Toprim_C_rpt - PFAM28P - GREMLIN Contacts

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Toprim_C_rpt - Topoisomerase C-terminal repeat

PFAM:	PF13368	Sequences: DPETGEPIVVRNGRFGPYVQHGEKNASLPKGDDPETITLEEALELLALPRAKGGRP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (53)
Sequences:	34287 (15866)
Seq/√Len:	2179.4
META:	0.878

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_D	41_E	3.078	1.00
38_T	41_E	2.132	1.00
20_Q	25_N	2.123	1.00
11_R	20_Q	2.078	1.00
9_V	20_Q	2.056	1.00
44_E	48_L	1.926	1.00
13_G	18_Y	1.902	1.00
39_L	43_L	1.895	1.00
41_E	44_E	1.803	1.00
1_D	21_H	1.710	1.00
33_D	36_T	1.704	1.00
8_I	39_L	1.634	1.00
29_P	32_D	1.548	1.00
11_R	25_N	1.512	1.00
44_E	47_A	1.476	1.00
6_E	22_G	1.476	1.00
4_T	21_H	1.469	1.00
21_H	24_K	1.427	1.00
26_A	46_L	1.280	1.00
1_D	4_T	1.220	1.00
12_N	17_P	1.183	1.00
3_E	47_A	1.146	1.00
21_H	46_L	1.110	1.00
19_V	42_A	1.087	1.00
6_E	21_H	1.082	1.00
26_A	49_P	1.067	1.00
40_E	44_E	1.046	1.00
10_V	19_V	0.998	1.00
43_L	47_A	0.993	1.00
49_P	52_K	0.929	1.00
26_A	45_L	0.878	1.00
24_K	49_P	0.876	1.00
10_V	34_P	0.875	1.00
49_P	53_G	0.872	1.00
40_E	43_L	0.871	1.00
8_I	46_L	0.838	1.00
2_P	43_L	0.814	1.00
19_V	46_L	0.807	1.00
37_I	45_L	0.796	1.00
37_I	41_E	0.795	1.00
1_D	43_L	0.784	1.00
48_L	51_A	0.778	1.00
12_N	35_E	0.775	1.00
8_I	43_L	0.770	1.00
32_D	36_T	0.765	1.00
20_Q	23_E	0.761	1.00
48_L	52_K	0.760	1.00
29_P	33_D	0.732	1.00
36_T	41_E	0.726	1.00
8_I	42_A	0.726	1.00
47_A	50_R	0.709	1.00
10_V	28_L	0.702	1.00
19_V	45_L	0.690	1.00
28_L	37_I	0.677	1.00
30_K	33_D	0.659	1.00
11_R	35_E	0.654	1.00
12_N	34_P	0.652	1.00
32_D	37_I	0.650	1.00
28_L	45_L	0.637	1.00
47_A	51_A	0.634	1.00
39_L	42_A	0.629	1.00
17_P	34_P	0.619	1.00
29_P	48_L	0.617	1.00
19_V	26_A	0.616	1.00
50_R	53_G	0.614	1.00
24_K	50_R	0.602	1.00
21_H	43_L	0.590	1.00
12_N	25_N	0.587	1.00
18_Y	25_N	0.566	1.00
18_Y	27_S	0.559	1.00
14_R	17_P	0.552	1.00
21_H	50_R	0.549	1.00
10_V	37_I	0.537	1.00
8_I	21_H	0.526	1.00
10_V	17_P	0.523	1.00
6_E	23_E	0.522	1.00
29_P	45_L	0.514	1.00
33_D	41_E	0.513	1.00
19_V	37_I	0.512	1.00
10_V	25_N	0.500	1.00

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
3fz4A	1	1	23.1	0.813	Contact Map
3gkxA	2	1	15.6	0.827	Contact Map
3rdwA	1	0.9643	15.4	0.827	Contact Map
2m46A	1	1	15.4	0.828	Contact Map
2mu0A	1	0.9643	14	0.83	Contact Map
1s3cA	2	0.9643	12.5	0.834	Contact Map
2kokA	1	0.9821	12.3	0.835	Contact Map
2gaiA	1	0.5714	11	0.838	Contact Map
3f0iA	1	0.9643	10.7	0.839	Contact Map
3i9v3	1	0.9643	10.1	0.841	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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