GREMLIN Database
TraC_F_IV - F pilus assembly Type-IV secretion system for plasmid transfer
PFAM: PF11130 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 237 (231)
Sequences: 2350 (1830)
Seq/√Len: 120.4
META: 0.768

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
31_E122_R4.7081.00
71_D103_D3.9361.00
166_D169_D3.4741.00
19_F167_P3.4171.00
21_N25_S3.2851.00
152_E164_R3.2091.00
13_D16_S2.8671.00
29_V165_L2.8421.00
66_A119_R2.8261.00
163_R169_D2.8181.00
171_I199_L2.7881.00
19_F166_D2.7711.00
165_L169_D2.6841.00
29_V126_S2.5841.00
63_I126_S2.5611.00
210_I219_F2.4541.00
194_D197_R2.4171.00
62_F125_V2.3241.00
170_L174_L2.2911.00
66_A121_F2.2451.00
17_G164_R2.2421.00
74_L99_G2.2391.00
28_F148_R2.2321.00
32_L125_V2.2141.00
152_E162_P2.1541.00
179_N208_T2.1141.00
105_G110_L2.0891.00
67_S176_R2.0461.00
78_R96_R2.0441.00
97_R100_L1.9921.00
12_Y19_F1.9831.00
9_Y170_L1.9601.00
167_P193_Y1.9541.00
92_R96_R1.9461.00
232_L235_F1.9381.00
32_L123_L1.9101.00
30_F162_P1.8901.00
17_G166_D1.8681.00
30_F152_E1.8391.00
9_Y174_L1.8371.00
212_V217_L1.7871.00
62_F123_L1.7811.00
213_E216_G1.7151.00
98_R102_L1.7101.00
12_Y17_G1.6851.00
104_K108_G1.6521.00
25_S128_K1.6371.00
21_N24_G1.6261.00
171_I193_Y1.6251.00
124_F173_W1.6181.00
171_I203_L1.6121.00
19_F165_L1.5671.00
174_L203_L1.5661.00
69_D176_R1.5541.00
99_G103_D1.5301.00
49_L154_T1.4911.00
9_Y21_N1.4791.00
148_R164_R1.4651.00
32_L162_P1.4551.00
31_E124_F1.4151.00
67_S120_D1.4131.00
219_F227_V1.4091.00
100_L104_K1.3871.00
17_G148_R1.3471.00
124_F165_L1.3381.00
77_Y81_R1.3321.00
31_E163_R1.3321.00
78_R99_G1.3261.00
193_Y199_L1.3251.00
70_I74_L1.3101.00
213_E218_R1.3091.00
10_R200_R1.3031.00
28_F127_V1.3001.00
210_I217_L1.2991.00
28_F164_R1.2971.00
180_P225_R1.2671.00
16_S141_L1.2651.00
30_F164_R1.2540.99
218_R226_V1.2460.99
93_A96_R1.2130.99
171_I202_Q1.2080.99
60_L127_V1.2080.99
152_E156_K1.2030.99
193_Y202_Q1.2000.99
10_R22_D1.1910.99
100_L103_D1.1900.99
30_F148_R1.1790.99
67_S122_R1.1740.99
179_N205_D1.1740.99
174_L178_F1.1730.99
16_S145_N1.1420.99
116_G119_R1.1250.99
23_D128_K1.1220.99
35_L42_T1.1010.99
197_R201_E1.0950.99
64_L123_L1.0940.99
29_V124_F1.0920.99
96_R100_L1.0780.98
60_L125_V1.0700.98
81_R95_A1.0570.98
18_L28_F1.0560.98
75_D79_A1.0560.98
21_N27_G1.0510.98
28_F144_L1.0480.98
3_F204_I1.0460.98
71_D75_D1.0440.98
19_F169_D1.0420.98
33_T161_P1.0240.98
9_Y203_L0.9980.97
19_F170_L0.9970.97
38_A42_T0.9910.97
35_L38_A0.9800.97
54_L58_T0.9800.97
211_D218_R0.9660.97
69_D172_R0.9560.97
