GREMLIN Database
YCED - Uncharacterized protein YceD
UniProt: P0AB28 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11119
Length: 173 (162)
Sequences: 712 (530)
Seq/√Len: 41.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
118_D121_A5.3891.00
71_L82_H4.2681.00
33_R125_D4.0111.00
45_V67_V3.8871.00
63_G88_Y3.5741.00
76_C137_H3.4561.00
66_K85_Y3.1601.00
25_I44_D2.9231.00
68_T81_T2.8321.00
15_T22_Y2.7881.00
46_E66_K2.5481.00
71_L80_F2.4071.00
95_S98_Q2.2371.00
21_D50_S2.2171.00
96_D99_A2.2081.00
69_V84_V2.1320.99
37_S128_I2.1040.99
47_C63_G2.1040.99
76_C142_C2.0410.99
23_Q48_S1.9520.99
8_L118_D1.8540.98
137_H142_C1.8540.98
62_N89_C1.7230.97
28_P67_V1.7120.97
15_T51_F1.7120.97
166_V169_S1.6710.97
39_V72_E1.6550.97
164_F167_L1.6020.96
165_A168_A1.5010.94
26_Y31_V1.4850.94
12_P16_A1.4650.93
51_F106_Y1.4540.93
49_M119_L1.4420.93
65_A86_T1.4390.93
48_S64_D1.4380.93
102_L108_P1.4190.92
60_V103_P1.4000.92
102_L106_Y1.3680.91
25_I46_E1.3610.91
91_S102_L1.3540.90
74_Q128_I1.3510.90
10_L90_F1.3390.90
28_P84_V1.3090.89
27_T30_Q1.3030.89
34_V69_V1.3010.88
10_L51_F1.2710.87
68_T83_Q1.2700.87
80_F137_H1.2640.87
33_R124_E1.2570.87
58_L106_Y1.2350.86
6_L51_F1.2340.86
103_P108_P1.2280.85
70_T81_T1.1940.84
40_S70_T1.1750.83
126_E129_L1.1430.81
23_Q46_E1.1210.80
61_L122_M1.1160.79
21_D48_S1.1100.79
51_F61_L1.1080.79
45_V65_A1.1010.78
38_V84_V1.0970.78
9_T80_F1.0970.78
103_P126_E1.0860.77
94_R107_E1.0830.77
163_P167_L1.0810.77
34_V127_I1.0390.74
52_A62_N1.0180.73
98_Q101_A1.0160.73
12_P92_P1.0100.72
63_G108_P1.0080.72
27_T32_E1.0030.72
64_D87_T0.9920.71
96_D110_E0.9880.70
71_L74_Q0.9660.69
9_T123_V0.9590.68
28_P39_V0.9510.67
13_V94_R0.9450.67
12_P54_D0.9380.66
38_V128_I0.9160.64
6_L63_G0.9110.64
36_E104_E0.9050.64
65_A146_E0.9030.63
76_C80_F0.9030.63
35_A131_L0.9010.63
67_V127_I0.8980.63
26_Y50_S0.8930.62
107_E169_S0.8920.62
13_V117_I0.8850.62
54_D91_S0.8830.62
86_T126_E0.8770.61
97_E131_L0.8740.61
24_G123_V0.8710.61
24_G28_P0.8630.60
78_K153_E0.8550.59
17_Q53_I0.8550.59
19_R91_S0.8540.59
38_V43_S0.8490.59
26_Y45_V0.8460.58
50_S123_V0.8450.58
128_I162_N0.8430.58
64_D85_Y0.8410.58
105_A129_L0.8360.57
24_G103_P0.8330.57
63_G89_C0.8320.57
69_V86_T0.8260.56
14_R112_N0.8200.56
78_K87_T0.8190.56
37_S119_L0.8160.56
58_L142_C0.8150.55
123_V138_D0.8110.55
57_R154_L0.8100.55
57_R102_L0.8040.54
24_G113_E0.8040.54
125_D156_E0.8040.54
11_D169_S0.7900.53
159_Q162_N0.7890.53
167_L171_K0.7870.53
15_T20_L0.7750.52
26_Y120_L0.7740.52
103_P129_L0.7710.51
110_E135_P0.7690.51
17_Q162_N0.7640.51
82_H99_A0.7530.50
40_S81_T0.7500.49
112_N115_G0.7490.49
51_F109_I0.7450.49
56_Q89_C0.7450.49
90_F108_P0.7430.49
135_P139_S0.7420.49
