GREMLIN Database
T4SS_TraI - Type IV secretory system, conjugal DNA-protein transfer
PFAM: PF16932 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 212 (211)
Sequences: 726 (585)
Seq/√Len: 40.3
META: 0.789

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
58_I169_V4.3801.00
23_R140_D4.0981.00
42_F151_T3.7751.00
101_R146_N3.6631.00
98_Y153_D3.5631.00
20_L142_I3.4451.00
32_E35_A3.3091.00
85_P201_P3.2971.00
15_G19_G3.2931.00
77_D191_G3.2731.00
74_R192_D3.1271.00
54_L89_V2.9751.00
123_I127_A2.9411.00
23_R26_E2.8701.00
39_D96_R2.6751.00
184_D205_T2.3721.00
17_Q106_P2.3091.00
73_A88_F2.3081.00
160_Y171_P2.2601.00
176_E193_R2.2421.00
60_E159_R2.1550.99
7_L127_A2.1280.99
43_D46_P2.1240.99
65_L90_S2.0950.99
183_G203_L2.0630.99
54_L93_P1.9220.99
153_D157_M1.8750.98
22_W136_V1.8010.98
81_K187_E1.7830.98
175_A196_R1.7780.98
204_Q209_K1.7700.98
47_L55_P1.7640.97
85_P200_L1.7630.97
181_V207_S1.7410.97
13_S16_A1.7310.97
71_Q200_L1.7300.97
22_W26_E1.7170.97
182_T192_D1.7020.97
168_M188_M1.6650.96
6_A9_E1.6590.96
11_A127_A1.6570.96
26_E136_V1.5560.95
121_R125_R1.5360.94
20_L138_Q1.5050.94
48_L89_V1.5040.94
142_I146_N1.4700.93
148_A151_T1.4570.93
185_G202_Q1.4500.92
60_E78_R1.4480.92
175_A198_T1.4390.92
19_G136_V1.4310.92
62_R78_R1.4280.92
90_S132_W1.4230.92
88_F174_V1.4210.92
164_L171_P1.4170.92
16_A138_Q1.4090.91
47_L50_P1.4000.91
133_E137_E1.3790.90
84_R153_D1.3740.90
30_E147_L1.3610.90
167_G204_Q1.3520.89
58_I159_R1.3470.89
72_T196_R1.3350.89
62_R169_V1.3130.88
6_A113_L1.3130.88
126_K130_E1.2810.87
191_G203_L1.2550.86
94_T97_D1.2380.85
2_I9_E1.1900.82
13_S17_Q1.1860.82
49_L52_G1.1810.82
8_R130_E1.1310.79
154_Y158_V1.1210.78
134_E137_E1.1210.78
149_R152_R1.1200.78
56_P86_A1.0970.77
119_E123_I1.0940.77
31_L149_R1.0790.76
117_N121_R1.0770.76
59_S83_V1.0750.75
85_P186_N1.0530.74
169_V172_P1.0470.73
4_L123_I1.0400.73
196_R202_Q1.0370.73
76_A189_R1.0340.73
7_L29_E1.0140.71
11_A35_A1.0130.71
115_P120_E1.0110.71
29_E64_A1.0100.71
155_T159_R1.0050.70
86_A200_L0.9850.69
127_A130_E0.9790.68
103_Y146_N0.9650.67
67_L70_G0.9600.67
24_S101_R0.9550.66
8_R126_K0.9430.65
93_P174_V0.9350.65
140_D144_E0.9270.64
151_T155_T0.9270.64
31_L160_Y0.9230.64
184_D187_E0.9190.63
35_A39_D0.9130.63
3_R120_E0.9110.63
80_Y88_F0.9110.63
65_L73_A0.9110.63
8_R127_A0.9100.63
151_T170_S0.9010.62
58_I80_Y0.8980.62
93_P152_R0.8950.61
114_L124_W0.8940.61
4_L7_L0.8880.61
144_E169_V0.8840.60
130_E133_E0.8840.60
125_R129_R0.8840.60
23_R48_L0.8820.60
203_L212_P0.8790.60
4_L117_N0.8770.60
21_A24_S0.8760.60
53_V197_I0.8760.60
118_D126_K0.8760.60
118_D125_R0.8720.59
87_R140_D0.8720.59
181_V188_M0.8600.58
70_G170_S0.8590.58
44_F157_M0.8560.58
119_E209_K0.8550.58
22_W25_R0.8520.57
160_Y183_G0.8510.57
122_A126_K0.8500.57
83_V152_R0.8440.57
2_I181_V0.8430.57
164_L192_D0.8380.56
51_A69_D0.8360.56
143_F192_D0.8210.55
86_A201_P0.8090.54
57_V157_M0.8070.53
5_Q8_R0.8070.53
20_L103_Y0.7990.53
191_G211_K0.7980.53
170_S209_K0.7970.52
72_T88_F0.7930.52
11_A15_G0.7870.52
123_I185_G0.7870.52
24_S28_N0.7840.51
64_A79_V0.7800.51
124_W156_G0.7800.51
29_E33_R0.7770.51
18_G128_V0.7770.51
146_N149_R0.7720.50
23_R27_I0.7700.50
30_E169_V0.7690.50
109_P142_I0.7670.50
57_V156_G0.7640.49
177_T196_R0.7630.49
67_L89_V0.7620.49
141_E167_G0.7560.49
191_G194_V0.7550.49
159_R162_K0.7530.48
205_T209_K0.7510.48
18_G142_I0.7480.48
46_P154_Y0.7460.48
60_E143_F0.7400.47
86_A172_P0.7380.47
20_L24_S0.7370.47
