RNP4 - SULSO - GREMLIN Contacts

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RNP4 - Ribonuclease P protein component 4

UniProt:	Q97WJ1	Sequences: MRRKNQIKKRIIELIELAYNTAKSGNLELAREYVKLAEMYSRKGKVEIPLKYKRMFCRKCYTPLIIGVTERRRMRSKILIRTCLICNWQRRYVLSGNKRSDKENES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	106 (84)
Sequences:	3028 (2638)
Seq/√Len:	287.8

ECOLI - YAJD INSA1 INSA5 INSA6 SPRT INSA2 INSA3 INSA4 INSA7
HALSA - F2Z681 O51967 RNP4 Q9HSS9 Q9HPK4 Q9HR14 Q9HNY6
SULSO - RNP4 Q97ZR7 Q97XN0 Q97ZR5 Q97XU6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_K	85_I	3.582	1.00
58_R	84_L	3.196	1.00
29_L	32_E	2.762	1.00
60_C	75_R	2.037	1.00
17_L	20_N	2.032	1.00
67_G	93_V	2.013	1.00
85_I	94_L	1.967	1.00
92_Y	95_S	1.958	1.00
60_C	71_R	1.956	1.00
63_P	89_Q	1.861	1.00
83_C	86_C	1.845	1.00
56_F	82_T	1.793	1.00
28_E	31_R	1.793	1.00
59_K	72_R	1.665	1.00
57_C	60_C	1.643	1.00
61_Y	87_N	1.610	1.00
82_T	87_N	1.590	1.00
91_R	95_S	1.586	1.00
71_R	75_R	1.579	1.00
57_C	71_R	1.575	1.00
15_I	18_A	1.570	1.00
29_L	33_Y	1.537	1.00
17_L	21_T	1.440	1.00
82_T	89_Q	1.437	1.00
62_T	90_R	1.433	1.00
69_T	97_N	1.422	1.00
57_C	75_R	1.372	1.00
55_M	60_C	1.276	1.00
45_K	49_P	1.220	1.00
58_R	72_R	1.219	1.00
60_C	64_L	1.210	1.00
14_L	17_L	1.192	1.00
86_C	90_R	1.153	1.00
93_V	97_N	1.149	1.00
57_C	64_L	1.142	1.00
76_S	79_L	1.122	1.00
82_T	85_I	1.100	1.00
18_A	21_T	1.045	1.00
21_T	27_L	1.043	1.00
73_R	80_I	1.032	1.00
27_L	30_A	1.023	1.00
69_T	72_R	1.015	1.00
36_L	42_R	0.987	1.00
23_K	29_L	0.983	1.00
14_L	18_A	0.981	1.00
18_A	23_K	0.977	1.00
77_K	80_I	0.964	1.00
22_A	25_G	0.961	1.00
42_R	46_V	0.929	1.00
86_C	96_G	0.921	1.00
15_I	19_Y	0.883	1.00
14_L	25_G	0.875	1.00
15_I	20_N	0.869	1.00
15_I	21_T	0.865	1.00
32_E	35_K	0.864	1.00
30_A	35_K	0.859	1.00
83_C	90_R	0.852	1.00
16_E	20_N	0.851	1.00
81_R	93_V	0.850	1.00
16_E	21_T	0.847	1.00
54_R	65_I	0.840	1.00
73_R	78_I	0.837	1.00
32_E	42_R	0.834	1.00
25_G	28_E	0.834	1.00
25_G	34_V	0.819	1.00
42_R	45_K	0.802	0.99
19_Y	22_A	0.797	0.99
56_F	63_P	0.788	0.99
79_L	88_W	0.775	0.99
18_A	24_S	0.773	0.99
15_I	22_A	0.769	0.99
35_K	38_E	0.754	0.99
24_S	31_R	0.750	0.99
36_L	40_Y	0.748	0.99
22_A	28_E	0.745	0.99
27_L	37_A	0.732	0.99
84_L	89_Q	0.727	0.99
17_L	22_A	0.717	0.99
29_L	38_E	0.704	0.99
33_Y	36_L	0.704	0.99
62_T	76_S	0.700	0.99
18_A	22_A	0.698	0.99
62_T	71_R	0.696	0.98
73_R	77_K	0.691	0.98
19_Y	27_L	0.669	0.98
28_E	32_E	0.668	0.98
74_M	91_R	0.666	0.98
72_R	82_T	0.663	0.98
79_L	95_S	0.661	0.98
91_R	94_L	0.642	0.97
20_N	25_G	0.630	0.97
24_S	27_L	0.629	0.97
46_V	49_P	0.619	0.97
37_A	42_R	0.614	0.97
66_I	95_S	0.603	0.96
37_A	43_K	0.597	0.96
66_I	70_E	0.590	0.96
64_L	75_R	0.588	0.96
26_N	29_L	0.586	0.96
16_E	49_P	0.585	0.96
94_L	97_N	0.582	0.95
62_T	88_W	0.582	0.95
30_A	33_Y	0.574	0.95
16_E	25_G	0.572	0.95
67_G	77_K	0.570	0.95
26_N	31_R	0.568	0.95
39_M	43_K	0.567	0.95
36_L	44_G	0.563	0.95
30_A	36_L	0.561	0.95
64_L	88_W	0.560	0.94
78_I	90_R	0.560	0.94
18_A	27_L	0.557	0.94
46_V	61_Y	0.553	0.94
20_N	27_L	0.550	0.94
89_Q	92_Y	0.549	0.94
32_E	36_L	0.549	0.94
71_R	76_S	0.549	0.94
20_N	23_K	0.536	0.93
76_S	81_R	0.529	0.93
23_K	37_A	0.527	0.93
29_L	43_K	0.523	0.92
43_K	47_E	0.519	0.92
76_S	80_I	0.517	0.92
26_N	36_L	0.513	0.91
56_F	59_K	0.512	0.91
72_R	85_I	0.500	0.90

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
2kmkA	1	0.7547	99.2	0.417	Contact Map
4x9jA	1	0.7736	99.2	0.422	Contact Map
2ee8A	1	0.9151	99.2	0.422	Contact Map
2dmdA	1	0.8302	99.2	0.424	Contact Map
3w5kB	1	0.8868	99.2	0.426	Contact Map
2m9aA	1	0.7925	99.2	0.432	Contact Map
1x6hA	1	0.6321	99.2	0.434	Contact Map
2lv2A	1	0.7547	99.2	0.434	Contact Map
2ctdA	1	0.8019	99.2	0.435	Contact Map
2n25A	1	0.2736	99.2	0.441	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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