A	1	0.4551	61.2	0.913	Contact Map
4c92A	1	0.4038	56.6	0.915	Contact Map
4m77A	1	0.391	45.2	0.92	Contact Map
4m7dA	1	0.3782	44.9	0.921	Contact Map
3fb9A	1	0.5256	44.7	0.921	Contact Map
3j1zP	8	0.5577	44.6	0.921	Contact Map
4c92C	1	0.4103	39	0.924	Contact Map
3h90A	3	0.5321	36	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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