GREMLIN Database
YSDA - Uncharacterized protein YsdA
UniProt: P94519 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 89 (80)
Sequences: 1074 (928)
Seq/√Len: 103.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
19_G56_F3.1751.00
17_V40_I3.0701.00
46_A76_E2.9721.00
14_G49_V2.8591.00
15_F55_T2.8001.00
18_M49_V2.7161.00
14_G40_I2.3551.00
20_I24_K2.2381.00
41_A49_V1.9591.00
72_L76_E1.8951.00
23_R27_Q1.7621.00
38_W69_V1.7131.00
14_G18_M1.7021.00
46_A72_L1.6911.00
68_G72_L1.6511.00
33_S36_R1.6511.00
49_V69_V1.6221.00
38_W64_S1.5571.00
6_Y44_F1.4881.00
54_Q66_K1.4451.00
39_L43_V1.3971.00
6_Y10_I1.3721.00
38_W72_L1.3270.99
10_I43_V1.3250.99
16_W20_I1.3210.99
19_G23_R1.3200.99
63_A67_Y1.2990.99
50_W69_V1.2970.99
18_M38_W1.2900.99
7_L76_E1.2820.99
20_I32_I1.2790.99
23_R26_Q1.1770.99
24_K32_I1.1450.98
50_W73_L1.1330.98
52_G56_F1.0690.97
46_A73_L1.0680.97
63_A66_K1.0480.97
53_M69_V1.0330.97
19_G52_G0.9650.95
69_V72_L0.9260.94
73_L76_E0.9190.94
24_K29_K0.9010.93
53_M70_P0.8970.93
46_A69_V0.8860.92
23_R29_K0.8850.92
15_F56_F0.8760.92
64_S69_V0.8690.92
17_V32_I0.8620.91
42_I72_L0.8480.91
46_A70_P0.8280.89
18_M69_V0.8260.89
20_I74_V0.8160.89
78_I82_I0.8130.89
22_K31_R0.8110.88
6_Y43_V0.7960.88
10_I13_C0.7960.88
57_R60_T0.7920.87
53_M62_H0.7870.87
7_L11_N0.7860.87
67_Y71_L0.7850.87
21_D58_H0.7720.86
11_N47_L0.7650.85
53_M68_G0.7580.85
22_K58_H0.7380.83
41_A69_V0.7330.83
61_K66_K0.7320.83
20_I43_V0.7160.81
37_L49_V0.7090.81
18_M41_A0.7060.80
69_V73_L0.7040.80
22_K65_F0.7030.80
40_I44_F0.6910.79
50_W54_Q0.6810.78
41_A72_L0.6540.75
25_A58_H0.6540.75
74_V78_I0.6530.75
58_H65_F0.6410.74
30_W64_S0.6380.73
14_G17_V0.6370.73
31_R65_F0.6360.73
35_D82_I0.6320.73
31_R58_H0.6320.73
50_W66_K0.6270.72
62_H68_G0.6270.72
15_F52_G0.6270.72
56_F60_T0.6220.72
71_L75_I0.6200.71
28_H61_K0.6190.71
38_W41_A0.6080.70
41_A65_F0.6070.70
18_M52_G0.6050.69
56_F62_H0.6050.69
22_K25_A0.5950.68
42_I75_I0.5900.68
54_Q57_R0.5840.67
21_D31_R0.5840.67
21_D25_A0.5800.66
20_I39_L0.5790.66
71_L74_V0.5740.65
46_A53_M0.5740.65
21_D65_F0.5720.65
55_T80_I0.5680.65
14_G44_F0.5670.64
48_G52_G0.5660.64
16_W83_Y0.5620.64
15_F20_I0.5620.64
10_I51_L0.5620.64
16_W26_Q0.5600.64
25_A31_R0.5530.63
12_L78_I0.5390.61
8_V11_N0.5380.60
35_D39_L0.5350.60
75_I82_I0.5280.59
15_F19_G0.5280.59
77_A81_A0.5250.59
22_K34_E0.5150.57
38_W68_G0.5140.57
4_A8_V0.5130.57
18_M62_H0.5090.56
7_L80_I0.5000.55
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  
4cofA 3 0.2135 8.8 0.922 Contact Map
2ks1B 1 0.4045 5.5 0.929 Contact Map
4pypA 1 0.9438 4.7 0.931 Contact Map
4l6rA 1 0.9775 4.6 0.931 Contact Map
4zw9A 1 0.9326 4.3 0.932 Contact Map
2yiuB 1 0.2809 3.5 0.935 Contact Map
4j05A 3 0.9888 3 0.938 Contact Map
1fftB 1 0.764 2.8 0.938 Contact Map
2l2tA 2 0.4045 2.6 0.94 Contact Map
3wdoA 1 1 2.6 0.94 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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