GREMLIN Database
TraD - Conjugal transfer protein TraD
PFAM: PF06412 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 61 (59)
Sequences: 3194 (1541)
Seq/√Len: 200.6
META: 0.813

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
34_A38_A4.8971.00
7_R11_L3.5751.00
8_T12_I3.1531.00
40_E54_R2.7301.00
37_E41_K2.4761.00
29_A56_A2.2201.00
10_H24_D1.8441.00
31_L35_L1.7991.00
14_L18_V1.7091.00
56_A60_Q1.7051.00
27_D30_T1.6571.00
3_A6_L1.6111.00
27_D52_R1.5881.00
9_R13_E1.5481.00
36_L58_A1.4981.00
2_K6_L1.2591.00
10_H13_E1.2351.00
18_V35_L1.1491.00
37_E51_W1.1041.00
29_A52_R1.0991.00
15_G18_V1.0641.00
13_E28_R1.0251.00
46_E49_A0.9801.00
20_K32_L0.9730.99
6_L10_H0.9640.99
46_E50_A0.9600.99
12_I16_G0.9560.99
30_T42_L0.9470.99
43_D46_E0.9430.99
32_L36_L0.9350.99
30_T52_R0.9220.99
53_R57_A0.9160.99
20_K58_A0.9160.99
26_L30_T0.8810.99
7_R19_V0.8710.99
52_R56_A0.8350.98
10_H28_R0.8220.98
48_E51_W0.8200.98
43_D48_E0.7660.97
47_R50_A0.7660.97
41_K47_R0.7540.97
44_S47_R0.7510.97
11_L19_V0.7490.97
8_T11_L0.7470.97
4_R12_I0.7440.97
45_D49_A0.7400.97
57_A60_Q0.7230.96
21_A32_L0.7210.96
14_L19_V0.7180.96
9_R16_G0.7130.96
44_S48_E0.7120.96
42_L47_R0.7120.96
19_V24_D0.7060.96
28_R32_L0.6960.95
30_T51_W0.6910.95
41_K48_E0.6870.95
8_T16_G0.6820.95
41_K46_E0.6620.94
20_K59_F0.6450.93
7_R12_I0.6430.93
40_E43_D0.6360.93
15_G23_L0.6310.92
5_R11_L0.6300.92
45_D53_R0.6030.90
36_L54_R0.6010.90
24_D27_D0.5960.90
16_G20_K0.5860.89
4_R16_G0.5830.89
16_G19_V0.5760.88
32_L59_F0.5740.88
14_L24_D0.5730.88
23_L32_L0.5700.88
8_T13_E0.5670.88
4_R8_T0.5630.87
29_A58_A0.5620.87
41_K49_A0.5590.87
18_V31_L0.5510.86
5_R12_I0.5450.86
6_L53_R0.5360.85
31_L56_A0.5360.85
37_E50_A0.5350.84
39_A47_R0.5230.83
3_A38_A0.5170.82
14_L31_L0.5120.82
13_E20_K0.5090.81
50_A56_A0.5070.81
55_G59_F0.5040.81
26_L42_L0.5000.80
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  
4o5pA 1 0.0492 12.7 0.827 Contact Map
3i9wA 1 0.541 5 0.856 Contact Map
2j0jA 1 1 3.3 0.868 Contact Map
1rm6B 1 0.918 3 0.871 Contact Map
3ilkA 2 0.6721 3 0.871 Contact Map
3nr7A 2 0.5738 3 0.871 Contact Map
3mkqB 1 0.7705 2.7 0.874 Contact Map
3mkqA 2 1 2.6 0.874 Contact Map
3onpA 2 0 2.3 0.879 Contact Map
3gjxA 1 0.2131 2.2 0.879 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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