GREMLIN Database
YPMS - Uncharacterized protein YpmS
UniProt: P54179 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 187 (181)
Sequences: 300 (250)
Seq/√Len: 18.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
172_N175_K4.6301.00
109_V171_I4.0341.00
12_L15_N3.7151.00
170_K177_E2.8990.99
169_D181_S2.8620.99
173_L178_I2.8150.98
108_D156_S2.8090.98
55_A59_N2.6870.98
118_L121_L2.6130.97
43_Y181_S2.4590.96
8_F11_L2.3420.95
145_H148_D2.3330.95
26_V149_K2.2860.94
55_A72_Y2.2460.94
61_Y136_Y2.1870.93
76_I178_I2.1660.93
62_L167_K2.1310.92
72_Y142_V2.1300.92
125_I149_K2.0950.91
9_F13_A1.9950.89
70_L114_T1.9600.88
128_V168_A1.9220.87
107_G111_L1.9090.87
145_H150_S1.8560.85
138_L151_I1.8470.85
8_F12_L1.8050.83
113_V171_I1.7590.82
70_L177_E1.6780.79
7_L133_D1.6670.78
49_S170_K1.6630.78
108_D154_R1.6570.78
3_K7_L1.6360.77
23_V145_H1.6360.77
10_I18_L1.6340.77
84_G136_Y1.5860.74
40_E109_V1.5860.74
36_K148_D1.5480.73
107_G124_P1.5380.72
61_Y131_Y1.5240.71
30_G96_F1.5230.71
113_V152_E1.5050.70
113_V129_L1.4640.68
62_L165_Y1.4590.68
16_F26_V1.4570.68
51_K176_D1.4150.65
123_I127_F1.4050.65
7_L15_N1.3870.64
53_S89_F1.3710.63
45_F123_I1.3510.62
85_K92_S1.3470.62
47_V86_I1.3330.61
20_A37_D1.3270.60
19_A33_A1.3030.59
23_V77_D1.3030.59
143_H157_E1.2960.58
104_K108_D1.2870.58
84_G151_I1.2730.57
58_V182_Y1.2610.56
38_A75_E1.2580.56
54_L74_V1.2360.55
72_Y136_Y1.2360.55
77_D81_H1.2260.54
131_Y142_V1.2210.54
153_V156_S1.2140.53
59_N109_V1.2110.53
57_F116_F1.1980.52
111_L119_G1.1490.49
102_T114_T1.1410.49
71_D153_V1.1330.48
102_T110_E1.1220.48
49_S153_V1.1190.47
123_I139_P1.1170.47
99_F139_P1.1080.47
99_F111_L1.1070.47
36_K63_N1.1030.46
78_D110_E1.0760.45
110_E152_E1.0720.45
18_L24_A1.0640.44
13_A154_R1.0630.44
50_T53_S1.0390.43
125_I182_Y1.0360.42
76_I153_V1.0310.42
55_A123_I1.0230.42
49_S89_F1.0200.41
126_S144_V1.0060.41
84_G95_A1.0020.40
169_D182_Y1.0000.40
26_V130_N0.9980.40
50_T144_V0.9970.40
47_V161_T0.9960.40
58_V72_Y0.9950.40
74_V113_V0.9870.39
23_V27_L0.9850.39
4_W8_F0.9820.39
125_I129_L0.9770.39
22_F63_N0.9750.39
12_L34_Q0.9620.38
50_T81_H0.9600.38
34_Q62_L0.9590.38
49_S53_S0.9580.38
116_F125_I0.9400.37
111_L173_L0.9400.37
107_G178_I0.9350.36
134_S162_N0.9330.36
47_V182_Y0.9240.36
39_S73_K0.9000.34
113_V141_F0.9000.34
105_K157_E0.8990.34
114_T182_Y0.8900.34
53_S113_V0.8870.34
70_L153_V0.8850.33
104_K164_M0.8830.33
33_A37_D0.8820.33
53_S171_I0.8800.33
49_S95_A0.8800.33
36_K40_E0.8760.33
44_G49_S0.8700.33
60_S106_N0.8650.32
54_L117_S0.8540.32
112_N146_P0.8510.32
80_V146_P0.8450.31
58_V76_I0.8430.31
12_L177_E0.8290.30
158_M163_G0.8270.30
46_Q50_T0.8190.30
22_F144_V0.8180.30
11_L77_D0.7990.29
123_I179_E0.7990.29
49_S181_S0.7940.29
140_S177_E0.7900.28
13_A22_F0.7870.28
45_F152_E0.7850.28
94_D116_F0.7830.28
30_G78_D0.7830.28
97_I153_V0.7760.28
16_F88_A0.7750.28
132_M136_Y0.7710.27
92_S105_K0.7660.27
83_A94_D0.7650.27
107_G173_L0.7600.27
20_A23_V0.7580.27
41_S149_K0.7470.26
89_F153_V0.7460.26
