RPOH - HALSA - GREMLIN Contacts

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RPOH - DNA-directed RNA polymerase subunit H

UniProt:	P0CX06	Sequences: MVDVSQHELVPEHTVLDEETLDGVLADYDIDRTELPKIKYKDPALPDNAEIGDVVEIVRDSRTTDEAVVYRLVIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	75 (72)
Sequences:	390 (218)
Seq/√Len:	25.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_T	56_E	5.101	1.00
21_L	54_V	4.246	1.00
14_T	58_V	3.429	1.00
10_V	13_H	2.098	0.96
49_A	53_D	1.993	0.95
3_D	47_D	1.939	0.94
61_S	64_T	1.927	0.94
10_V	59_R	1.710	0.90
18_E	22_D	1.665	0.88
45_L	49_A	1.574	0.85
10_V	57_I	1.516	0.83
6_Q	40_Y	1.479	0.81
31_D	57_I	1.424	0.79
40_Y	50_E	1.399	0.78
59_R	63_T	1.397	0.77
45_L	48_N	1.374	0.76
43_P	61_S	1.352	0.75
18_E	31_D	1.324	0.73
10_V	43_P	1.316	0.73
38_I	55_V	1.283	0.71
6_Q	23_G	1.276	0.71
38_I	73_V	1.242	0.68
16_L	70_Y	1.222	0.67
45_L	69_V	1.220	0.67
38_I	59_R	1.211	0.66
16_L	69_V	1.199	0.66
30_I	34_E	1.135	0.61
20_T	23_G	1.134	0.61
30_I	37_K	1.122	0.60
3_D	17_D	1.112	0.60
57_I	69_V	1.106	0.59
17_D	30_I	1.087	0.58
21_L	32_R	1.087	0.58
16_L	24_V	1.055	0.56
5_S	47_D	1.038	0.54
27_D	56_E	1.012	0.52
38_I	72_L	1.009	0.52
48_N	55_V	0.982	0.50
13_H	61_S	0.979	0.50
10_V	61_S	0.929	0.46
23_G	27_D	0.923	0.46
6_Q	47_D	0.915	0.45
35_L	71_R	0.913	0.45
12_E	41_K	0.908	0.45
24_V	30_I	0.883	0.43
25_L	52_G	0.883	0.43
49_A	55_V	0.850	0.41
15_V	53_D	0.841	0.40
24_V	54_V	0.840	0.40
37_K	51_I	0.833	0.40
35_L	70_Y	0.826	0.39
37_K	67_A	0.824	0.39
27_D	66_E	0.820	0.39
4_V	44_A	0.817	0.38
31_D	41_K	0.811	0.38
32_R	53_D	0.798	0.37
43_P	59_R	0.789	0.36
33_T	39_K	0.787	0.36
44_A	55_V	0.786	0.36
9_L	16_L	0.784	0.36
56_E	72_L	0.784	0.36
34_E	45_L	0.771	0.35
37_K	56_E	0.769	0.35
38_I	45_L	0.769	0.35
16_L	21_L	0.757	0.34
59_R	72_L	0.757	0.34
31_D	34_E	0.753	0.34
57_I	68_V	0.729	0.32
4_V	27_D	0.726	0.32
4_V	12_E	0.724	0.32
40_Y	73_V	0.714	0.32
18_E	54_V	0.696	0.30
44_A	47_D	0.677	0.29
5_S	12_E	0.673	0.29
9_L	24_V	0.670	0.29
13_H	43_P	0.666	0.29
52_G	70_Y	0.658	0.28
34_E	54_V	0.635	0.27
15_V	26_A	0.627	0.26
3_D	6_Q	0.625	0.26
45_L	51_I	0.611	0.25
38_I	44_A	0.601	0.25
24_V	27_D	0.594	0.24
61_S	65_D	0.589	0.24
25_L	64_T	0.578	0.24
18_E	30_I	0.570	0.23
23_G	56_E	0.570	0.23
9_L	68_V	0.566	0.23
12_E	58_V	0.563	0.23
59_R	65_D	0.560	0.23
28_Y	56_E	0.559	0.23
14_T	20_T	0.558	0.23
21_L	24_V	0.547	0.22
28_Y	54_V	0.546	0.22
5_S	44_A	0.538	0.22
15_V	33_T	0.536	0.21
21_L	39_K	0.532	0.21
8_E	12_E	0.529	0.21
30_I	33_T	0.528	0.21
10_V	17_D	0.528	0.21
8_E	60_D	0.525	0.21
28_Y	33_T	0.515	0.20
47_D	53_D	0.515	0.20
4_V	34_E	0.512	0.20
33_T	53_D	0.506	0.20
18_E	58_V	0.505	0.20
11_P	70_Y	0.505	0.20
28_Y	67_A	0.500	0.20

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
4qiwH	1	1	100	0.087	Contact Map
1eikA	1	1	100	0.089	Contact Map
3h0gE	1	0.9867	100	0.101	Contact Map
1dzfA	1	0.9867	100	0.101	Contact Map
1hmjA	1	0.8667	100	0.102	Contact Map
4aybH	1	1	100	0.173	Contact Map
2mgvA	1	0.7333	45	0.897	Contact Map
2gu1A	1	0.88	34.9	0.903	Contact Map
4rnzA	1	0.84	31	0.905	Contact Map
2ekdA	5	0.48	23.2	0.911	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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