GREMLIN Database
YVYD - Putative sigma-54 modulation protein
UniProt: P28368 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 189 (176)
Sequences: 2135 (1291)
Seq/√Len: 97.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
70_N76_A5.6031.00
16_L73_M3.6421.00
55_V80_A2.8501.00
20_V41_V2.6321.00
7_G12_V2.5681.00
165_N172_N2.2551.00
14_P18_D2.2291.00
89_R93_T2.2161.00
43_L51_S2.1621.00
150_I174_V2.1571.00
133_I146_S2.1531.00
12_V17_K2.0261.00
162_V173_V2.0261.00
2_N36_D2.0041.00
51_S73_M1.9841.00
52_K69_H1.9071.00
133_I150_I1.8831.00
19_H77_I1.8211.00
50_E69_H1.7931.00
53_V76_A1.7701.00
65_R158_H1.7191.00
132_D181_K1.6611.00
68_V79_L1.6531.00
104_S107_Y1.6491.00
13_T16_L1.6441.00
131_L181_K1.6331.00
162_V171_T1.6101.00
24_I55_V1.5931.00
164_T170_L1.5861.00
43_L73_M1.5591.00
56_T158_H1.5571.00
131_L154_N1.5521.00
37_A57_I1.5511.00
146_S163_F1.5141.00
63_A156_L1.4821.00
153_M156_L1.4801.00
86_R90_K1.4721.00
20_V39_V1.4671.00
148_E152_Q1.4651.00
41_V53_V1.4381.00
66_S80_A1.4321.00
145_D148_E1.4311.00
18_D22_R1.4231.00
70_N75_N1.4030.99
144_M152_Q1.3900.99
164_T171_T1.3890.99
137_K158_H1.3860.99
7_G13_T1.3740.99
106_K110_A1.3730.99
133_I184_L1.3630.99
106_K111_N1.3530.99
16_L77_I1.3520.99
164_T169_N1.3520.99
13_T74_Y1.3380.99
131_L150_I1.3210.99
93_T97_R1.3210.99
39_V55_V1.3200.99
44_K52_K1.3040.99
107_Y111_N1.2990.99
177_R183_G1.2950.99
6_R38_D1.2750.99
29_R85_E1.2650.99
162_V187_P1.2490.99
173_V185_I1.2470.99
138_R186_E1.2420.99
106_K109_L1.2290.99
160_F173_V1.2240.99
145_D166_A1.2210.99
5_I20_V1.2080.98
16_L41_V1.2060.98
159_N176_R1.1950.98
25_G28_E1.1940.98
148_E151_L1.1920.98
172_N187_P1.1900.98
30_Y85_E1.1890.98
73_M77_I1.1880.98
137_K161_F1.1710.98
158_H161_F1.1640.98
7_G10_I1.1550.98
15_A74_Y1.1530.98
90_K93_T1.1300.98
23_K26_K1.1210.97
165_N186_E1.1160.97
104_S110_A1.0980.97
150_I154_N1.0770.97
150_I182_Y1.0580.96
105_P108_L1.0460.96
124_D127_E1.0370.96
136_Q146_S1.0350.96
79_L83_K1.0280.96
121_V124_D1.0200.96
65_R137_K1.0130.95
56_T63_A1.0090.95
67_E137_K1.0050.95
24_I39_V1.0000.95
14_P17_K0.9980.95
10_I50_E0.9850.95
2_N37_A0.9810.95
146_S184_L0.9770.94
86_R93_T0.9770.94
6_R40_N0.9750.94
136_Q184_L0.9690.94
107_Y110_A0.9550.94
103_G106_K0.9540.94
19_H74_Y0.9520.94
16_L74_Y0.9490.94
142_K152_Q0.9480.93
136_Q186_E0.9470.93
94_K179_D0.9400.93
5_I12_V0.9290.93
125_I128_E0.9270.93
56_T65_R0.9230.93
137_K156_L0.9190.92
137_K153_M0.9170.92
19_H75_N0.9160.92
31_F34_S0.9090.92
105_P109_L0.9060.92
5_I83_K0.9000.92
68_V83_K0.8990.92
41_V73_M0.8820.91
10_I73_M0.8800.91
10_I74_Y0.8790.91
134_V181_K0.8790.91
160_F185_I0.8720.90
175_Y183_G0.8690.90
99_F102_Q0.8540.89
31_F95_V0.8490.89
56_T161_F0.8430.89
45_F50_E0.8410.89
88_I97_R0.8320.88
74_Y77_I0.8320.88
122_Q128_E0.8250.88
54_E158_H0.8190.87
174_V182_Y0.8190.87
24_I37_A0.8180.87
102_Q107_Y0.8170.87
123_D126_E0.8170.87
72_D75_N0.8160.87
83_K87_Q0.8010.86