27_L164_M0.7460.26
83_A128_V0.7430.26
34_Q93_I0.7400.26
58_V151_I0.7380.26
22_F170_K0.7380.26
40_E140_S0.7340.26
167_K183_Y0.7330.26
138_L175_K0.7300.25
10_I46_Q0.7280.25
79_D106_N0.7230.25
58_V74_V0.7200.25
53_S109_V0.7190.25
50_T60_S0.7170.25
51_K61_Y0.7050.24
99_F183_Y0.7010.24
40_E58_V0.7010.24
139_P168_A0.6990.24
62_L71_D0.6960.24
77_D163_G0.6950.24
53_S152_E0.6930.24
7_L108_D0.6910.24
26_V54_L0.6890.24
16_F33_A0.6840.23
49_S86_I0.6780.23
5_K95_A0.6770.23
99_F146_P0.6740.23
54_L158_M0.6740.23
143_H154_R0.6730.23
51_K177_E0.6710.23
5_K111_L0.6700.23
32_Q79_D0.6600.22
3_K6_R0.6580.22
70_L85_K0.6580.22
109_V131_Y0.6570.22
12_L115_K0.6560.22
57_F98_A0.6550.22
87_K148_D0.6540.22
41_S63_N0.6530.22
131_Y136_Y0.6510.22
97_I177_E0.6500.22
5_K9_F0.6500.22
55_A182_Y0.6470.22
126_S160_L0.6460.22
79_D93_I0.6430.22
96_F117_S0.6430.22
54_L180_F0.6420.22
100_E104_K0.6410.21
110_E150_S0.6410.21
76_I168_A0.6390.21
17_I140_S0.6390.21
82_V88_A0.6380.21
7_L77_D0.6360.21
140_S157_E0.6350.21
50_T178_I0.6320.21
97_I113_V0.6270.21
6_R13_A0.6260.21
88_A142_V0.6230.21
55_A95_A0.6220.21
97_I118_L0.6210.21
3_K9_F0.6210.21
94_D139_P0.6180.21
112_N140_S0.6170.20
17_I175_K0.6140.20
7_L47_V0.6140.20
84_G117_S0.6130.20
19_A151_I0.6110.20
62_L157_E0.6100.20
42_E172_N0.6090.20
62_L105_K0.6070.20
36_K62_L0.6040.20
65_K97_I0.5980.20
3_K12_L0.5980.20
108_D155_L0.5980.20
14_I172_N0.5970.20
10_I14_I0.5960.20
84_G142_V0.5950.20
75_E144_V0.5950.20
4_W11_L0.5950.20
64_D135_F0.5940.20
111_L124_P0.5940.20
159_P165_Y0.5830.19
11_L48_T0.5830.19
18_L176_D0.5790.19
82_V86_I0.5760.19
20_A48_T0.5750.19
42_E135_F0.5740.19
11_L178_I0.5720.19
87_K97_I0.5710.19
78_D97_I0.5660.18
58_V153_V0.5660.18
54_L147_G0.5650.18
27_L76_I0.5620.18
146_P166_V0.5620.18
168_A180_F0.5600.18
95_A158_M0.5590.18
114_T157_E0.5550.18
94_D125_I0.5540.18
27_L45_F0.5530.18
139_P142_V0.5500.18
78_D182_Y0.5460.18
71_D134_S0.5450.18
99_F155_L0.5430.18
96_F171_I0.5420.18
53_S66_A0.5390.17
130_N134_S0.5360.17
44_G151_I0.5360.17
31_E130_N0.5330.17
113_V125_I0.5320.17
13_A102_T0.5320.17
59_N116_F0.5310.17
102_T112_N0.5290.17
71_D84_G0.5260.17
47_V57_F0.5230.17
80_V154_R0.5210.17
21_G133_D0.5210.17
27_L182_Y0.5210.17
16_F69_K0.5160.17
110_E123_I0.5160.17
70_L80_V0.5160.17
74_V80_V0.5150.17
51_K107_G0.5140.17
15_N28_L0.5140.17
15_N19_A0.5130.17
58_V166_V0.5100.16
44_G181_S0.5070.16
10_I69_K0.5060.16
154_R164_M0.5060.16
59_N82_V0.5060.16
6_R90_S0.5000.16
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  
1q8kA 1 0.4064 8.6 0.958 Contact Map
4uu4A 1 0.6631 8.6 0.958 Contact Map
2g8sA 2 0.2941 8.2 0.958 Contact Map
1pfoA 2 0.5401 8.1 0.958 Contact Map
4tphA 2 0.1765 7.6 0.959 Contact Map
1twyA 5 0.7059 7.2 0.959 Contact Map
3aevA 1 0.3636 7.1 0.959 Contact Map
4nngA 1 0.4171 7 0.959 Contact Map
1wi5A 1 0.4439 6.4 0.96 Contact Map
3cw2C 1 0.3957 6.2 0.96 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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