27_I31_L0.7350.47
59_S152_R0.7290.46
25_R35_A0.7290.46
143_F176_E0.7270.46
40_R48_L0.7270.46
47_L158_V0.7260.46
107_E202_Q0.7250.46
62_R128_V0.7230.46
113_L147_L0.7230.46
120_E138_Q0.7220.46
49_L161_R0.7150.45
162_K166_Q0.7150.45
118_D122_A0.7150.45
8_R138_Q0.7050.44
178_D191_G0.7040.44
45_N68_D0.7030.44
14_Y109_P0.7030.44
16_A189_R0.7020.44
17_Q64_A0.7000.44
102_D114_L0.6980.43
111_D116_K0.6970.43
100_W146_N0.6960.43
76_A79_V0.6940.43
87_R121_R0.6930.43
54_L87_R0.6900.43
185_G203_L0.6870.42
179_L194_V0.6860.42
100_W103_Y0.6850.42
108_P154_Y0.6840.42
12_L134_E0.6830.42
19_G148_A0.6740.41
124_W128_V0.6740.41
79_V86_A0.6700.41
88_F195_L0.6640.40
77_D180_G0.6640.40
89_V205_T0.6620.40
89_V94_T0.6610.40
13_S92_P0.6590.40
118_D121_R0.6570.40
27_I179_L0.6550.40
53_V101_R0.6520.39
121_R126_K0.6520.39
42_F143_F0.6500.39
28_N100_W0.6500.39
107_E205_T0.6500.39
48_L54_L0.6490.39
99_L150_L0.6450.39
76_A130_E0.6410.38
8_R12_L0.6400.38
63_D66_N0.6360.38
144_E204_Q0.6340.38
44_F98_Y0.6330.38
98_Y157_M0.6320.38
80_Y206_N0.6300.37
192_D203_L0.6290.37
117_N126_K0.6280.37
15_G192_D0.6260.37
97_D130_E0.6190.36
7_L150_L0.6170.36
171_P177_T0.6150.36
173_Y192_D0.6150.36
29_E209_K0.6110.36
106_P114_L0.6110.36
57_V149_R0.6110.36
39_D94_T0.6090.36
31_L147_L0.6090.36
165_A195_L0.6080.36
21_A82_I0.6060.35
61_A64_A0.6050.35
37_Y41_I0.6040.35
72_T177_T0.6020.35
129_R133_E0.5990.35
67_L90_S0.5970.35
63_D130_E0.5970.35
35_A204_Q0.5820.33
67_L188_M0.5810.33
76_A154_Y0.5800.33
41_I101_R0.5800.33
164_L183_G0.5780.33
160_Y164_L0.5750.33
92_P172_P0.5740.33
34_R37_Y0.5740.33
111_D121_R0.5730.33
2_I207_S0.5700.32
86_A197_I0.5670.32
16_A171_P0.5660.32
165_A168_M0.5640.32
16_A20_L0.5630.32
73_A174_V0.5630.32
10_A140_D0.5630.32
200_L212_P0.5630.32
121_R146_N0.5620.32
157_M164_L0.5610.32
173_Y195_L0.5600.32
86_A198_T0.5600.32
69_D72_T0.5600.32
81_K97_D0.5590.31
88_F159_R0.5580.31
54_L74_R0.5580.31
8_R133_E0.5570.31
41_I113_L0.5560.31
32_E100_W0.5550.31
74_R93_P0.5530.31
119_E125_R0.5510.31
147_L150_L0.5510.31
25_R29_E0.5510.31
42_F50_P0.5510.31
27_I197_I0.5500.31
29_E133_E0.5480.31
204_Q207_S0.5480.31
78_R86_A0.5470.31
143_F147_L0.5460.30
63_D178_D0.5450.30
88_F168_M0.5400.30
59_S114_L0.5400.30
53_V86_A0.5380.30
52_G90_S0.5370.30
43_D126_K0.5350.30
76_A88_F0.5350.30
113_L172_P0.5340.30
42_F154_Y0.5330.29
9_E166_Q0.5330.29
92_P212_P0.5320.29
96_R191_G0.5300.29
177_T199_A0.5260.29
193_R197_I0.5260.29
60_E63_D0.5260.29
50_P69_D0.5220.29
181_V205_T0.5210.29
19_G188_M0.5170.28
55_P157_M0.5170.28
27_I139_A0.5160.28
125_R176_E0.5150.28
180_G190_I0.5150.28
137_E140_D0.5130.28
182_T195_L0.5110.28
67_L87_R0.5110.28
177_T191_G0.5100.28
6_A12_L0.5090.28
31_L36_R0.5070.28
13_S131_G0.5070.28
12_L22_W0.5060.27
35_A96_R0.5040.27
16_A134_E0.5040.27
204_Q210_W0.5030.27
37_Y40_R0.5030.27
98_Y131_G0.5030.27
31_L161_R0.5030.27
119_E208_K0.5030.27
101_R142_I0.5020.27
148_A211_K0.5020.27
115_P156_G0.5000.27
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  
1g92A 1 0.1085 17.4 0.957 Contact Map
4dwsA 1 0.2736 6.1 0.965 Contact Map
5rubA 2 0.2311 5.7 0.965 Contact Map
3o0yA 3 0.3208 4.6 0.967 Contact Map
3u24A 1 0.2972 3.4 0.969 Contact Map
1mskA 1 0.6038 3.4 0.969 Contact Map
4pacA 1 0.2689 3.1 0.97 Contact Map
2azeC 2 0.2075 2.5 0.971 Contact Map
1s6iA 1 0.3396 2.4 0.971 Contact Map
2x5hA 2 0.2123 2.4 0.971 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.

Page generated in 0.0073 seconds.