GREMLIN Database
TraV - Type IV conjugative transfer system lipoprotein (TraV)
PFAM: PF09676 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 134 (127)
Sequences: 1092 (917)
Seq/√Len: 81.4
META: 0.745

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
106_R124_Y2.9631.00
99_R128_V2.9201.00
28_L31_Q2.8121.00
128_V132_G2.7501.00
113_E117_G2.6871.00
111_P122_P2.6791.00
14_M19_A2.5561.00
105_M127_V2.5491.00
15_S18_G2.2871.00
107_V127_V2.1861.00
5_C13_C2.0911.00
114_D120_H2.0821.00
106_R126_Y2.0321.00
102_P119_L1.9371.00
53_A58_A1.8131.00
99_R102_P1.7821.00
121_M126_Y1.7451.00
120_H123_R1.7401.00
55_S64_P1.7271.00
51_S55_S1.7141.00
12_K22_N1.6471.00
100_S130_D1.6291.00
52_S56_G1.6161.00
102_P132_G1.5971.00
97_P126_Y1.5661.00
66_P69_A1.5160.99
19_A110_A1.5160.99
54_A62_G1.5040.99
23_A128_V1.4670.99
59_P65_A1.4430.99
19_A23_A1.4360.99
18_G22_N1.4060.99
120_H128_V1.3960.99
16_V100_S1.3910.99
15_S113_E1.3510.99
11_G14_M1.3380.99
102_P128_V1.3090.98
99_R117_G1.3020.98
101_P104_V1.2860.98
55_S58_A1.2790.98
4_A8_P1.2570.98
118_D127_V1.2440.98
62_G69_A1.2420.98
14_M22_N1.2200.97
64_P70_A1.2140.97
107_V112_W1.2070.97
35_V56_G1.1820.97
109_I123_R1.1810.97
63_A66_P1.1650.97
112_W120_H1.1400.96
99_R113_E1.1350.96
128_V131_P1.1020.95
102_P112_W1.1010.95
110_A120_H1.0950.95
68_A77_Y1.0930.95
58_A68_A1.0920.95
53_A56_G1.0880.95
51_S66_P1.0660.94
114_D118_D1.0650.94
121_M132_G1.0620.94
11_G19_A1.0370.93
16_V132_G1.0330.93
71_G74_D1.0250.93
29_P32_R1.0240.93
102_P133_R1.0180.93
99_R108_W1.0150.93
52_S64_P1.0070.92
102_P106_R0.9960.92
6_K16_V0.9900.92
57_P60_A0.9830.91
107_V124_Y0.9720.91
14_M18_G0.9530.90
61_A65_A0.9510.90
7_A10_G0.9480.90
51_S54_A0.9180.88
108_W124_Y0.9140.88
51_S62_G0.9070.88
57_P61_A0.9060.88
26_G33_K0.8970.87
122_P127_V0.8750.86
12_K19_A0.8740.86
4_A20_Y0.8710.86
12_K16_V0.8710.86
1_S25_A0.8610.85
58_A63_A0.8570.85
51_S57_P0.8470.84
62_G66_P0.8460.84
117_G132_G0.8450.84
76_L80_L0.8440.84
105_M132_G0.8420.84
11_G112_W0.8410.84
112_W132_G0.8400.83
48_A51_S0.8400.83
28_L32_R0.8360.83
81_A84_L0.8270.83
1_S32_R0.8250.82
84_L88_V0.8180.82
52_S59_P0.8160.82
54_A71_G0.8100.81
64_P68_A0.8070.81
58_A64_P0.8020.81
21_A25_A0.8010.80
51_S65_A0.7950.80
68_A75_S0.7930.80
17_S21_A0.7920.80
108_W112_W0.7820.79
1_S9_D0.7810.79
17_S23_A0.7770.78
57_P67_A0.7760.78
17_S126_Y0.7750.78
54_A59_P0.7740.78
1_S99_R0.7730.78
67_A71_G0.7710.78
126_Y132_G0.7580.77
106_R119_L0.7570.77
7_A132_G0.7550.76
104_V127_V0.7340.74
25_A123_R0.7340.74
12_K120_H0.7270.74
109_I125_V0.7200.73
54_A63_A0.7200.73
118_D125_V0.7160.73
121_M127_V0.7130.72
56_G64_P0.7080.72
113_E128_V0.7020.71
127_V132_G0.6940.70
112_W123_R0.6940.70
45_T49_A0.6860.69
47_G55_S0.6840.69
85_E88_V0.6750.68
83_L88_V0.6730.68
48_A59_P0.6690.67
15_S22_N0.6690.67
63_A70_A0.6670.67
84_L89_T0.6670.67
53_A63_A0.6650.67
15_S99_R0.6610.66
78_R81_A0.6590.66
60_A64_P0.6570.66
52_S60_A0.6560.66
104_V123_R0.6450.65
110_A123_R0.6430.64
30_S125_V0.6380.64
82_G89_T0.6370.64
105_M124_Y0.6340.63
12_K110_A0.6260.62
107_V126_Y0.6190.61
61_A66_P0.6120.61
103_R125_V0.6020.59
108_W121_M0.5840.57
22_N132_G0.5810.57
100_S121_M0.5780.56
111_P121_M0.5760.56
121_M124_Y0.5760.56
52_S62_G0.5740.56
57_P70_A0.5720.55
23_A123_R0.5690.55
56_G62_G0.5630.54
6_K10_G0.5590.54
9_D104_V0.5580.54
52_S61_A0.5580.54
105_M113_E0.5550.53
16_V98_L0.5530.53
48_A52_S0.5520.53
71_G75_S0.5510.53
51_S56_G0.5480.52
20_Y102_P0.5470.52
11_G20_Y0.5460.52
20_Y98_L0.5450.52
3_F105_M0.5440.52
80_L85_E0.5430.52
4_A121_M0.5360.51
55_S59_P0.5350.51
17_S26_G0.5340.50
61_A64_P0.5330.50
50_V55_S0.5240.49
76_L79_E0.5240.49
20_Y118_D0.5230.49
19_A24_V0.5220.49
24_V131_P0.5210.49
17_S107_V0.5130.48
20_Y105_M0.5120.48
86_A89_T0.5100.47
98_L103_R0.5090.47
44_T53_A0.5070.47
28_L33_K0.5060.47
99_R132_G0.5050.47
55_S68_A0.5020.46
27_N31_Q0.5010.46
60_A66_P0.5000.46
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  
1xi7A 1 0.1343 4.1 0.925 Contact Map
3ic3A 4 0.3433 3.7 0.927 Contact Map
3afhA 1 0.2164 2.7 0.932 Contact Map
1ffyA 1 0.4254 2 0.936 Contact Map
1y7uA 5 0.2985 1.9 0.937 Contact Map
4ncpA 5 0.2985 1.8 0.938 Contact Map
2b9sA 1 0.9478 1.7 0.938 Contact Map
3bjkA 5 0.291 1.7 0.939 Contact Map
2dybA 1 0.306 1.6 0.94 Contact Map
2i71A 2 0.2463 1.5 0.941 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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