81_T138_D0.7410.49
90_F136_V0.7400.48
65_A74_Q0.7280.47
24_G49_M0.7270.47
103_P125_D0.7250.47
27_T125_D0.7240.47
110_E125_D0.7200.47
63_G76_C0.7170.46
51_F63_G0.7160.46
108_P122_M0.7140.46
24_G31_V0.7130.46
91_S108_P0.7100.46
83_Q86_T0.7040.45
65_A127_I0.7040.45
27_T46_E0.6960.44
68_T166_V0.6900.44
84_V130_A0.6830.43
45_V127_I0.6810.43
44_D84_V0.6800.43
46_E68_T0.6800.43
13_V69_V0.6780.43
72_E169_S0.6770.43
67_V131_L0.6740.42
8_L11_D0.6720.42
34_V57_R0.6630.41
162_N166_V0.6620.41
109_I117_I0.6570.41
34_V124_E0.6520.40
57_R104_E0.6480.40
135_P168_A0.6480.40
70_T79_P0.6460.40
136_V172_R0.6460.40
164_F170_L0.6450.40
27_T86_T0.6450.40
121_A169_S0.6440.40
110_E165_A0.6420.39
61_L92_P0.6360.39
93_V108_P0.6360.39
54_D93_V0.6320.39
158_A161_P0.6300.38
74_Q102_L0.6290.38
45_V144_V0.6270.38
111_V158_A0.6180.37
29_D130_A0.6150.37
35_A91_S0.6150.37
48_S84_V0.6130.37
67_V71_L0.6120.37
16_A22_Y0.6110.37
39_V172_R0.6090.37
109_I112_N0.6080.36
16_A170_L0.6060.36
99_A110_E0.6050.36
36_E40_S0.6050.36
58_L93_V0.6040.36
22_Y113_E0.6030.36
26_Y79_P0.6020.36
10_L13_V0.6010.36
16_A59_A0.5970.35
42_D81_T0.5960.35
41_V72_E0.5960.35
60_V91_S0.5950.35
120_L134_V0.5910.35
47_C51_F0.5900.35
49_M63_G0.5880.35
57_R165_A0.5850.34
22_Y51_F0.5830.34
16_A162_N0.5800.34
142_C171_K0.5800.34
64_D81_T0.5780.34
75_R124_E0.5770.34
47_C88_Y0.5760.34
104_E165_A0.5760.34
125_D135_P0.5750.34
31_V121_A0.5750.34
93_V99_A0.5670.33
7_P12_P0.5670.33
69_V82_H0.5610.32
38_V66_K0.5600.32
6_L107_E0.5560.32
107_E158_A0.5540.32
62_N87_T0.5530.32
100_E104_E0.5530.32
100_E110_E0.5520.32
51_F91_S0.5490.31
22_Y138_D0.5480.31
53_I168_A0.5480.31
154_L159_Q0.5460.31
85_Y92_P0.5460.31
74_Q77_G0.5440.31
12_P47_C0.5440.31
14_R71_L0.5440.31
11_D170_L0.5400.31
43_S123_V0.5400.31
12_P117_I0.5370.31
60_V101_A0.5330.30
19_R168_A0.5330.30
15_T61_L0.5300.30
118_D131_L0.5300.30
41_V62_N0.5260.30
18_K30_Q0.5250.30
30_Q41_V0.5230.29
27_T64_D0.5220.29
42_D68_T0.5200.29
34_V86_T0.5200.29
153_E156_E0.5170.29
60_V111_V0.5160.29
7_P113_E0.5140.29
17_Q109_I0.5110.28
54_D58_L0.5090.28
86_T97_E0.5080.28
46_E50_S0.5050.28
12_P133_V0.5040.28
90_F162_N0.5010.28
9_T116_E0.5000.28
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  
4u9pA 3 0.3642 10.9 0.949 Contact Map
3owtC 1 0.0809 5.3 0.956 Contact Map
1n9rA 4 0.0462 4.5 0.957 Contact Map
4ww4A 2 0.3179 2.3 0.963 Contact Map
1yycA 1 0.4451 2.1 0.964 Contact Map
2i5oA 1 0.1792 2 0.964 Contact Map
1xo8A 1 0.4451 2 0.964 Contact Map
4gpsA 1 0.3988 1.8 0.965 Contact Map
4toiA 2 0.2832 1.8 0.965 Contact Map
1bm4A 1 0.1445 1.7 0.966 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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