GREMLIN Database
VirB3 - Type IV secretory pathway, VirB3-like protein
PFAM: PF05101 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 84 (78)
Sequences: 7800 (4264)
Seq/√Len: 482.8
META: 0.887

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
26_N50_H3.6651.00
22_L53_A3.3671.00
18_V23_F3.2311.00
56_A63_F2.3291.00
26_N49_L2.2901.00
19_P64_F2.2581.00
21_E65_D2.0821.00
62_Q65_D1.9811.00
30_A46_A1.9321.00
50_H54_R1.8251.00
51_G55_L1.6791.00
38_L42_G1.6461.00
12_P62_Q1.6231.00
60_D66_V1.5101.00
18_V50_H1.4951.00
28_T32_A1.4861.00
22_L64_F1.4751.00
23_F50_H1.4741.00
39_S42_G1.4081.00
5_V10_T1.4021.00
68_L72_R1.3991.00
15_L23_F1.3441.00
7_R11_R1.3211.00
18_V26_N1.3191.00
7_R10_T1.3021.00
70_R73_T1.2821.00
36_L39_S1.2381.00
37_G40_L1.2011.00
49_L53_A1.1591.00
18_V54_R1.0981.00
69_L73_T1.0801.00
18_V53_A1.0741.00
19_P57_A1.0581.00
38_L41_W1.0461.00
53_A57_A1.0451.00
54_R58_K1.0391.00
74_R77_V1.0331.00
21_E25_L1.0301.00
56_A59_R1.0101.00
76_R79_N1.0001.00
14_L57_A0.9941.00
44_L48_V0.9881.00
18_V57_A0.9841.00
19_P65_D0.9831.00
70_R74_R0.9781.00
37_G42_G0.9761.00
57_A63_F0.9711.00
14_L19_P0.9031.00
26_N46_A0.8921.00
75_R79_N0.8881.00
43_L47_L0.8861.00
77_V80_R0.8771.00
26_N53_A0.8751.00
45_L49_L0.8701.00
55_L59_R0.8641.00
75_R78_R0.8631.00
74_R80_R0.8541.00
51_G54_R0.8541.00
32_A35_L0.8521.00
3_D6_H0.8391.00
76_R80_R0.8311.00
30_A49_L0.8301.00
3_D7_R0.8291.00
52_V56_A0.8261.00
38_L43_L0.8111.00
74_R78_R0.8001.00
22_L26_N0.7941.00
20_R24_I0.7771.00
26_N30_A0.7471.00
43_L46_A0.7371.00
44_L47_L0.7341.00
13_L20_R0.7221.00
71_L75_R0.7161.00
41_W44_L0.7121.00
42_G46_A0.7061.00
41_W46_A0.6901.00
8_A13_L0.6601.00
62_Q66_V0.6591.00
69_L72_R0.6581.00
3_D10_T0.6541.00
15_L20_R0.6501.00
30_A34_F0.6441.00
21_E68_L0.6371.00
55_L58_K0.6361.00
68_L71_L0.6301.00
38_L44_L0.6200.99
40_L44_L0.6180.99
8_A19_P0.6070.99
69_L74_R0.5990.99
72_R76_R0.5860.99
16_L23_F0.5730.99
23_F27_G0.5680.99
12_P65_D0.5670.99
30_A47_L0.5580.99
16_L50_H0.5550.99
48_V52_V0.5540.99
29_L32_A0.5530.99
36_L44_L0.5530.99
52_V55_L0.5520.99
24_I28_T0.5510.99
14_L18_V0.5500.99
75_R80_R0.5440.99
51_G65_D0.5290.98
13_L16_L0.5280.98
24_I27_G0.5260.98
63_F66_V0.5260.98
37_G41_W0.5250.98
57_A61_P0.5250.98
72_R75_R0.5250.98
26_N29_L0.5220.98
14_L60_D0.5180.98
19_P22_L0.5130.98
59_R63_F0.5110.98
34_F50_H0.5090.98
56_A67_L0.5070.98
69_L75_R0.5070.98
59_R67_L0.5000.98
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  
2w0cP 4 0.0357 3 0.894 Contact Map
2aq4A 1 0.3333 2.4 0.899 Contact Map
3ne5A 3 0.8452 1.6 0.909 Contact Map
3ujzA 2 0.5 1.3 0.913 Contact Map
1m8oB 1 0.2143 1.3 0.913 Contact Map
3hieA 2 0.3333 1.2 0.916 Contact Map
3wu2X 1 0.4524 1.2 0.916 Contact Map
2q2eA 2 0.9405 1.1 0.918 Contact Map
1efpA 1 0.3333 1 0.92 Contact Map
3j7y9 1 0.2143 1 0.92 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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