GREMLIN Database
YCSD - Uncharacterized protein YcsD
UniProt: P42961 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 130 (123)
Sequences: 3487 (1916)
Seq/√Len: 172.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
84_G117_Q2.7731.00
22_E25_K2.7621.00
29_A59_T2.5421.00
79_K123_E2.3061.00
30_Y91_R2.2861.00
28_A93_D2.2641.00
55_A94_L2.2431.00
56_L94_L2.2311.00
77_V80_A2.1491.00
39_F47_M2.0601.00
111_K118_P2.0411.00
52_V92_L1.9701.00
97_E109_H1.9431.00
113_S118_P1.8961.00
80_A122_A1.8351.00
95_T113_S1.8271.00
109_H123_E1.8141.00
28_A95_T1.7931.00
60_A108_G1.7171.00
99_T109_H1.6671.00
113_S116_E1.6651.00
30_Y93_D1.6641.00
52_V120_A1.6191.00
44_Q85_E1.6041.00
26_H97_E1.5891.00
38_W41_T1.5841.00
26_H95_T1.5521.00
19_T30_Y1.5501.00
95_T111_K1.5471.00
20_D26_H1.4941.00
17_G30_Y1.4841.00
27_A63_T1.4741.00
32_L91_R1.4591.00
96_F110_A1.4571.00
20_D28_A1.4511.00
22_E26_H1.4051.00
106_V126_I1.3611.00
18_V62_F1.3401.00
10_Y41_T1.3371.00
73_L85_E1.2911.00
31_K37_D1.2741.00
47_M51_L1.2721.00
93_D113_S1.2241.00
25_K97_E1.2061.00
44_Q87_V1.2051.00
90_D114_V1.1511.00
94_L112_A1.1451.00
46_E73_L1.1441.00
101_N106_V1.1401.00
83_L121_E1.1361.00
110_A124_I1.1281.00
18_V29_A1.0901.00
76_S125_G1.0891.00
15_I59_T1.0851.00
84_G119_V1.0841.00
44_Q71_L1.0741.00
10_Y36_N1.0711.00
44_Q73_L1.0661.00
33_I47_M1.0641.00
93_D116_E1.0611.00
52_V112_A1.0571.00
27_A59_T1.0511.00
19_T93_D1.0400.99
75_S125_G1.0310.99
112_A120_A1.0280.99
72_G126_I1.0260.99
60_A96_F1.0260.99
47_M55_A1.0250.99
17_G32_L1.0020.99
92_L112_A0.9970.99
5_S62_F0.9920.99
10_Y35_E0.9920.99
53_I77_V0.9870.99
5_S65_I0.9860.99
19_T28_A0.9820.99
74_L77_V0.9640.99
86_A119_V0.9420.99
99_T107_F0.9380.99
118_P121_E0.9280.99
65_I106_V0.9060.99
91_R115_G0.8970.98
108_G126_I0.8870.98
98_V106_V0.8850.98
67_D70_S0.8800.98
101_N104_G0.8700.98
111_K121_E0.8690.98
21_S27_A0.8680.98
107_F125_G0.8650.98
81_E125_G0.8650.98
56_L122_A0.8610.98
27_A62_F0.8570.98
53_I80_A0.8530.98
78_K123_E0.8500.98
10_Y32_L0.8430.98
97_E111_K0.8420.98
21_S66_T0.8330.97
8_H14_F0.8290.97
99_T123_E0.8240.97
78_K107_F0.8190.97
42_D50_S0.8130.97
15_I62_F0.8090.97
6_L61_A0.8070.97
80_A120_A0.8050.97
75_S126_I0.7900.96
75_S105_F0.7790.96
86_A92_L0.7540.95
56_L120_A0.7520.95
100_R103_R0.7500.95
64_G106_V0.7480.95
46_E49_F0.7400.95
17_G91_R0.7280.94
39_F51_L0.7170.94
83_L118_P0.6970.93
109_H121_E0.6920.93
31_K34_S0.6900.93
102_R105_F0.6890.93
33_I39_F0.6890.93
34_S37_D0.6860.93
5_S66_T0.6840.92
8_H12_F0.6830.92
35_E45_T0.6800.92
18_V59_T0.6800.92
63_T108_G0.6760.92
42_D49_F0.6710.92
35_E39_F0.6710.92
31_K36_N0.6630.91
10_Y17_G0.6620.91
10_Y34_S0.6550.91
84_G87_V0.6520.91
53_I122_A0.6490.90
40_I49_F0.6480.90
72_G108_G0.6430.90
8_H61_A0.6380.90
64_G126_I0.6360.89
77_V82_K0.6350.89
36_N39_F0.6300.89
87_V90_D0.6280.89
23_P66_T0.6280.89
64_G108_G0.6280.89
14_F51_L0.6250.89
27_A60_A0.6230.88
64_G72_G0.6230.88
33_I86_A0.6180.88
35_E38_W0.6180.88
50_S81_E0.6150.88
15_I94_L0.6100.87
56_L112_A0.6020.87
35_E41_T0.6010.87
4_L43_T0.6010.87
56_L110_A0.5960.86
76_S81_E0.5960.86
81_E121_E0.5960.86
45_T49_F0.5920.86
32_L36_N0.5880.85
60_A110_A0.5870.85
59_T94_L0.5780.84
49_F81_E0.5770.84
67_D126_I0.5670.83
105_F125_G0.5650.83
40_I88_P0.5610.83
93_D115_G0.5610.83
49_F83_L0.5570.82
46_E50_S0.5520.82
17_G115_G0.5520.82
100_R107_F0.5470.81
62_F66_T0.5460.81
59_T63_T0.5440.81
5_S70_S0.5400.80
42_D46_E0.5350.80
72_G106_V0.5320.79
6_L96_F0.5210.78
74_L124_I0.5190.78
49_F86_A0.5190.78
32_L35_E0.5180.77
96_F108_G0.5180.77
21_S26_H0.5170.77
4_L66_T0.5140.77
24_G98_V0.5130.77
72_G75_S0.5090.76
84_G115_G0.5060.76
34_S89_G0.5050.76
63_T66_T0.5010.75
65_I108_G0.5010.75
59_T96_F0.5000.75
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  
2gllA 3 1 100 0.228 Contact Map
1u1zA 3 1 100 0.234 Contact Map
1z6bA 3 0.9846 100 0.279 Contact Map
2cf2C 2 0.9923 100 0.283 Contact Map
3d6xA 3 1 100 0.292 Contact Map
3q62A 2 0.9923 100 0.311 Contact Map
4h4gA 3 0.9846 100 0.332 Contact Map
4i83A 3 0.9846 100 0.335 Contact Map
4b0bA 2 0.9923 99.9 0.359 Contact Map
3esiA 4 0.8923 99.8 0.536 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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