GREMLIN Database
TrbL - TrbL/VirB6 plasmid conjugal transfer protein
PFAM: PF04610 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 216 (213)
Sequences: 7718 (5625)
Seq/√Len: 385.4
META: 0.795

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
147_P150_R4.4631.00
155_G158_G4.2681.00
144_L153_F3.8531.00
133_L159_A3.5631.00
151_F154_E2.9781.00
137_G156_W2.6211.00
33_F37_L2.6161.00
81_D84_D2.5591.00
129_A163_Y2.5411.00
50_D54_G2.4311.00
46_T50_D2.3781.00
7_L11_R2.3751.00
150_R154_E2.2541.00
140_F152_L2.1971.00
26_K30_K2.1901.00
81_D85_P2.1061.00
129_A166_K2.0011.00
151_F155_G2.0001.00
136_L169_V1.9951.00
154_E158_G1.9931.00
133_L160_V1.9601.00
75_L78_L1.8691.00
35_L39_T1.8271.00
79_G83_A1.8081.00
143_F152_L1.8061.00
119_A213_L1.8001.00
4_Y27_K1.7591.00
44_Y137_G1.7331.00
159_A163_Y1.6661.00
151_F158_G1.6571.00
159_A162_S1.6421.00
36_A44_Y1.6131.00
6_A10_L1.6111.00
34_F144_L1.5801.00
177_G209_L1.5661.00
10_L14_L1.5571.00
89_Q92_S1.5441.00
5_I9_G1.5321.00
108_A115_A1.5211.00
136_L172_L1.5071.00
205_A209_L1.5021.00
130_L160_V1.4981.00
24_L28_I1.4931.00
142_P145_L1.4901.00
41_W44_Y1.4891.00
17_I20_P1.4701.00
136_L168_V1.4651.00
41_W45_A1.4621.00
43_A47_I1.4291.00
80_F84_D1.4251.00
178_L182_D1.3981.00
48_I51_S1.3771.00
152_L158_G1.3681.00
140_F153_F1.3641.00
11_R16_R1.3501.00
126_A166_K1.3461.00
57_L61_G1.3401.00
197_A200_L1.3331.00
167_L171_A1.3131.00
85_P88_D1.3061.00
74_A78_L1.2971.00
68_D71_A1.2881.00
123_L127_K1.2871.00
140_F143_F1.2841.00
146_F149_T1.2681.00
135_A138_P1.2641.00
9_G13_A1.2461.00
166_K170_L1.2441.00
162_S166_K1.2361.00
153_F157_L1.2341.00
84_D88_D1.2191.00
51_S54_G1.2151.00
200_L208_V1.2141.00
54_G57_L1.2131.00
2_T6_A1.2001.00
36_A40_N1.1991.00
204_L209_L1.1891.00
138_P156_W1.1761.00
75_L79_G1.1741.00
202_L206_A1.1701.00
54_G58_E1.1671.00
140_F165_L1.1591.00
57_L60_A1.1591.00
201_A209_L1.1521.00
85_P89_Q1.1481.00
52_F160_V1.1271.00
90_A93_L1.1271.00
80_F83_A1.1221.00
102_I106_L1.1071.00
22_A26_K1.1001.00
199_A202_L1.0971.00
22_A25_V1.0781.00
49_V53_T1.0711.00
127_K131_A1.0701.00
197_A201_A1.0681.00
50_D53_T1.0681.00
210_L214_I1.0671.00
111_I203_L1.0661.00
51_S55_L1.0611.00
157_L161_L1.0601.00
140_F156_W1.0591.00
7_L14_L1.0561.00
8_A24_L1.0471.00
171_A175_G1.0431.00
29_L32_G1.0431.00
52_F164_G1.0321.00
202_L209_L1.0291.00
55_L58_E1.0281.00
15_G18_G1.0231.00
130_L134_L1.0221.00
129_A133_L1.0161.00
88_D92_S1.0091.00
153_F156_W0.9911.00
53_T56_G0.9821.00
196_L200_L0.9811.00
163_Y167_L0.9761.00
141_I153_F0.9631.00
201_A205_A0.9581.00
186_A190_A0.9571.00
207_L211_L0.9521.00
55_L59_A0.9471.00
29_L33_F0.9421.00
34_F145_L0.9381.00
96_F99_I0.9371.00
44_Y48_I0.9291.00
145_L156_W0.9291.00
200_L204_L0.9241.00
99_I103_L0.9221.00
191_G198_D0.9191.00
144_L147_P0.9141.00
89_Q93_L0.9071.00
187_A190_A0.9021.00
125_L129_A0.9011.00
168_V172_L0.9001.00
10_L13_A0.8961.00
98_N101_A0.8911.00
77_Q81_D0.8911.00
200_L203_L0.8901.00
3_I7_L0.8841.00
10_L29_L0.8831.00
95_F99_I0.8811.00
27_K31_I0.8771.00
198_D202_L0.8691.00
4_Y8_A0.8631.00
41_W55_L0.8581.00
17_I23_E0.8581.00
8_A27_K0.8561.00
32_G35_L0.8541.00
118_I121_A0.8531.00
158_G162_S0.8531.00
103_L107_L0.8521.00
11_R14_L0.8521.00
47_I51_S0.8441.00
40_N44_Y0.8441.00
99_I102_I0.8421.00
118_I122_Q0.8361.00
179_T182_D0.8351.00
30_K150_R0.8331.00
36_A39_T0.8331.00
137_G141_I0.8281.00
198_D201_A0.8281.00
8_A11_R0.8271.00
9_G12_L0.8251.00
32_G36_A0.8231.00
165_L168_V0.8201.00
42_P45_A0.8111.00
164_G167_L0.8021.00
