GREMLIN Database
Toprim_C_rpt - Topoisomerase C-terminal repeat
PFAM: PF13368 Sequences:
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_D41_E3.0781.00
38_T41_E2.1321.00
20_Q25_N2.1231.00
11_R20_Q2.0781.00
9_V20_Q2.0561.00
44_E48_L1.9261.00
13_G18_Y1.9021.00
39_L43_L1.8951.00
41_E44_E1.8031.00
1_D21_H1.7101.00
33_D36_T1.7041.00
8_I39_L1.6341.00
29_P32_D1.5481.00
11_R25_N1.5121.00
44_E47_A1.4761.00
6_E22_G1.4761.00
4_T21_H1.4691.00
21_H24_K1.4271.00
26_A46_L1.2801.00
1_D4_T1.2201.00
12_N17_P1.1831.00
3_E47_A1.1461.00
21_H46_L1.1101.00
19_V42_A1.0871.00
6_E21_H1.0821.00
26_A49_P1.0671.00
40_E44_E1.0461.00
10_V19_V0.9981.00
43_L47_A0.9931.00
49_P52_K0.9291.00
26_A45_L0.8781.00
24_K49_P0.8761.00
10_V34_P0.8751.00
49_P53_G0.8721.00
40_E43_L0.8711.00
8_I46_L0.8381.00
2_P43_L0.8141.00
19_V46_L0.8071.00
37_I45_L0.7961.00
37_I41_E0.7951.00
1_D43_L0.7841.00
48_L51_A0.7781.00
12_N35_E0.7751.00
8_I43_L0.7701.00
32_D36_T0.7651.00
20_Q23_E0.7611.00
48_L52_K0.7601.00
29_P33_D0.7321.00
36_T41_E0.7261.00
8_I42_A0.7261.00
47_A50_R0.7091.00
10_V28_L0.7021.00
19_V45_L0.6901.00
28_L37_I0.6771.00
30_K33_D0.6591.00
11_R35_E0.6541.00
12_N34_P0.6521.00
32_D37_I0.6501.00
28_L45_L0.6371.00
47_A51_A0.6341.00
39_L42_A0.6291.00
17_P34_P0.6191.00
29_P48_L0.6171.00
19_V26_A0.6161.00
50_R53_G0.6141.00
24_K50_R0.6021.00
21_H43_L0.5901.00
12_N25_N0.5871.00
18_Y25_N0.5661.00
18_Y27_S0.5591.00
14_R17_P0.5521.00
21_H50_R0.5491.00
10_V37_I0.5371.00
8_I21_H0.5261.00
10_V17_P0.5231.00
6_E23_E0.5221.00
29_P45_L0.5141.00
33_D41_E0.5131.00
19_V37_I0.5121.00
10_V25_N0.5001.00
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

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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