GREMLIN Database
YCJD - Uncharacterized protein YcjD
UniProt: P45736 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12653
Length: 117 (105)
Sequences: 1298 (1061)
Seq/√Len: 103.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
77_T81_E3.5731.00
51_A85_W3.3241.00
58_V85_W3.0281.00
19_Q96_D2.7531.00
90_F105_N2.6531.00
48_L58_V2.4771.00
94_E98_N2.4071.00
44_G79_W2.3861.00
98_N101_T2.3841.00
35_F52_C2.2841.00
38_R41_H2.2701.00
55_A110_L2.2341.00
35_F110_L2.2151.00
9_A42_P2.1301.00
38_R53_C2.0201.00
79_W83_Q2.0151.00
23_L27_L1.9011.00
61_L95_I1.8841.00
88_L106_I1.7541.00
12_L16_L1.7481.00
65_Q91_W1.7391.00
86_T109_E1.7151.00
26_Y99_E1.6931.00
43_V48_L1.6851.00
23_L61_L1.6681.00
53_C85_W1.6641.00
65_Q69_A1.4471.00
46_Y79_W1.4281.00
33_S107_L1.3751.00
94_E105_N1.3530.99
105_N108_Q1.3460.99
99_E103_L1.3210.99
19_Q92_N1.2690.99
77_T87_V1.2060.99
58_V80_L1.1920.99
58_V87_V1.1920.99
35_F55_A1.1850.99
32_F103_L1.1790.99
74_S78_S1.1430.98
26_Y103_L1.1380.98
8_N11_D1.1290.98
30_R36_K1.0890.98
22_K96_D1.0790.97
45_S79_W1.0780.97
22_K25_R1.0740.97
18_L96_D1.0710.97
104_E108_Q1.0590.97
48_L80_L1.0040.96
51_A58_V0.9930.96
93_N97_C0.9740.95
26_Y100_E0.9720.95
104_E107_L0.9640.95
67_D70_V0.9640.95
88_L109_E0.9500.95
22_K26_Y0.9370.94
10_R29_S0.9070.93
17_T47_I0.8960.93
30_R54_S0.8930.93
62_D66_H0.8810.92
81_E87_V0.8800.92
18_L22_K0.8710.92
64_G91_W0.8670.91
79_W82_S0.8660.91
99_E102_V0.8340.90
6_K42_P0.8330.90
25_R31_R0.8310.90
48_L85_W0.8310.90
21_R25_R0.8260.89
26_Y31_R0.8240.89
91_W94_E0.8170.89
17_T92_N0.8110.88
44_G83_Q0.8100.88
31_R34_D0.7970.88
90_F102_V0.7900.87
71_A74_S0.7810.86
9_A13_R0.7790.86
36_K41_H0.7700.86
12_L47_I0.7670.85
90_F106_I0.7670.85
74_S77_T0.7650.85
41_H53_C0.7550.85
66_H73_D0.7410.83
24_W39_R0.7390.83
41_H51_A0.7320.83
75_R78_S0.7290.82
23_L106_I0.7240.82
77_T80_L0.7230.82
16_L39_R0.7040.80
71_A75_R0.6990.80
62_D73_D0.6940.79
65_Q93_N0.6930.79
11_D15_N0.6920.79
18_L21_R0.6770.78
25_R28_R0.6770.78
64_G93_N0.6760.77
43_V58_V0.6730.77
43_V51_A0.6680.77
77_T88_L0.6660.76
23_L103_L0.6520.75
56_R85_W0.6520.75
32_F107_L0.6510.75
30_R34_D0.6490.75
101_T104_E0.6480.74
61_L90_F0.6450.74
29_S36_K0.6430.74
8_N12_L0.6420.74
94_E101_T0.6340.73
18_L64_G0.6300.72
105_N109_E0.6270.72
37_F52_C0.6150.71
56_R84_G0.6140.70
28_R31_R0.6070.70
61_L91_W0.6010.69
62_D76_R0.5950.68
6_K41_H0.5950.68
32_F35_F0.5950.68
23_L40_Q0.5930.68
40_Q73_D0.5910.68
72_Y79_W0.5900.67
106_I109_E0.5800.66
7_S11_D0.5780.66
72_Y75_R0.5770.66
46_Y72_Y0.5720.65
32_F106_I0.5660.64
8_N47_I0.5650.64
67_D71_A0.5630.64
98_N107_L0.5620.64
86_T108_Q0.5610.64
6_K36_K0.5540.63
78_S82_S0.5540.63
41_H85_W0.5520.62
59_V80_L0.5480.62
78_S81_E0.5460.61
30_R37_F0.5450.61
17_T80_L0.5440.61
25_R86_T0.5370.60
75_R82_S0.5360.60
19_Q95_I0.5350.60
68_L71_A0.5330.60
59_V97_C0.5320.60
37_F59_V0.5280.59
26_Y34_D0.5280.59
14_R100_E0.5240.58
27_L61_L0.5240.58
18_L65_Q0.5220.58
36_K47_I0.5150.57
60_E66_H0.5120.57
52_C57_V0.5100.56
19_Q65_Q0.5100.56
22_K99_E0.5100.56
48_L51_A0.5080.56
63_G66_H0.5080.56
45_S78_S0.5070.56
66_H76_R0.5060.56
23_L32_F0.5050.56
6_K38_R0.5030.55
63_G73_D0.5010.55
77_T89_R0.5000.55
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  
4oq2A 1 0.9744 100 0.354 Contact Map
4parB 3 0.9487 100 0.355 Contact Map
1cw0A 1 0.9744 100 0.433 Contact Map
3hrlA 1 0.8034 99.9 0.477 Contact Map
1vsrA 1 0.8291 99.9 0.48 Contact Map
3r3pA 3 0.812 99.9 0.543 Contact Map
4glwA 2 0.7949 17.2 0.94 Contact Map
2owoA 1 0.8803 12.9 0.943 Contact Map
1qf6A 1 0.7778 12.2 0.943 Contact Map
1zauA 1 0.8718 11.2 0.944 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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