93_A97_R0.9490.96
76_R79_A0.9460.96
9_Y126_S0.9380.96
58_T129_L0.9350.96
77_Y90_H0.9340.96
26_V131_G0.9280.96
7_L179_N0.9250.96
187_D190_P0.9190.96
173_W177_L0.9180.96
14_P17_G0.9100.95
22_D200_R0.9070.95
165_L173_W0.9040.95
27_G119_R0.9040.95
165_L170_L0.8900.95
153_S157_S0.8850.95
45_A157_S0.8850.95
132_K137_S0.8840.95
20_L26_V0.8770.94
41_E45_A0.8760.94
72_P76_R0.8740.94
141_L145_N0.8720.94
77_Y80_Y0.8530.94
31_E120_D0.8440.93
40_E44_D0.8410.93
188_A192_D0.8410.93
167_P171_I0.8400.93
209_R221_G0.8350.93
75_D78_R0.8260.93
32_L160_L0.8220.92
38_A43_R0.8190.92
182_P220_D0.8180.92
41_E44_D0.8170.92
220_D224_H0.8170.92
49_L121_F0.8050.92
155_L160_L0.8050.92
30_F165_L0.8020.91
74_L103_D0.7970.91
89_E94_L0.7860.91
215_D218_R0.7830.90
153_S184_A0.7830.90
227_V234_R0.7820.90
71_D106_V0.7780.90
32_L155_L0.7780.90
202_Q207_D0.7770.90
89_E92_R0.7750.90
38_A101_F0.7740.90
66_A126_S0.7730.90
171_I175_R0.7650.89
84_L88_G0.7620.89
175_R205_D0.7600.89
19_F29_V0.7550.89
39_G42_T0.7520.89
18_L26_V0.7470.88
129_L144_L0.7440.88
34_P155_L0.7410.88
65_F68_P0.7390.88
63_I177_L0.7370.88
210_I233_K0.7340.87
59_P128_K0.7250.87
216_G226_V0.7240.87
22_D26_V0.7230.87
94_L98_R0.7200.86
71_D74_L0.7190.86
48_G158_A0.7100.86
7_L125_V0.7090.85
177_L180_P0.7090.85
145_N164_R0.7080.85
111_S114_W0.7070.85
172_R185_G0.7060.85
47_E157_S0.7060.85
65_F177_L0.7010.85
24_G124_F0.6980.85
149_E152_E0.6900.84
113_P116_G0.6860.84
29_V170_L0.6850.83
4_S204_I0.6840.83
19_F199_L0.6840.83
213_E219_F0.6830.83
168_E171_I0.6820.83
168_E172_R0.6800.83
65_F173_W0.6740.82
35_L123_L0.6730.82
60_L204_I0.6730.82
58_T130_P0.6690.82
131_G136_P0.6690.82
11_A20_L0.6660.82
72_P75_D0.6640.82
77_Y98_R0.6640.82
167_P199_L0.6620.81
69_D160_L0.6600.81
170_L193_Y0.6580.81
178_F203_L0.6570.81
101_F105_G0.6560.81
109_S178_F0.6540.81
180_P205_D0.6520.80
3_F7_L0.6490.80
60_L214_P0.6450.80
216_G228_R0.6440.80
149_E156_K0.6430.79
17_G169_D0.6420.79
63_I67_S0.6410.79
64_L121_F0.6400.79
220_D223_P0.6390.79
90_H173_W0.6380.79
6_L187_D0.6360.79
211_D216_G0.6350.79
50_L228_R0.6350.79
111_S115_R0.6350.79
225_R235_F0.6320.78
2_S5_D0.6310.78
90_H114_W0.6300.78
78_R88_G0.6290.78
19_F193_Y0.6260.78
228_R234_R0.6260.78
19_F164_R0.6240.77
25_S144_L0.6200.77
32_L35_L0.6190.77
204_I208_T0.6150.76
103_D106_V0.6130.76
30_F39_G0.6090.76
117_P178_F0.6080.76
54_L59_P0.6070.75
151_L192_D0.6060.75
50_L106_V0.6060.75
85_G143_E0.6060.75
55_P170_L0.6050.75
79_A86_R0.6050.75
145_N148_R0.6050.75
39_G56_E0.6040.75
