GREMLIN Database
CtnDOT_TraJ - Homologues of TraJ from Bacteroides conjugative transposon
PFAM: PF07863 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 66 (60)
Sequences: 1087 (735)
Seq/√Len: 94.8
META: 0.853

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
53_M56_D3.5101.00
26_G29_L3.3041.00
27_A30_R2.5601.00
18_Y22_A2.1111.00
56_D60_N1.9411.00
57_A60_N1.9271.00
47_A50_G1.8901.00
18_Y21_H1.8231.00
33_T36_A1.7631.00
54_A57_A1.7141.00
43_A46_A1.6851.00
7_V31_K1.6191.00
52_G58_M1.5311.00
2_M11_T1.4841.00
18_Y28_L1.4721.00
18_Y26_G1.3840.99
31_K35_L1.3680.99
40_G43_A1.3540.99
27_A31_K1.3100.99
14_S22_A1.2610.99
44_G47_A1.2060.98
15_V22_A1.1940.98
53_M60_N1.1650.98
17_N21_H1.1470.98
30_R34_S1.1010.97
16_A20_V1.0790.97
55_A58_M1.0750.96
26_G30_R1.0600.96
52_G55_A1.0400.96
42_S45_S1.0240.95
16_A19_I0.9650.94
53_M57_A0.9470.93
51_A55_A0.9450.93
2_M17_N0.9370.93
37_S40_G0.9320.92
24_G29_L0.9220.92
2_M35_L0.9150.92
52_G57_A0.8750.90
48_G51_A0.8680.89
36_A39_A0.8610.89
7_V21_H0.8590.89
19_I23_G0.8470.88
29_L32_V0.8420.88
9_Y16_A0.8140.86
50_G54_A0.8070.86
44_G48_G0.8000.85
11_T19_I0.7960.85
28_L31_K0.7950.85
5_G14_S0.7950.85
48_G54_A0.7790.84
10_F33_T0.7600.82
15_V18_Y0.7510.81
22_A30_R0.7460.81
25_G31_K0.7080.77
25_G28_L0.7050.77
40_G44_G0.7010.77
21_H44_G0.6990.77
14_S20_V0.6920.76
41_S45_S0.6780.74
29_L35_L0.6730.74
11_T27_A0.6680.73
35_L39_A0.6670.73
37_S41_S0.6650.73
12_V15_V0.6610.73
8_G15_V0.6530.72
29_L37_S0.6450.71
5_G10_F0.6440.71
16_A28_L0.6270.69
35_L38_S0.6200.68
2_M8_G0.6130.67
34_S37_S0.6060.66
5_G36_A0.6020.65
55_A59_G0.5960.65
22_A34_S0.5940.64
7_V14_S0.5920.64
18_Y27_A0.5880.64
16_A42_S0.5720.61
16_A37_S0.5700.61
2_M55_A0.5630.60
3_I7_V0.5470.58
11_T28_L0.5440.58
14_S26_G0.5420.57
12_V28_L0.5310.56
7_V35_L0.5220.55
54_A58_M0.5170.54
48_G52_G0.5140.54
17_N25_G0.5100.53
47_A52_G0.5080.53
32_V36_A0.5060.52
18_Y31_K0.5000.52
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  
3mp7B 1 0.3182 24.7 0.85 Contact Map
4w252 1 0.3333 14.2 0.866 Contact Map
2ww9B 1 0.3485 7 0.883 Contact Map
1ciiA 1 0.4697 7 0.884 Contact Map
1rh5B 1 0.3485 6.7 0.884 Contact Map
3hzqA 3 0.3333 6.3 0.885 Contact Map
1colA 1 0.5 2.7 0.904 Contact Map
3fewX 1 0.5455 1.5 0.917 Contact Map
1y43A 1 0.2727 1.5 0.917 Contact Map
1tpxA 1 0.2273 1.3 0.92 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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