11_R26_K0.8011.00
106_L110_L0.8011.00
155_G162_S0.7971.00
108_A112_V0.7901.00
142_P151_F0.7891.00
208_V211_L0.7861.00
204_L208_V0.7831.00
95_F98_N0.7801.00
91_S94_S0.7791.00
31_I35_L0.7781.00
110_L114_L0.7761.00
43_A46_T0.7741.00
129_A159_A0.7741.00
211_L214_I0.7721.00
184_F188_L0.7711.00
122_Q125_L0.7691.00
199_A211_L0.7681.00
143_F149_T0.7651.00
205_A210_L0.7601.00
70_L73_P0.7551.00
11_R17_I0.7551.00
100_G103_L0.7541.00
38_A41_W0.7531.00
8_A23_E0.7431.00
3_I6_A0.7421.00
152_L159_A0.7391.00
25_V32_G0.7391.00
8_A12_L0.7271.00
122_Q170_L0.7241.00
62_A65_G0.7241.00
60_A70_L0.7211.00
11_R27_K0.7181.00
197_A206_A0.7171.00
27_K30_K0.7121.00
51_S56_G0.7091.00
60_A64_L0.7061.00
136_L140_F0.7061.00
201_A208_V0.7051.00
114_L118_I0.7031.00
208_V212_L0.7021.00
116_F120_A0.7011.00
182_D186_A0.6991.00
126_A167_L0.6940.99
79_G112_V0.6920.99
84_D197_A0.6890.99
4_Y147_P0.6880.99
163_Y166_K0.6870.99
88_D91_S0.6850.99
58_E62_A0.6830.99
55_L63_I0.6810.99
197_A202_L0.6800.99
83_A109_W0.6780.99
206_A210_L0.6750.99
59_A168_V0.6740.99
203_L206_A0.6730.99
119_A122_Q0.6670.99
69_L73_P0.6670.99
141_I156_W0.6670.99
173_I177_G0.6620.99
69_L72_S0.6620.99
160_V164_G0.6590.99
30_K33_F0.6590.99
196_L201_A0.6580.99
199_A209_L0.6550.99
197_A203_L0.6550.99
187_A191_G0.6520.99
16_R26_K0.6440.99
44_Y47_I0.6430.99
67_A70_L0.6400.99
19_E22_A0.6390.99
199_A210_L0.6350.99
52_F55_L0.6340.99
197_A208_V0.6330.99
83_A87_L0.6290.99
199_A204_L0.6260.99
5_I12_L0.6220.99
115_A210_L0.6200.99
201_A204_L0.6200.99
109_W112_V0.6190.99
35_L38_A0.6170.99
196_L203_L0.6160.99
15_G19_E0.6130.99
118_I123_L0.6110.99
200_L205_A0.6100.99
145_L152_L0.6070.99
6_A14_L0.6030.99
97_G100_G0.6020.99
199_A203_L0.6010.99
76_D84_D0.6000.98
195_T198_D0.6000.98
188_L197_A0.5950.98
177_G180_L0.5880.98
16_R30_K0.5860.98
42_P46_T0.5860.98
96_F100_G0.5820.98
97_G101_A0.5810.98
152_L161_L0.5810.98
209_L213_L0.5800.98
79_G84_D0.5790.98
97_G106_L0.5780.98
44_Y51_S0.5780.98
80_F86_L0.5760.98
76_D79_G0.5740.98
189_A192_A0.5740.98
129_A167_L0.5740.98
119_A174_V0.5710.98
98_N102_I0.5710.98
60_A65_G0.5690.98
180_L184_F0.5660.98
8_A13_A0.5660.98
172_L176_I0.5650.98
48_I52_F0.5650.98
56_G59_A0.5650.98
48_I55_L0.5640.98
88_D94_S0.5620.98
6_A12_L0.5590.98
206_A213_L0.5580.98
87_L90_A0.5570.98
59_A65_G0.5560.98
84_D92_S0.5530.97
108_A113_L0.5520.97
134_L138_P0.5490.97
56_G60_A0.5480.97
11_R22_A0.5480.97
4_Y146_F0.5460.97
130_L138_P0.5420.97
131_A172_L0.5380.97
83_A86_L0.5380.97
183_S186_A0.5350.97
201_A207_L0.5350.97
126_A163_Y0.5320.97
37_L41_W0.5320.97
90_A94_S0.5320.97
74_A77_Q0.5270.97
56_G61_G0.5270.97
204_L207_L0.5260.97
144_L150_R0.5250.97
122_Q166_K0.5240.97
6_A9_G0.5230.96
87_L93_L0.5220.96
23_E26_K0.5220.96
196_L206_A0.5190.96
11_R15_G0.5180.96
85_P93_L0.5170.96
194_P200_L0.5130.96
101_A106_L0.5100.96
89_Q94_S0.5080.96
81_D88_D0.5070.96
18_G22_A0.5050.96
198_D203_L0.5030.96
33_F36_A0.5030.96
20_P23_E0.5020.96
5_I31_I0.5000.95
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  
3wu2Y 1 0.1296 3.6 0.925 Contact Map
3zdqA 2 0.338 1.4 0.94 Contact Map
2mc7A 1 0.1296 1.2 0.942 Contact Map
4pj0Y 1 0.1343 1 0.945 Contact Map
4a82A 2 0.3287 0.9 0.946 Contact Map
3rkoM 1 0.3102 0.8 0.948 Contact Map
2ifoA 8 0.0787 0.8 0.948 Contact Map
2ksdA 1 0.2639 0.7 0.95 Contact Map
4he8M 1 0.3009 0.7 0.95 Contact Map
2nwlA 3 0.3981 0.7 0.95 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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