RPOK - HALSA - GREMLIN Contacts

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

RPOK - DNA-directed RNA polymerase subunit K

UniProt:	Q9HQJ0	Sequences: MSDSQHFSRYEKARIIGARALQVAYGAPVLVDTDQTEPILIAAEEYDADALPFTVRREGT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	60 (53)
Sequences:	173 (72)
Seq/√Len:	9.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_F	55_V	2.682	0.87
16_I	50_A	2.265	0.76
18_A	26_G	2.151	0.72
23_V	29_V	1.975	0.65
18_A	21_L	1.768	0.57
35_Q	44_E	1.744	0.55
33_T	41_I	1.712	0.54
20_A	56_R	1.639	0.51
14_R	21_L	1.558	0.47
26_G	40_L	1.521	0.45
31_V	34_D	1.478	0.43
31_V	38_P	1.469	0.43
30_L	55_V	1.412	0.40
30_L	54_T	1.390	0.40
6_H	10_Y	1.385	0.39
14_R	18_A	1.343	0.38
44_E	48_A	1.320	0.37
24_A	34_D	1.287	0.35
26_G	54_T	1.284	0.35
12_K	30_L	1.282	0.35
10_Y	30_L	1.277	0.35
8_S	37_E	1.273	0.35
18_A	54_T	1.211	0.32
49_D	57_R	1.205	0.32
40_L	48_A	1.144	0.29
12_K	53_F	1.124	0.29
39_I	44_E	1.115	0.28
49_D	53_F	1.080	0.27
7_F	56_R	1.072	0.27
34_D	44_E	1.067	0.27
15_I	54_T	1.058	0.26
20_A	46_Y	1.040	0.26
25_Y	39_I	1.034	0.25
9_R	55_V	0.952	0.23
12_K	46_Y	0.947	0.23
38_P	49_D	0.942	0.22
26_G	53_F	0.884	0.21
13_A	18_A	0.875	0.20
37_E	41_I	0.868	0.20
5_Q	24_A	0.863	0.20
16_I	35_Q	0.862	0.20
25_Y	51_L	0.862	0.20
17_G	22_Q	0.854	0.20
35_Q	41_I	0.847	0.20
12_K	50_A	0.825	0.19
29_V	32_D	0.816	0.19
7_F	53_F	0.815	0.19
8_S	46_Y	0.814	0.19
43_A	47_D	0.791	0.18
16_I	43_A	0.773	0.18
25_Y	43_A	0.759	0.17
15_I	55_V	0.754	0.17
24_A	32_D	0.717	0.16
8_S	23_V	0.693	0.16
23_V	46_Y	0.681	0.15
29_V	33_T	0.679	0.15
27_A	44_E	0.654	0.15
6_H	44_E	0.649	0.14
7_F	31_V	0.636	0.14
40_L	51_L	0.630	0.14
10_Y	38_P	0.625	0.14
14_R	29_V	0.622	0.14
15_I	33_T	0.609	0.14
10_Y	39_I	0.608	0.14
38_P	43_A	0.596	0.13
15_I	22_Q	0.596	0.13
24_A	56_R	0.584	0.13
16_I	56_R	0.579	0.13
35_Q	56_R	0.563	0.13
15_I	28_P	0.550	0.12
32_D	40_L	0.549	0.12
49_D	55_V	0.547	0.12
29_V	37_E	0.536	0.12
32_D	53_F	0.530	0.12
17_G	21_L	0.529	0.12
43_A	48_A	0.527	0.12
5_Q	44_E	0.523	0.12
8_S	22_Q	0.518	0.12
6_H	14_R	0.505	0.12
24_A	46_Y	0.500	0.11

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
1twfF	1	1	99.5	0.487	Contact Map
3h0gF	1	1	99.4	0.507	Contact Map
1qklA	1	1	99.4	0.52	Contact Map
4qiwK	1	0.9167	99.3	0.532	Contact Map
4aybK	1	1	99.2	0.545	Contact Map
4yfkE	1	0.9667	98.1	0.69	Contact Map
2a6hE	1	0.9667	93.9	0.804	Contact Map
4c2mB	1	0.9	32.6	0.888	Contact Map
4qiwB	1	0.9	16.3	0.903	Contact Map
4aybB	1	0.9	15.7	0.904	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.