GREMLIN Database
XKDU - Phage-like element PBSX protein XkdU
UniProt: P54340 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 192 (167)
Sequences: 377 (337)
Seq/√Len: 26.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
165_L173_A4.7341.00
156_T165_L4.5421.00
156_T173_A4.5261.00
49_P80_I4.0301.00
112_L115_E4.0061.00
118_F141_K3.5951.00
45_Q52_T3.1701.00
55_L79_L2.8501.00
15_L21_M2.8221.00
160_K169_R2.5030.99
51_A55_L2.4970.99
41_D52_T2.4080.99
70_D78_R2.4070.99
45_Q53_W2.3360.98
62_L83_M2.2540.98
67_E70_D2.2160.98
41_D45_Q2.0500.96
59_E75_R1.9720.95
164_I167_H1.8630.93
23_E26_K1.8170.92
55_L76_R1.7960.92
141_K147_Y1.6930.90
137_I147_Y1.6850.89
138_E141_K1.6660.89
11_L25_L1.6480.88
55_L72_D1.6030.87
118_F145_L1.5870.86
14_F17_S1.5680.85
48_V83_M1.5450.85
58_W83_M1.5430.85
168_R171_R1.5060.83
163_V168_R1.5050.83
9_A79_L1.5040.83
27_A40_F1.4800.82
165_L172_T1.4660.81
25_L28_E1.4530.81
168_R173_A1.4520.81
160_K171_R1.4030.78
157_L166_N1.3970.78
165_L171_R1.3830.77
95_E99_N1.3820.77
7_M25_L1.3800.77
7_M29_A1.3530.76
118_F138_E1.3460.75
48_V79_L1.3410.75
157_L160_K1.3070.73
156_T168_R1.2930.72
165_L169_R1.2700.71
88_P111_L1.2600.70
142_P145_L1.2540.70
15_L24_L1.2420.69
170_Y174_S1.2040.67
163_V171_R1.1990.66
41_D53_W1.1810.65
48_V62_L1.1550.63
46_L144_H1.1460.63
169_R174_S1.1380.62
111_L145_L1.1220.61
10_Y31_E1.1200.61
91_Y111_L1.1190.61
74_I78_R1.1030.60
82_K139_N1.0780.58
126_D149_L1.0580.57
133_L149_L1.0470.56
119_N150_R1.0420.55
159_I172_T1.0380.55
50_T76_R1.0360.55
160_K173_A1.0340.55
51_A76_R1.0280.54
8_R22_A1.0250.54
90_T116_Y1.0180.54
71_T81_S1.0150.53
167_H170_Y1.0150.53
6_D33_D1.0140.53
28_E32_F1.0050.53
169_R173_A0.9980.52
95_E108_Q0.9870.51
163_V173_A0.9870.51
101_F133_L0.9850.51
112_L119_N0.9850.51
160_K168_R0.9650.50
160_K174_S0.9570.49
6_D29_A0.9560.49
159_I162_T0.9550.49
155_E168_R0.9550.49
84_S97_A0.9460.48
45_Q58_W0.9460.48
53_W144_H0.9410.48
155_E158_R0.9370.48
171_R174_S0.9350.47
158_R174_S0.9260.47
159_I163_V0.9030.45
53_W82_K0.8910.44
45_Q54_G0.8890.44
8_R25_L0.8840.44
160_K166_N0.8710.43
107_A126_D0.8690.43
70_D132_E0.8560.42
64_V111_L0.8560.42
98_V105_P0.8430.41
167_H171_R0.8420.41
99_N119_N0.8400.41
134_I149_L0.8350.40
127_L151_G0.8340.40
56_S66_R0.8300.40
156_T163_V0.8190.39
137_I141_K0.8120.39
116_Y145_L0.8120.39
163_V167_H0.8110.38
85_N139_N0.8080.38
17_S22_A0.8080.38
90_T104_N0.8070.38
170_Y173_A0.8050.38
156_T160_K0.8050.38
15_L18_L0.8000.38
31_E47_F0.7980.38
54_G66_R0.7890.37
6_D79_L0.7860.37
118_F147_Y0.7850.37
156_T159_I0.7830.37
102_L124_V0.7810.36
166_N169_R0.7800.36
29_A33_D0.7740.36
163_V170_Y0.7720.36
99_N112_L0.7710.36
112_L117_R0.7650.35
21_M92_R0.7630.35
70_D74_I0.7620.35
118_F137_I0.7590.35
102_L123_N0.7590.35
138_E147_Y0.7560.35
109_V120_V0.7560.35