13_D155_L0.6020.75
62_F121_F0.6020.75
49_L151_L0.6010.75
59_P126_S0.6000.75
183_D186_G0.5970.74
131_G140_P0.5960.74
89_E141_L0.5930.74
179_N203_L0.5920.74
65_F122_R0.5910.73
184_A233_K0.5900.73
21_N128_K0.5900.73
25_S38_A0.5890.73
20_L166_D0.5880.73
25_S46_L0.5860.73
86_R89_E0.5860.73
53_D150_R0.5850.73
65_F176_R0.5840.73
146_D156_K0.5840.73
78_R95_A0.5830.72
69_D181_D0.5780.72
33_T40_E0.5780.72
13_D26_V0.5770.72
119_R122_R0.5760.72
102_L207_D0.5740.71
209_R214_P0.5740.71
47_E124_F0.5720.71
73_Y120_D0.5720.71
40_E186_G0.5700.71
35_L39_G0.5690.71
52_F154_T0.5690.71
178_F210_I0.5630.70
167_P202_Q0.5630.70
136_P140_P0.5620.70
88_G92_R0.5620.70
132_K136_P0.5620.70
48_G167_P0.5610.70
46_L206_S0.5600.69
123_L176_R0.5600.69
214_P218_R0.5560.69
46_L73_Y0.5550.69
32_L180_P0.5540.69
229_V234_R0.5530.69
231_S235_F0.5510.68
48_G157_S0.5500.68
68_P167_P0.5500.68
218_R223_P0.5480.68
225_R229_V0.5460.68
168_E190_P0.5450.67
184_A220_D0.5450.67
90_H101_F0.5450.67
18_L145_N0.5440.67
142_E229_V0.5410.67
50_L154_T0.5410.67
105_G114_W0.5400.67
184_A187_D0.5400.67
135_D192_D0.5390.67
178_F204_I0.5380.66
25_S59_P0.5370.66
54_L127_V0.5370.66
48_G150_R0.5370.66
42_T45_A0.5370.66
87_Q91_L0.5360.66
153_S156_K0.5350.66
17_G168_E0.5350.66
7_L203_L0.5350.66
46_L134_K0.5340.66
157_S230_L0.5340.66
5_D61_Q0.5330.66
99_G178_F0.5280.65
167_P170_L0.5280.65
69_D229_V0.5270.65
41_E57_G0.5250.65
93_A166_D0.5240.64
67_S109_S0.5240.64
103_D195_P0.5220.64
12_Y214_P0.5190.64
41_E209_R0.5190.64
3_F183_D0.5180.64
180_P220_D0.5180.64
41_E153_S0.5170.63
26_V205_D0.5170.63
96_R113_P0.5150.63
46_L197_R0.5150.63
34_P39_G0.5140.63
218_R221_G0.5110.62
45_A121_F0.5100.62
156_K210_I0.5100.62
132_K145_N0.5090.62
105_G118_L0.5070.62
180_P184_A0.5070.62
86_R108_G0.5070.62
122_R169_D0.5070.62
135_D153_S0.5070.62
16_S148_R0.5070.62
29_V174_L0.5060.62
5_D201_E0.5060.62
50_L125_V0.5050.62
85_G88_G0.5040.61
104_K188_A0.5040.61
198_P201_E0.5040.61
45_A158_A0.5000.61
86_R163_R0.5000.61
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  
3jygA 4 0.3165 10.2 0.946 Contact Map
3g1jA 1 0.2068 5 0.953 Contact Map
4p5eA 2 0.346 4.3 0.955 Contact Map
4ks9A 2 0.7384 3.8 0.956 Contact Map
3rnvA 3 0.2574 3.7 0.956 Contact Map
2e29A 1 0.2278 3.5 0.956 Contact Map
2m3dA 1 0.2363 2.7 0.959 Contact Map
4m2aA 1 0.3544 2.7 0.959 Contact Map
1wf3A 1 0.5949 2.6 0.959 Contact Map
2ejsA 1 0.2447 2.6 0.959 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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