GREMLIN Database
zf-RVT - zinc-binding in reverse transcriptase
PFAM: PF13966 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 85 (85)
Sequences: 10614 (9176)
Seq/√Len: 995.3
META: 0.637

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
1_F6_A3.1571.00
47_K62_P2.9781.00
51_A59_D2.7751.00
49_N53_R2.6811.00
42_N71_I2.5551.00
72_D77_E2.3471.00
48_D70_T2.1521.00
59_D68_E2.0941.00
48_D68_E2.0371.00
72_D76_F2.0341.00
50_L55_I1.9951.00
39_A75_F1.7991.00
45_P49_N1.7911.00
29_P32_I1.7731.00
49_N52_R1.7711.00
66_E79_P1.6291.00
69_E74_L1.5021.00
46_T74_L1.4901.00
51_A68_E1.3581.00
34_F38_L1.3491.00
4_K8_K1.3451.00
34_F43_R1.3371.00
7_Y11_R1.3261.00
2_S5_S1.3201.00
47_K50_L1.3181.00
8_K11_R1.3171.00
30_P33_K1.3121.00
79_P82_R1.2971.00
11_R14_S1.2971.00
60_L65_G1.2861.00
47_K58_D1.2571.00
51_A57_L1.1871.00
60_L67_E1.1561.00
26_L33_K1.1251.00
35_F44_L1.1201.00
6_A9_L1.1111.00
48_D52_R1.0721.00
30_P34_F1.0501.00
31_K37_W1.0481.00
32_I35_F1.0351.00
38_L45_P1.0231.00
38_L43_R1.0171.00
74_L81_A1.0101.00
63_L80_F1.0061.00
60_L68_E0.9961.00
51_A58_D0.9961.00
20_W23_I0.9921.00
5_S8_K0.9771.00
28_A32_I0.9651.00
61_C64_C0.9491.00
42_N49_N0.9481.00
7_Y10_L0.9461.00
80_F83_E0.9251.00
51_A56_Q0.9141.00
8_K12_G0.8851.00
20_W40_L0.8831.00
70_T77_E0.8751.00
38_L41_H0.8701.00
46_T71_I0.8631.00
1_F7_Y0.8631.00
37_W41_H0.8571.00
45_P55_I0.8321.00
13_G16_S0.8251.00
28_A33_K0.8201.00
47_K51_A0.8121.00
63_L81_A0.7891.00
34_F37_W0.7881.00
9_L12_G0.7751.00
38_L42_N0.7711.00
36_L43_R0.7651.00
82_R85_W0.7641.00
60_L66_E0.7631.00
10_L13_G0.7581.00
45_P53_R0.7511.00
46_T75_F0.7461.00
16_S19_W0.7451.00
11_R15_P0.7381.00
46_T69_E0.7331.00
39_A44_L0.7331.00
39_A71_I0.7201.00
43_R46_T0.7031.00
35_F39_A0.7031.00
48_D51_A0.6991.00
20_W24_W0.6981.00
18_P22_L0.6961.00
51_A54_G0.6961.00
36_L40_L0.6831.00
23_I36_L0.6711.00
47_K59_D0.6691.00
42_N48_D0.6621.00
25_K28_A0.6431.00
62_P80_F0.6371.00
31_K34_F0.6311.00
15_P18_P0.6191.00
17_V20_W0.6171.00
47_K57_L0.6141.00
62_P65_G0.6041.00
47_K69_E0.6011.00
9_L13_G0.5941.00
38_L44_L0.5901.00
23_I29_P0.5881.00
8_K13_G0.5831.00
7_Y25_K0.5821.00
74_L80_F0.5761.00
57_L60_L0.5741.00
43_R49_N0.5621.00
29_P36_L0.5551.00
42_N45_P0.5511.00
39_A46_T0.5491.00
4_K13_G0.5481.00
27_K32_I0.5481.00
1_F63_L0.5431.00
49_N71_I0.5391.00
5_S9_L0.5341.00
50_L56_Q0.5331.00
3_V11_R0.5301.00
22_L26_L0.5241.00
14_S18_P0.5201.00
4_K12_G0.5161.00
9_L14_S0.5141.00
7_Y12_G0.5141.00
30_P43_R0.5061.00
35_F75_F0.5041.00
27_K30_P0.5031.00
21_K25_K0.5021.00
35_F38_L0.5011.00
6_A14_S0.5011.00
77_E80_F0.5001.00
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  
2aklA 1 0.3765 3.6 0.894 Contact Map
3rj2X 1 0.3294 3.4 0.896 Contact Map
3bvoA 1 0.3176 2.7 0.901 Contact Map
3zpvA 2 0.3647 2.4 0.903 Contact Map
4nn2A 1 0.3294 2.2 0.905 Contact Map
3kv4A 1 0.3176 2 0.907 Contact Map
4rv9A 1 0.3765 1.9 0.909 Contact Map
2wx4A 3 0.3765 1.8 0.91 Contact Map
4nxiA 2 0.4235 1.7 0.911 Contact Map
2wx3A 3 0.4 1.7 0.911 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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