HrpB_C - PFAM28P - GREMLIN Contacts

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HrpB_C - ATP-dependent helicase C-terminal

PFAM:	PF08482	Sequences: WLAPYLAGVRSLADLKRLDLLAALRALLPWEQRRRLDRLAPEHLTVPSGSRIRIDYEADGPPVLAVRLQELFGLAETPRIAGGRVPLLLHLLSPAGRPVQVTRDLAGFWRGSYPEVRKELRGRYPKHPWPEDP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	133 (133)
Sequences:	14917 (8029)
Seq/√Len:	696.2
META:	0.886

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_P	32_Q	3.326	1.00
45_T	51_R	2.651	1.00
63_V	90_H	2.637	1.00
25_R	33_R	2.559	1.00
66_V	71_L	2.344	1.00
19_D	22_A	2.294	1.00
76_E	106_A	2.255	1.00
99_V	120_L	2.211	1.00
43_H	51_R	2.096	1.00
35_R	38_R	2.041	1.00
107_G	111_G	2.011	1.00
65_A	90_H	1.981	1.00
76_E	79_R	1.940	1.00
71_L	74_L	1.935	1.00
35_R	39_L	1.920	1.00
39_L	82_G	1.920	1.00
71_L	89_L	1.897	1.00
21_L	25_R	1.891	1.00
115_E	118_K	1.788	1.00
111_G	114_P	1.777	1.00
106_A	110_R	1.762	1.00
117_R	121_R	1.685	1.00
54_I	62_P	1.660	1.00
77_T	106_A	1.653	1.00
68_L	113_Y	1.653	1.00
18_L	23_A	1.647	1.00
47_P	74_L	1.569	1.00
88_L	103_R	1.566	1.00
117_R	131_E	1.551	1.00
38_R	82_G	1.524	1.00
46_V	52_I	1.513	1.00
25_R	37_D	1.508	1.00
46_V	66_V	1.506	1.00
79_R	86_P	1.500	1.00
67_R	96_G	1.480	1.00
115_E	119_E	1.469	1.00
75_A	110_R	1.445	1.00
54_I	64_L	1.416	1.00
9_V	14_D	1.415	1.00
100_Q	112_S	1.389	1.00
54_I	87_L	1.380	1.00
64_L	89_L	1.357	1.00
34_R	38_R	1.347	1.00
61_P	103_R	1.328	1.00
67_R	128_P	1.320	1.00
5_Y	26_A	1.313	1.00
81_A	85_V	1.313	1.00
107_G	112_S	1.303	1.00
22_A	25_R	1.293	1.00
90_H	101_V	1.285	1.00
10_R	14_D	1.274	1.00
30_W	34_R	1.271	1.00
57_E	60_G	1.259	1.00
32_Q	35_R	1.252	1.00
11_S	14_D	1.246	1.00
52_I	64_L	1.232	1.00
33_R	37_D	1.224	1.00
9_V	18_L	1.218	1.00
58_A	61_P	1.214	1.00
55_D	63_V	1.207	1.00
104_D	107_G	1.117	1.00
116_V	119_E	1.103	1.00
31_E	34_R	1.099	1.00
50_S	70_E	1.092	1.00
48_S	70_E	1.084	1.00
72_F	128_P	1.076	1.00
29_P	33_R	1.059	1.00
66_V	70_E	1.052	1.00
35_R	82_G	1.048	1.00
31_E	35_R	1.027	1.00
44_L	54_I	1.026	1.00
121_R	131_E	1.025	1.00
43_H	53_R	1.016	1.00
114_P	118_K	1.007	1.00
68_L	99_V	1.006	1.00
75_A	106_A	1.006	1.00
71_L	91_L	0.992	1.00
20_L	23_A	0.958	1.00
112_S	116_V	0.947	1.00
13_A	17_R	0.934	1.00
15_L	18_L	0.931	1.00
14_D	17_R	0.922	1.00
44_L	87_L	0.919	1.00
114_P	117_R	0.907	1.00
12_L	15_L	0.905	1.00
22_A	26_A	0.904	1.00
12_L	16_K	0.896	1.00
40_A	85_V	0.888	1.00
5_Y	23_A	0.882	1.00
77_T	89_L	0.880	1.00
30_W	33_R	0.874	1.00
2_L	6_L	0.846	1.00
40_A	81_A	0.846	1.00
86_P	103_R	0.846	1.00
34_R	37_D	0.841	1.00
63_V	88_L	0.840	1.00
55_D	90_H	0.834	1.00
57_E	63_V	0.833	1.00
88_L	101_V	0.828	1.00
55_D	65_A	0.827	1.00
79_R	83_G	0.822	1.00
