GREMLIN Database
Radical_SAM_C - Radical_SAM C-terminal domain
PFAM: PF16199 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 82 (80)
Sequences: 24223 (15839)
Seq/√Len: 1770.9
META: 0.917

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
18_A64_V3.2791.00
39_A79_E2.8601.00
18_A22_K2.7951.00
20_L25_E2.2981.00
16_P20_L2.2091.00
3_G52_H2.1511.00
70_P73_R2.1081.00
29_L37_L2.1031.00
30_S33_E1.9611.00
71_N74_Q1.7671.00
19_K23_R1.6681.00
28_P65_A1.6591.00
36_D79_E1.5881.00
31_L35_V1.5241.00
8_P69_H1.5121.00
9_L17_L1.5031.00
6_I41_F1.4961.00
13_K18_A1.4851.00
45_L51_I1.4541.00
46_P49_I1.4181.00
40_D44_R1.4061.00
16_P19_K1.3701.00
59_P62_L1.3701.00
40_D43_E1.3131.00
13_K64_V1.2921.00
42_L51_I1.2841.00
11_V26_Y1.2381.00
29_L34_Y1.2301.00
42_L45_L1.2141.00
19_K22_K1.2061.00
8_P55_T1.2051.00
42_L77_E1.1571.00
13_K22_K1.1561.00
39_A43_E1.1101.00
35_V39_A1.0431.00
31_L73_R1.0421.00
36_D39_A1.0321.00
34_Y67_P1.0321.00
21_Y65_A1.0291.00
37_L41_F1.0131.00
11_V18_A1.0031.00
21_Y64_V0.9951.00
29_L33_E0.9931.00
10_L55_T0.9911.00
35_V79_E0.9751.00
73_R77_E0.9691.00
42_L54_L0.9671.00
3_G50_R0.9531.00
58_I63_L0.9471.00
10_L56_G0.9431.00
71_N75_L0.9391.00
11_V21_Y0.9341.00
17_L20_L0.9331.00
60_S70_P0.9311.00
6_I38_V0.9201.00
20_L23_R0.9201.00
37_L40_D0.9151.00
1_P4_V0.8951.00
4_V44_R0.8921.00
69_H75_L0.8591.00
31_L68_W0.8511.00
41_F44_R0.8411.00
72_L75_L0.8081.00
4_V51_I0.8071.00
12_V58_I0.7901.00
35_V76_I0.7871.00
12_V15_T0.7771.00
39_A80_L0.7701.00
60_S63_L0.7611.00
18_A21_Y0.7601.00
34_Y38_V0.7531.00
70_P74_Q0.7521.00
11_V28_P0.7421.00
9_L26_Y0.7331.00
58_I62_L0.7291.00
20_L24_G0.7251.00
8_P56_G0.7221.00
74_Q78_K0.7121.00
42_L80_L0.7121.00
33_E37_L0.7081.00
32_E79_E0.6881.00
3_G55_T0.6731.00
27_K33_E0.6631.00
45_L49_I0.6541.00
74_Q77_E0.6481.00
7_H56_G0.6431.00
21_Y26_Y0.6271.00
22_K64_V0.6261.00
11_V17_L0.6211.00
2_D50_R0.6151.00
39_A76_I0.6101.00
31_L67_P0.6061.00
12_V63_L0.6061.00
10_L69_H0.6061.00
54_L76_I0.6041.00
1_P49_I0.6031.00
36_D40_D0.6001.00
52_H55_T0.6001.00
63_L66_G0.5991.00
43_E47_P0.5841.00
42_L76_I0.5841.00
30_S34_Y0.5831.00
8_P12_V0.5811.00
10_L58_I0.5581.00
31_L34_Y0.5581.00
22_K25_E0.5541.00
76_I80_L0.5531.00
12_V62_L0.5451.00
2_D49_I0.5421.00
31_L69_H0.5401.00
33_E36_D0.5381.00
6_I51_I0.5351.00
10_L63_L0.5311.00
30_S65_A0.5291.00
21_Y28_P0.5261.00
75_L78_K0.5241.00
39_A42_L0.5191.00
70_P75_L0.5191.00
43_E80_L0.5161.00
15_T20_L0.5001.00
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  
1r30A 2 0.9024 30.5 0.867 Contact Map
4wcxA 1 0.9268 16.7 0.882 Contact Map
3d0jA 2 0.561 13.9 0.887 Contact Map
4rtbA 2 0.9024 11.6 0.89 Contact Map
3iixA 1 0.9146 9.2 0.895 Contact Map
3t7vA 1 0.9024 8.5 0.897 Contact Map
1xdxA 2 0.6951 7.8 0.898 Contact Map
1oltA 1 0.9878 6.9 0.901 Contact Map
4mafA 2 0.5854 6.5 0.902 Contact Map
4g1gA 2 0.378 5.9 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.

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