GREMLIN Database
YRKI - UPF0033 protein YrkI
UniProt: P54436 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 75 (72)
Sequences: 1201 (708)
Seq/√Len: 83.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
57_D73_Q3.3821.00
29_E32_Q3.0431.00
4_D32_Q3.0151.00
10_K67_I2.8831.00
35_E69_K2.6481.00
6_V35_E2.3031.00
33_I71_W2.0251.00
10_K37_H1.9641.00
51_S72_I1.9021.00
5_K27_E1.7041.00
5_K28_L1.6281.00
63_D66_D1.5971.00
28_L32_Q1.5511.00
37_H67_I1.4970.99
36_V47_L1.4670.99
10_K39_T1.4430.99
21_T34_L1.4170.99
33_I59_L1.3840.99
48_T52_K1.3220.99
21_T47_L1.2440.98
58_L70_F1.2420.98
6_V37_H1.2390.98
5_K32_Q1.2160.98
44_K61_Q1.2150.98
19_V50_W1.2010.97
43_A70_F1.1440.96
43_A68_L1.1350.96
44_K63_D1.1320.96
12_L20_R1.1300.96
23_K27_E1.1250.96
25_M50_W1.1090.96
16_M19_V1.0950.95
37_H69_K1.0660.95
35_E71_W1.0510.94
38_A43_A1.0300.94
22_K26_N1.0130.93
62_T69_K1.0120.93
60_E71_W1.0120.93
33_I73_Q0.9970.92
51_S55_G0.9910.92
24_A27_E0.9890.92
24_A28_L0.9740.92
44_K68_L0.9450.90
21_T36_V0.9320.90
16_M20_R0.9250.89
18_I53_S0.9150.89
41_K68_L0.9150.89
22_K42_G0.8810.87
61_Q70_F0.8710.86
7_L34_L0.8420.84
38_A68_L0.8300.84
5_K24_A0.8190.83
18_I22_K0.8170.83
19_V25_M0.8150.82
7_L24_A0.8070.82
12_L16_M0.8010.81
48_T70_F0.7870.80
4_D28_L0.7840.80
13_A22_K0.7510.77
28_L34_L0.7430.76
25_M28_L0.7370.76
30_S74_K0.7350.75
51_S58_L0.7330.75
44_K48_T0.7090.73
64_E69_K0.7050.72
64_E67_I0.7040.72
7_L36_V0.6910.71
3_S35_E0.6890.71
63_D68_L0.6720.69
45_N49_A0.6720.69
37_H71_W0.6620.68
48_T61_Q0.6620.68
3_S6_V0.6600.67
18_I21_T0.6580.67
22_K43_A0.6560.67
41_K53_S0.6500.66
19_V43_A0.6410.65
58_L68_L0.6310.64
9_A21_T0.6260.63
42_G49_A0.6150.62
25_M53_S0.6130.62
45_N54_G0.6120.62
25_M74_K0.6120.62
45_N48_T0.6090.61
18_I42_G0.6070.61
13_A43_A0.6070.61
42_G50_W0.6040.61
22_K54_G0.6000.60
44_K47_L0.5970.60
62_T71_W0.5910.59
3_S71_W0.5900.59
39_T54_G0.5830.58
5_K20_R0.5820.58
28_L74_K0.5720.56
33_I60_E0.5670.56
18_I23_K0.5620.55
38_A73_Q0.5520.54
21_T74_K0.5360.52
26_N56_H0.5310.51
6_V69_K0.5260.50
26_N50_W0.5250.50
24_A36_V0.5250.50
61_Q71_W0.5230.50
18_I54_G0.5210.50
9_A49_A0.5170.49
13_A16_M0.5080.48
27_E65_G0.5030.47
70_F74_K0.5000.47
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  
1je3A 1 0.9867 99.9 0.297 Contact Map
1jdqA 1 1 99.9 0.297 Contact Map
1pavA 1 1 99.9 0.306 Contact Map
3lvjC 1 1 99.9 0.306 Contact Map
3hz7A 1 0.96 99.9 0.335 Contact Map
2lxrA 1 0.92 99.8 0.405 Contact Map
1okgA 1 0.7333 98.6 0.676 Contact Map
2vd8A 2 0.9333 32.3 0.899 Contact Map
1xfcA 2 0.96 31.5 0.9 Contact Map
4bhyA 2 0.92 22.2 0.907 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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