152_Q161_F0.8010.86
24_I82_N0.7890.85
67_E158_H0.7880.85
67_E155_M0.7840.85
88_I99_F0.7820.85
139_F158_H0.7770.84
135_R139_F0.7760.84
2_N33_H0.7730.84
165_N187_P0.7680.84
65_R135_R0.7670.84
68_V80_A0.7670.84
35_V64_L0.7610.83
40_N54_E0.7500.82
81_T101_E0.7490.82
10_I53_V0.7480.82
53_V73_M0.7440.82
17_K21_E0.7420.82
19_H34_S0.7420.82
153_M182_Y0.7410.81
31_F88_I0.7400.81
65_R161_F0.7330.81
27_L30_Y0.7320.81
56_T155_M0.7320.81
135_R159_N0.7300.80
54_E67_E0.7290.80
5_I21_E0.7290.80
100_R104_S0.7280.80
24_I81_T0.7280.80
153_M161_F0.7140.79
43_L74_Y0.7140.79
97_R100_R0.7080.78
56_T67_E0.7060.78
41_V44_K0.7060.78
91_H95_V0.7050.78
10_I16_L0.7030.78
38_D57_I0.7020.78
33_H37_A0.7010.78
4_N38_D0.6980.77
160_F182_Y0.6930.77
154_N181_K0.6880.76
65_R156_L0.6870.76
26_K90_K0.6830.76
135_R154_N0.6750.75
168_T186_E0.6720.75
168_T172_N0.6710.75
165_N168_T0.6700.75
153_M178_N0.6680.74
152_Q155_M0.6620.74
56_T137_K0.6590.73
19_H78_D0.6550.73
102_Q106_K0.6490.72
104_S108_L0.6440.72
137_K159_N0.6430.71
141_L179_D0.6430.71
18_D21_E0.6400.71
67_E153_M0.6310.70
14_P21_E0.6310.70
28_E57_I0.6290.70
101_E109_L0.6290.70
101_E110_A0.6260.69
61_D170_L0.6240.69
131_L145_D0.6210.69
19_H163_F0.6210.69
90_K132_D0.6180.68
135_R158_H0.6080.67
51_S76_A0.6050.67
31_F59_M0.6000.66
55_V84_L0.5990.66
15_A59_M0.5970.66
87_Q90_K0.5970.66
103_G107_Y0.5960.66
27_L81_T0.5940.65
70_N79_L0.5930.65
32_D90_K0.5880.65
25_G82_N0.5880.65
68_V86_R0.5860.64
97_R101_E0.5850.64
146_S150_I0.5800.64
32_D35_V0.5750.63
56_T135_R0.5740.63
8_E24_I0.5710.62
102_Q105_P0.5700.62
57_I108_L0.5690.62
108_L111_N0.5610.61
124_D128_E0.5610.61
15_A43_L0.5590.61
59_M88_I0.5500.60
1_M8_E0.5480.59
52_K67_E0.5460.59
93_T96_N0.5440.59
38_D60_T0.5440.59
91_H155_M0.5430.59
111_N126_E0.5430.59
91_H99_F0.5410.58
99_F104_S0.5400.58
13_T77_I0.5380.58
22_R124_D0.5370.58
20_V77_I0.5350.57
8_E40_N0.5330.57
102_Q110_A0.5320.57
143_P147_E0.5290.57
29_R33_H0.5290.57
110_A164_T0.5280.56
40_N44_K0.5280.56
15_A19_H0.5260.56
22_R25_G0.5220.56
67_E157_G0.5220.56
151_L155_M0.5190.55
28_E37_A0.5160.55
51_S74_Y0.5120.54
32_D66_S0.5120.54
162_V185_I0.5120.54
1_M61_D0.5120.54
54_E177_R0.5110.54
95_V151_L0.5100.54
153_M174_V0.5070.54
102_Q108_L0.5050.53
120_A124_D0.5050.53
84_L99_F0.5050.53
141_L171_T0.5040.53
59_M91_H0.5020.53
134_V180_G0.5010.53
54_E65_R0.5010.53
40_N61_D0.5000.53
137_K160_F0.5000.53
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  
1imuA 1 0.5661 100 0.547 Contact Map
3v26X 1 0.5026 100 0.551 Contact Map
3tqmA 1 0.4921 100 0.552 Contact Map
3v2cY 1 0.5026 100 0.552 Contact Map
2ywqA 1 0.4709 99.9 0.556 Contact Map
4heiA 1 0.4868 99.9 0.557 Contact Map
3ka5A 2 0.3069 99.9 0.583 Contact Map
3lyvA 2 0.3122 99.9 0.585 Contact Map
3k2tA 1 0.2804 99.9 0.591 Contact Map
1pu1A 1 0.4074 20.5 0.949 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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