45_Q144_H0.7560.35
169_R172_T0.7530.35
131_N134_I0.7400.34
157_L174_S0.7400.34
48_V107_A0.7370.33
157_L169_R0.7330.33
165_L168_R0.7300.33
101_F130_M0.7240.33
62_L79_L0.7220.32
44_D57_R0.7210.32
121_D150_R0.7190.32
166_N171_R0.7190.32
77_L100_R0.7170.32
47_F59_E0.7170.32
17_S137_I0.7140.32
27_A38_S0.7050.31
89_I92_R0.6970.31
154_N160_K0.6960.31
89_I93_A0.6890.30
111_L116_Y0.6870.30
162_T166_N0.6850.30
120_V155_E0.6850.30
133_L140_M0.6850.30
64_V67_E0.6800.30
28_E105_P0.6780.30
89_I98_V0.6770.30
6_D9_A0.6770.30
31_E54_G0.6750.29
165_L170_Y0.6750.29
155_E160_K0.6740.29
163_V169_R0.6670.29
7_M20_E0.6630.29
17_S37_D0.6520.28
159_I173_A0.6510.28
157_L171_R0.6480.28
166_N172_T0.6420.27
27_A121_D0.6420.27
73_E120_V0.6410.27
54_G58_W0.6400.27
88_P144_H0.6300.27
49_P78_R0.6280.27
72_D79_L0.6270.27
79_L83_M0.6250.27
97_A118_F0.6250.27
159_I165_L0.6220.26
159_I168_R0.6210.26
94_I130_M0.6200.26
51_A54_G0.6120.26
135_E140_M0.6110.26
155_E159_I0.6090.26
70_D87_P0.6090.26
20_E144_H0.6070.25
17_S30_P0.6060.25
110_R120_V0.6040.25
107_A130_M0.6040.25
58_W88_P0.6040.25
48_V80_I0.6040.25
20_E28_E0.6020.25
18_L21_M0.6020.25
28_E64_V0.5960.25
98_V137_I0.5960.25
101_F147_Y0.5950.25
8_R15_L0.5940.25
160_K165_L0.5920.25
121_D154_N0.5870.24
73_E76_R0.5840.24
151_G173_A0.5840.24
110_R115_E0.5830.24
44_D114_G0.5800.24
7_M18_L0.5800.24
158_R167_H0.5790.24
74_I132_E0.5750.24
64_V95_E0.5740.24
120_V133_L0.5710.24
88_P98_V0.5670.23
47_F75_R0.5650.23
27_A159_I0.5620.23
63_N94_I0.5620.23
162_T168_R0.5600.23
81_S132_E0.5580.23
89_I144_H0.5570.23
87_P98_V0.5570.23
94_I106_S0.5570.23
119_N148_T0.5530.23
151_G156_T0.5500.22
43_T47_F0.5480.22
114_G167_H0.5480.22
165_L174_S0.5440.22
81_S154_N0.5420.22
19_K22_A0.5400.22
111_L144_H0.5380.22
40_F73_E0.5380.22
41_D58_W0.5370.22
109_V136_A0.5370.22
68_S137_I0.5340.22
84_S100_R0.5320.21
155_E165_L0.5320.21
32_F158_R0.5310.21
166_N174_S0.5280.21
91_Y109_V0.5240.21
78_R97_A0.5230.21
77_L130_M0.5220.21
82_K85_N0.5220.21
164_I170_Y0.5210.21
46_L94_I0.5200.21
56_S76_R0.5190.21
133_L136_A0.5190.21
53_W109_V0.5160.21
145_L151_G0.5130.21
90_T111_L0.5100.20
48_V51_A0.5080.20
157_L168_R0.5080.20
40_F117_R0.5070.20
98_V102_L0.5060.20
71_T74_I0.5060.20
61_I68_S0.5060.20
155_E173_A0.5050.20
45_Q97_A0.5000.20
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  
3vlfB 1 0.3646 22.3 0.944 Contact Map
5afrA 2 0 12.8 0.95 Contact Map
1a3wA 3 0.5156 12.3 0.951 Contact Map
4kctB 3 0.5469 11.2 0.952 Contact Map
3n4sA 2 0.2031 10.8 0.952 Contact Map
2oqoA 2 0.4323 10.6 0.952 Contact Map
4e17B 1 0.1458 10.2 0.952 Contact Map
3a24A 1 0.4219 8.4 0.954 Contact Map
3khdA 3 0.5781 8.3 0.954 Contact Map
4jpoC 1 0.375 7.7 0.955 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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