RPON - HALSA - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

RPON - DNA-directed RNA polymerase subunit N

UniProt:	Q9HQJ1	Sequences: MMVPVRCFSCGTVVGEHWEAFKARAETHDGDEDPADVLDDLGVDRHCCRRMLIAHQDLVDVVSPYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	66 (62)
Sequences:	305 (148)
Seq/√Len:	18.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_R	37_V	2.997	0.99
3_V	52_L	2.648	0.98
18_W	61_V	2.504	0.97
21_F	25_A	2.182	0.93
24_R	40_D	2.137	0.92
24_R	32_E	2.052	0.91
25_A	37_V	1.867	0.86
38_L	53_I	1.659	0.78
32_E	40_D	1.632	0.77
14_V	51_M	1.565	0.74
2_M	55_H	1.563	0.74
13_V	58_L	1.528	0.72
32_E	37_V	1.465	0.69
35_A	39_D	1.427	0.67
12_T	16_E	1.394	0.65
43_V	53_I	1.313	0.60
14_V	52_L	1.236	0.55
19_E	35_A	1.228	0.55
21_F	29_D	1.224	0.54
21_F	33_D	1.174	0.51
45_R	50_R	1.165	0.51
31_D	34_P	1.149	0.50
9_S	54_A	1.090	0.46
3_V	55_H	1.087	0.46
3_V	14_V	1.084	0.46
6_R	45_R	1.060	0.44
32_E	36_D	1.059	0.44
13_V	50_R	1.052	0.44
15_G	21_F	1.045	0.43
13_V	54_A	1.036	0.43
37_V	63_S	1.008	0.41
7_C	10_C	1.004	0.41
22_K	57_D	0.997	0.40
9_S	20_A	0.991	0.40
15_G	43_V	0.990	0.40
3_V	12_T	0.990	0.40
12_T	43_V	0.985	0.40
32_E	52_L	0.962	0.38
23_A	30_G	0.936	0.37
1_M	63_S	0.931	0.36
55_H	65_Y	0.924	0.36
1_M	57_D	0.913	0.35
33_D	36_D	0.906	0.35
23_A	40_D	0.900	0.35
15_G	59_V	0.869	0.33
15_G	37_V	0.868	0.33
39_D	49_R	0.860	0.32
7_C	49_R	0.858	0.32
39_D	64_P	0.850	0.32
19_E	64_P	0.850	0.32
13_V	46_H	0.849	0.32
55_H	58_L	0.841	0.31
53_I	63_S	0.840	0.31
2_M	18_W	0.830	0.31
45_R	65_Y	0.826	0.31
9_S	45_R	0.823	0.30
6_R	50_R	0.813	0.30
54_A	65_Y	0.812	0.30
10_C	49_R	0.809	0.30
13_V	16_E	0.799	0.29
11_G	38_L	0.780	0.28
20_A	23_A	0.775	0.28
23_A	29_D	0.755	0.27
46_H	59_V	0.745	0.26
11_G	39_D	0.738	0.26
24_R	33_D	0.734	0.26
37_V	62_V	0.727	0.26
18_W	53_I	0.690	0.24
60_D	65_Y	0.683	0.23
43_V	54_A	0.674	0.23
16_E	62_V	0.663	0.23
12_T	61_V	0.656	0.22
42_G	56_Q	0.645	0.22
46_H	60_D	0.640	0.22
5_V	64_P	0.634	0.21
21_F	51_M	0.610	0.20
44_D	61_V	0.609	0.20
5_V	50_R	0.600	0.20
14_V	61_V	0.586	0.19
57_D	62_V	0.568	0.19
23_A	44_D	0.560	0.18
8_F	54_A	0.559	0.18
25_A	63_S	0.556	0.18
20_A	29_D	0.554	0.18
30_G	36_D	0.553	0.18
58_L	63_S	0.550	0.18
30_G	43_V	0.550	0.18
45_R	64_P	0.542	0.18
36_D	40_D	0.538	0.18
46_H	61_V	0.537	0.18
13_V	51_M	0.525	0.17
44_D	63_S	0.506	0.16
15_G	45_R	0.500	0.16

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
1twfJ	1	0.9545	100	0.099	Contact Map
4qiwN	1	0.9545	100	0.099	Contact Map
4aybN	1	0.9545	100	0.102	Contact Map
1ef4A	1	0.8333	100	0.203	Contact Map
4ex5A	2	0.8636	26	0.911	Contact Map
4xbaA	2	0.4545	18.6	0.917	Contact Map
3a5yA	2	0.803	17.9	0.917	Contact Map
3a74A	4	0.8636	17.6	0.918	Contact Map
4up7A	2	0.8636	16.9	0.918	Contact Map
4ycuA	3	0.9545	16.5	0.919	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.

Page generated in 0.0048 seconds.