68_L	72_F	0.814	1.00
112_S	115_E	0.801	1.00
28_L	33_R	0.800	1.00
55_D	58_A	0.794	1.00
110_R	114_P	0.781	1.00
46_V	50_S	0.774	1.00
119_E	122_G	0.760	1.00
118_K	122_G	0.759	1.00
9_V	15_L	0.751	1.00
119_E	123_R	0.745	1.00
48_S	74_L	0.735	1.00
42_E	53_R	0.729	1.00
44_L	74_L	0.729	1.00
96_G	99_V	0.729	1.00
128_P	132_D	0.720	1.00
60_G	103_R	0.720	1.00
93_S	99_V	0.717	1.00
90_H	98_P	0.715	1.00
13_A	16_K	0.715	1.00
16_K	19_D	0.712	1.00
6_L	9_V	0.710	1.00
65_A	96_G	0.700	1.00
65_A	92_L	0.698	1.00
28_L	32_Q	0.683	1.00
9_V	12_L	0.681	1.00
93_S	97_R	0.680	1.00
40_A	80_I	0.661	1.00
28_L	36_L	0.659	1.00
80_I	87_L	0.657	1.00
99_V	116_V	0.654	1.00
52_I	66_V	0.647	1.00
48_S	52_I	0.645	1.00
111_G	115_E	0.639	1.00
23_A	27_L	0.637	1.00
96_G	122_G	0.636	1.00
50_S	96_G	0.632	1.00
5_Y	9_V	0.631	1.00
68_L	71_L	0.628	1.00
130_P	133_P	0.623	1.00
57_E	61_P	0.619	1.00
74_L	89_L	0.619	1.00
93_S	120_L	0.614	1.00
93_S	124_Y	0.613	1.00
36_L	40_A	0.611	1.00
122_G	128_P	0.601	1.00
54_I	63_V	0.599	1.00
77_T	86_P	0.599	1.00
26_A	33_R	0.596	1.00
19_D	25_R	0.591	1.00
121_R	125_P	0.589	1.00
20_L	27_L	0.587	1.00
120_L	125_P	0.586	1.00
31_E	38_R	0.585	1.00
67_R	70_E	0.584	1.00
46_V	64_L	0.584	1.00
18_L	22_A	0.584	1.00
42_E	51_R	0.582	1.00
98_P	101_V	0.579	1.00
20_L	24_L	0.579	1.00
37_D	42_E	0.577	1.00
12_L	20_L	0.576	1.00
60_G	63_V	0.575	1.00
50_S	67_R	0.573	1.00
60_G	88_L	0.572	1.00
39_L	81_A	0.567	1.00
12_L	18_L	0.563	1.00
5_Y	18_L	0.561	1.00
99_V	112_S	0.561	1.00
69_Q	72_F	0.561	1.00
78_P	89_L	0.560	1.00
3_A	7_A	0.560	1.00
112_S	120_L	0.557	1.00
107_G	110_R	0.555	1.00
114_P	119_E	0.554	1.00
55_D	59_D	0.550	1.00
9_V	17_R	0.549	1.00
21_L	42_E	0.547	1.00
46_V	70_E	0.546	1.00
11_S	16_K	0.545	1.00
116_V	121_R	0.544	1.00
4_P	27_L	0.544	1.00
64_L	87_L	0.543	1.00
23_A	26_A	0.539	1.00
68_L	91_L	0.534	1.00
6_L	15_L	0.531	1.00
82_G	85_V	0.530	1.00
115_E	123_R	0.530	1.00
80_I	85_V	0.529	1.00
61_P	88_L	0.527	1.00
105_L	109_W	0.527	1.00
112_S	122_G	0.518	1.00
26_A	30_W	0.511	0.99
100_Q	119_E	0.505	0.99
12_L	17_R	0.505	0.99
22_A	27_L	0.504	0.99
70_E	92_L	0.502	0.99
70_E	128_P	0.501	0.99
48_S	66_V	0.501	0.99
96_G	128_P	0.500	0.99

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
4r0yA	1	0.8496	59.1	0.925	Contact Map
4v194	1	0.3383	21.4	0.942	Contact Map
5afrA	2	0.7444	16.7	0.945	Contact Map
1dwmA	1	0.5038	14.1	0.946	Contact Map
1mitA	1	0.5038	13.1	0.947	Contact Map
1vbwA	1	0.4962	12.2	0.948	Contact Map
4aeeA	1	0.4812	11.4	0.949	Contact Map
3cr8A	4	0.797	11.4	0.949	Contact Map
1v47A	2	0.8421	9.6	0.95	Contact Map
4bhxA	2	0.4211	9.3	0.951	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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