RPOZ - BACSU - GREMLIN Contacts

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RPOZ - DNA-directed RNA polymerase subunit omega

UniProt:	O35011	Sequences: MLDPSIDSLMNKLDSKYTLVTVSARRAREMQIKKDQMIEHTISHKYVGKALEEIDAGLLSFEKEDRE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	67 (63)
Sequences:	301 (186)
Seq/√Len:	23.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
38_I	41_T	3.446	1.00
1_M	6_I	2.813	0.99
30_M	36_Q	2.396	0.98
1_M	16_K	2.344	0.98
37_M	58_L	2.277	0.97
10_M	14_D	2.120	0.96
21_T	31_Q	2.073	0.95
13_L	59_L	1.626	0.84
18_T	61_F	1.621	0.84
2_L	20_V	1.594	0.83
12_K	57_G	1.569	0.82
8_S	11_N	1.543	0.81
44_H	49_K	1.539	0.81
16_K	20_V	1.506	0.79
60_S	63_K	1.399	0.74
2_L	48_G	1.367	0.72
31_Q	49_K	1.365	0.72
1_M	20_V	1.315	0.69
22_V	33_K	1.225	0.64
9_L	25_R	1.196	0.62
6_I	21_T	1.195	0.62
49_K	56_A	1.181	0.61
29_E	60_S	1.179	0.61
29_E	63_K	1.170	0.60
18_T	38_I	1.145	0.58
22_V	57_G	1.123	0.57
11_N	34_K	1.105	0.56
29_E	39_E	1.101	0.55
25_R	42_I	1.072	0.53
13_L	39_E	1.045	0.51
3_D	14_D	1.003	0.48
41_T	48_G	0.984	0.47
49_K	57_G	0.967	0.46
39_E	42_I	0.966	0.46
37_M	41_T	0.965	0.46
23_S	47_V	0.952	0.45
16_K	21_T	0.922	0.43
11_N	32_I	0.919	0.43
11_N	30_M	0.919	0.43
16_K	51_L	0.918	0.42
10_M	54_I	0.884	0.40
39_E	59_L	0.877	0.40
23_S	45_K	0.864	0.39
30_M	37_M	0.862	0.39
6_I	19_L	0.856	0.38
35_D	59_L	0.837	0.37
33_K	57_G	0.825	0.36
29_E	36_Q	0.824	0.36
46_Y	49_K	0.823	0.36
2_L	43_S	0.822	0.36
10_M	24_A	0.821	0.36
3_D	13_L	0.818	0.36
13_L	23_S	0.813	0.35
3_D	48_G	0.797	0.34
39_E	60_S	0.784	0.34
41_T	49_K	0.781	0.33
8_S	59_L	0.780	0.33
27_A	47_V	0.769	0.33
35_D	40_H	0.745	0.31
8_S	55_D	0.738	0.31
24_A	44_H	0.736	0.31
6_I	16_K	0.716	0.30
12_K	41_T	0.705	0.29
10_M	22_V	0.696	0.28
41_T	58_L	0.693	0.28
30_M	35_D	0.691	0.28
3_D	45_K	0.687	0.28
41_T	54_I	0.672	0.27
6_I	48_G	0.672	0.27
6_I	10_M	0.666	0.27
30_M	61_F	0.664	0.27
31_Q	46_Y	0.659	0.26
12_K	43_S	0.645	0.26
3_D	42_I	0.635	0.25
3_D	10_M	0.604	0.23
21_T	34_K	0.588	0.23
58_L	63_K	0.581	0.22
28_R	61_F	0.580	0.22
7_D	50_A	0.573	0.22
22_V	54_I	0.570	0.22
12_K	47_V	0.568	0.22
28_R	47_V	0.566	0.22
25_R	38_I	0.561	0.21
18_T	34_K	0.557	0.21
18_T	41_T	0.553	0.21
48_G	52_E	0.542	0.20
12_K	28_R	0.535	0.20
2_L	59_L	0.525	0.20
18_T	28_R	0.525	0.20
8_S	61_F	0.525	0.20
2_L	6_I	0.522	0.20
21_T	33_K	0.501	0.19
20_V	47_V	0.500	0.19
35_D	54_I	0.500	0.19

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
2a6hE	1	0.9851	99.8	0.351	Contact Map
4aybK	1	1	99.8	0.356	Contact Map
4yfkE	1	0.9701	99.8	0.361	Contact Map
1qklA	1	1	99.7	0.389	Contact Map
3h0gF	1	1	99.6	0.444	Contact Map
1twfF	1	1	99.5	0.494	Contact Map
4qiwK	1	0.8358	99.4	0.522	Contact Map
3rhzA	4	0.806	9.4	0.914	Contact Map
1snnA	2	0.3433	9.2	0.914	Contact Map
4ffjA	2	0.3582	8.5	0.915	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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