RNP4 - HALSA - GREMLIN Contacts

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RNP4 - Ribonuclease P protein component 4

UniProt:	Q9HRP7	Sequences: MASIAAERIDRLHTLARAAARTGDDDRAREYVRLARRLAERNRLTLPPAFRRFTCDDCDAVLVPGRNARVRTRSGHVVVTCDCGTHARYPYTG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	93 (75)
Sequences:	9323 (7912)
Seq/√Len:	913.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_D	82_D	3.942	1.00
80_T	86_H	2.800	1.00
27_R	30_E	2.536	1.00
65_G	90_P	2.518	1.00
54_T	80_T	2.235	1.00
61_V	86_H	2.025	1.00
59_D	84_G	1.929	1.00
60_A	85_T	1.905	1.00
80_T	84_G	1.880	1.00
57_D	70_V	1.825	1.00
64_P	67_N	1.806	1.00
17_R	20_A	1.694	1.00
55_C	69_R	1.679	1.00
54_T	61_V	1.677	1.00
64_P	89_Y	1.626	1.00
24_D	27_R	1.555	1.00
58_C	73_R	1.522	1.00
62_L	85_T	1.494	1.00
63_V	88_R	1.481	1.00
56_D	70_V	1.480	1.00
62_L	87_A	1.436	1.00
44_L	70_V	1.425	1.00
63_V	67_N	1.360	1.00
60_A	87_A	1.325	1.00
75_G	88_R	1.310	1.00
69_R	73_R	1.249	1.00
25_D	30_E	1.200	1.00
21_R	24_D	1.180	1.00
30_E	34_L	1.175	1.00
19_A	25_D	1.140	1.00
23_G	27_R	1.124	1.00
18_A	21_R	1.099	1.00
83_C	87_A	1.070	1.00
27_R	34_L	1.056	1.00
37_R	41_R	1.050	1.00
19_A	22_T	1.032	1.00
36_R	39_A	0.996	1.00
18_A	24_D	0.989	1.00
54_T	59_D	0.983	1.00
79_V	90_P	0.962	1.00
26_D	33_R	0.954	1.00
58_C	69_R	0.941	1.00
77_V	88_R	0.932	1.00
20_A	24_D	0.928	1.00
79_V	83_C	0.910	1.00
66_R	91_Y	0.899	1.00
71_R	76_H	0.895	1.00
21_R	25_D	0.890	1.00
17_R	24_D	0.879	1.00
19_A	24_D	0.873	1.00
72_T	88_R	0.872	1.00
40_E	43_R	0.869	1.00
51_R	77_V	0.853	1.00
81_C	87_A	0.850	1.00
79_V	86_H	0.830	1.00
18_A	22_T	0.829	1.00
22_T	25_D	0.794	1.00
25_D	28_A	0.776	1.00
34_L	41_R	0.746	1.00
33_R	41_R	0.745	1.00
17_R	21_R	0.744	1.00
72_T	77_V	0.743	1.00
27_R	43_R	0.735	1.00
75_G	78_V	0.732	1.00
28_A	43_R	0.724	1.00
39_A	42_N	0.721	1.00
23_G	26_D	0.719	1.00
72_T	76_H	0.715	1.00
19_A	28_A	0.706	1.00
55_C	73_R	0.704	1.00
74_S	78_V	0.700	1.00
35_A	39_A	0.694	1.00
30_E	40_E	0.692	1.00
78_V	86_H	0.690	1.00
27_R	33_R	0.650	1.00
19_A	23_G	0.648	1.00
58_C	62_L	0.648	1.00
18_A	26_D	0.631	1.00
28_A	56_D	0.630	1.00
18_A	28_A	0.623	1.00
60_A	74_S	0.616	1.00
21_R	27_R	0.614	1.00
34_L	38_L	0.610	1.00
24_D	34_L	0.608	1.00
27_R	40_E	0.607	1.00
41_R	44_L	0.607	1.00
74_S	77_V	0.604	1.00
26_D	29_R	0.604	1.00
31_Y	34_L	0.600	1.00
55_C	58_C	0.599	1.00
71_R	78_V	0.597	1.00
19_A	27_R	0.596	1.00
71_R	75_G	0.587	1.00
26_D	31_Y	0.584	1.00
21_R	26_D	0.581	1.00
25_D	37_R	0.575	1.00
49_A	52_R	0.571	1.00
43_R	47_P	0.570	1.00
62_L	69_R	0.552	1.00
29_R	44_L	0.552	1.00
33_R	36_R	0.542	1.00
72_T	75_G	0.538	1.00
32_V	35_A	0.537	1.00
36_R	40_E	0.534	1.00
39_A	43_R	0.528	1.00
34_L	39_A	0.525	1.00
25_D	34_L	0.523	1.00
20_A	25_D	0.522	1.00
30_E	37_R	0.520	1.00
34_L	40_E	0.514	1.00
49_A	63_V	0.504	1.00
32_V	37_R	0.500	1.00

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
3w5kB	1	0.871	99.1	0.413	Contact Map
4r2qA	1	0.7849	98.9	0.44	Contact Map
2dmdA	1	0.828	98.9	0.449	Contact Map
2ee8A	1	0.9247	98.9	0.452	Contact Map
2kmkA	1	0.7527	98.9	0.454	Contact Map
1tf6A	1	0.8065	98.9	0.456	Contact Map
4x9jA	1	0.7742	98.9	0.458	Contact Map
1ej6B	7	0.8387	98.8	0.465	Contact Map
2cshA	1	0.8387	98.8	0.465	Contact Map
2m9aA	1	0.7849	98.8	0.466	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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