RNPA - BACSU - GREMLIN Contacts

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RNPA - Ribonuclease P protein component

UniProt:	P25814	Sequences: MKKRNRLKKNEDFQKVFKHGTSVANRQFVLYTLDQPENDELRVGLSVSKKIGNAVMRNRIKRLIRQAFLEEKERLKEKDYIIIARKPASQLTYEETKKSLQHLFRKSSLYKKSSSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	116 (106)
Sequences:	2120 (1556)
Seq/√Len:	151.2

ECOLI - RNPA
BACSU - RNPA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_R	79_D	3.817	1.00
66_Q	69_L	2.867	1.00
45_L	64_I	2.843	1.00
92_T	95_E	2.820	1.00
25_N	99_S	2.679	1.00
43_V	68_F	2.503	1.00
59_R	63_L	2.455	1.00
58_N	61_K	2.449	1.00
66_Q	70_E	2.203	1.00
35_Q	38_N	2.132	1.00
71_E	101_Q	2.072	1.00
82_I	100_L	2.020	1.00
54_A	58_N	2.012	1.00
13_F	44_G	1.918	1.00
27_Q	91_L	1.837	1.00
10_N	14_Q	1.831	1.00
61_K	65_R	1.792	1.00
25_N	102_H	1.752	1.00
47_V	60_I	1.678	1.00
7_L	16_V	1.668	1.00
35_Q	79_D	1.604	1.00
5_N	40_E	1.599	1.00
67_A	96_T	1.585	1.00
27_Q	99_S	1.565	1.00
70_E	97_K	1.549	1.00
5_N	72_K	1.545	1.00
63_L	96_T	1.539	1.00
97_K	101_Q	1.490	1.00
64_I	82_I	1.460	1.00
34_D	78_K	1.446	1.00
71_E	97_K	1.386	1.00
23_V	32_T	1.373	1.00
15_K	33_L	1.285	1.00
17_F	46_S	1.283	1.00
94_E	97_K	1.257	1.00
71_E	74_R	1.238	1.00
24_A	85_R	1.237	1.00
32_T	78_K	1.203	1.00
91_L	99_S	1.166	1.00
74_R	101_Q	1.135	1.00
24_A	29_V	1.121	0.99
14_Q	18_K	1.102	0.99
32_T	107_S	1.077	0.99
63_L	66_Q	1.027	0.99
35_Q	40_E	0.997	0.99
56_M	60_I	0.993	0.99
67_A	100_L	0.976	0.99
12_D	15_K	0.955	0.98
67_A	93_Y	0.949	0.98
63_L	67_A	0.945	0.98
22_S	29_V	0.944	0.98
43_V	82_I	0.943	0.98
88_A	96_T	0.940	0.98
52_G	56_M	0.928	0.98
54_A	61_K	0.921	0.98
98_K	102_H	0.915	0.98
16_V	33_L	0.911	0.98
51_I	86_K	0.910	0.98
63_L	93_Y	0.901	0.98
93_Y	97_K	0.893	0.97
17_F	83_I	0.890	0.97
46_S	83_I	0.881	0.97
27_Q	87_P	0.878	0.97
28_F	100_L	0.874	0.97
22_S	85_R	0.870	0.97
80_Y	109_L	0.858	0.97
9_K	12_D	0.846	0.96
20_G	33_L	0.840	0.96
60_I	88_A	0.840	0.96
25_N	103_L	0.821	0.96
75_L	104_F	0.818	0.96
30_L	80_Y	0.817	0.96
3_K	8_K	0.814	0.96
23_V	106_K	0.814	0.96
28_F	64_I	0.798	0.95
78_K	109_L	0.790	0.95
31_Y	83_I	0.785	0.95
47_V	61_K	0.782	0.95
84_A	88_A	0.779	0.94
21_T	32_T	0.777	0.94
68_F	72_K	0.773	0.94
56_M	89_S	0.771	0.94
16_V	81_I	0.768	0.94
74_R	105_R	0.767	0.94
17_F	50_K	0.760	0.94
31_Y	85_R	0.755	0.93
30_L	103_L	0.753	0.93
100_L	104_F	0.743	0.93
102_H	106_K	0.739	0.93
41_L	77_E	0.738	0.93
14_Q	46_S	0.732	0.92
67_A	97_K	0.732	0.92
29_V	85_R	0.724	0.92
86_K	89_S	0.719	0.92
25_N	29_V	0.719	0.92
45_L	68_F	0.718	0.92
5_N	41_L	0.717	0.92
48_S	51_I	0.714	0.91
53_N	56_M	0.714	0.91
91_L	96_T	0.713	0.91
47_V	84_A	0.700	0.91
45_L	65_R	0.699	0.91
43_V	80_Y	0.698	0.90
41_L	72_K	0.687	0.90
13_F	65_R	0.683	0.90
4_R	40_E	0.683	0.90
95_E	98_K	0.677	0.89
29_V	51_I	0.675	0.89
76_K	109_L	0.668	0.88
63_L	92_T	0.664	0.88
60_I	89_S	0.663	0.88
46_S	52_G	0.657	0.88
19_H	33_L	0.657	0.88
65_R	100_L	0.657	0.88
74_R	108_S	0.655	0.88
17_F	31_Y	0.654	0.87
58_N	65_R	0.650	0.87
7_L	69_L	0.650	0.87
26_R	95_E	0.636	0.86
3_K	6_R	0.635	0.86
59_R	66_Q	0.631	0.86
12_D	79_D	0.630	0.85
46_S	85_R	0.626	0.85
60_I	84_A	0.615	0.84
102_H	105_R	0.610	0.84
15_K	19_H	0.604	0.83
51_I	56_M	0.597	0.82
67_A	104_F	0.594	0.82
38_N	108_S	0.592	0.82
91_L	95_E	0.591	0.82
77_E	90_Q	0.583	0.81
30_L	107_S	0.580	0.80
15_K	38_N	0.569	0.79
68_F	82_I	0.569	0.79
87_P	91_L	0.564	0.79
104_F	109_L	0.558	0.78
49_K	53_N	0.557	0.78
67_A	71_E	0.555	0.77
30_L	82_I	0.552	0.77
52_G	84_A	0.551	0.77
13_F	43_V	0.544	0.76
51_I	83_I	0.544	0.76
17_F	85_R	0.542	0.76
4_R	43_V	0.537	0.75
28_F	99_S	0.536	0.75
76_K	108_S	0.536	0.75
14_Q	44_G	0.533	0.75
24_A	99_S	0.533	0.75
14_Q	81_I	0.526	0.74
81_I	93_Y	0.520	0.73
16_V	46_S	0.519	0.73
99_S	102_H	0.519	0.73
23_V	103_L	0.518	0.73
6_R	82_I	0.514	0.72
28_F	67_A	0.511	0.71
6_R	43_V	0.508	0.71
34_D	37_E	0.502	0.70
26_R	102_H	0.501	0.70
51_I	89_S	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
4jg4A	1	0.9655	100	0.12	Contact Map
1d6tA	1	0.9914	100	0.136	Contact Map
2ljpA	1	0.9741	100	0.169	Contact Map
1nz0A	4	0.9138	100	0.17	Contact Map
4oxpA	1	0.8793	99	0.657	Contact Map
2bx2L	3	0.7845	69.1	0.882	Contact Map
2j5aA	1	0.3966	14.7	0.92	Contact Map
5aj3F	1	0.3534	12.3	0.923	Contact Map
1cqmA	1	0.3621	11.4	0.924	Contact Map
3uq8A	1	0.4655	8.2	0.929	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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