GREMLIN Database
Ycf4 - Ycf4
PFAM: PF02392 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 178 (176)
Sequences: 907 (477)
Seq/√Len: 35.9
META: 0.614

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
27_G68_G5.7251.00
91_N94_E5.1921.00
77_L81_W4.9181.00
97_V120_I4.8951.00
24_F72_S4.1201.00
81_W105_P3.5511.00
34_G62_G3.1451.00
55_I59_I3.0281.00
20_A76_W2.9541.00
97_V117_L2.8791.00
48_D51_Q2.8291.00
5_R89_E2.4271.00
18_F21_F2.2860.99
102_W110_R2.2740.99
137_I165_A2.1370.99
60_V63_F2.1140.99
124_R146_D2.0950.99
96_I114_T2.0270.99
35_L39_L1.9040.98
14_F18_F1.8860.98
45_P61_M1.8510.97
150_T153_G1.8050.97
152_V155_P1.7910.97
95_G117_L1.7730.97
42_N48_D1.7640.96
18_F22_I1.7480.96
49_P52_L1.6930.95
98_R112_E1.6790.95
135_R155_P1.6680.95
97_V141_L1.6370.95
59_I63_F1.6350.94
6_Q87_Y1.6250.94
33_A47_S1.5290.92
126_E134_R1.4730.91
31_L62_G1.4380.90
33_A44_L1.4190.89
97_V139_L1.4090.89
106_G109_R1.4010.88
77_L83_V1.3920.88
39_L45_P1.3810.88
28_L69_L1.3710.87
90_F128_K1.3200.85
34_G39_L1.2940.84
92_K171_F1.2780.83
130_G133_P1.2350.81
46_F61_M1.2300.81
120_I174_V1.2220.80
7_K82_D1.1990.79
141_L173_G1.1790.78
121_Q140_R1.1610.77
143_G146_D1.1600.77
115_Y144_R1.1560.76
23_L75_L1.1560.76
61_M137_I1.1370.75
135_R158_L1.1030.73
68_G90_F1.0870.72
6_Q165_A1.0830.72
72_S76_W1.0780.71
10_G16_N1.0780.71
140_R146_D1.0730.71
24_F76_W1.0720.71
16_N19_W1.0710.71
26_G91_N1.0470.69
96_I137_I1.0360.68
96_I116_P1.0290.68
92_K111_I1.0250.67
33_A52_L1.0240.67
162_E169_A1.0100.66
48_D127_I1.0090.66
73_L159_S1.0050.66
67_A137_I0.9850.64
2_N93_K0.9800.64
13_R85_S0.9790.64
87_Y108_N0.9750.63
119_D126_E0.9700.63
11_S104_F0.9640.62
17_Y171_F0.9490.61
122_S141_L0.9410.61
105_P109_R0.9360.60
71_L78_T0.9360.60
125_V143_G0.9340.60
87_Y112_E0.9260.59
139_L149_L0.9260.59
11_S83_V0.9230.59
115_Y145_R0.9230.59
130_G135_R0.9160.58
14_F28_L0.9140.58
147_I150_T0.9130.58
22_I28_L0.9120.58
29_G33_A0.9050.58
135_R150_T0.9030.57
156_L161_L0.8970.57
69_L142_K0.8960.57
87_Y98_R0.8950.57
165_A176_L0.8950.57
32_L36_S0.8940.57
49_P62_G0.8910.56
28_L79_I0.8880.56
102_W109_R0.8840.56
166_A170_R0.8820.56
161_L165_A0.8780.55
141_L146_D0.8770.55
74_Y157_T0.8730.55
61_M125_V0.8670.54
11_S15_S0.8660.54
45_P143_G0.8640.54
23_L71_L0.8630.54
114_T117_L0.8590.54
161_L170_R0.8570.53
26_G29_G0.8520.53
4_L7_K0.8480.53
53_V61_M0.8430.52
66_T167_E0.8240.51
122_S140_R0.8230.50
20_A75_L0.8170.50
44_L77_L0.8150.50
44_L49_P0.8040.49
19_W104_F0.8030.49
79_I82_D0.7990.48
55_I82_D0.7960.48
81_W106_G0.7920.48
21_F63_F0.7920.48
19_W81_W0.7900.48
59_I125_V0.7900.48
87_Y100_F0.7860.47
32_L107_K0.7860.47
70_L119_D0.7850.47
160_E174_V0.7810.47
168_L176_L0.7780.47
60_V78_T0.7770.46
174_V177_E0.7740.46
104_F130_G0.7700.46
19_W72_S0.7690.46
27_G63_F0.7630.45
6_Q168_L0.7630.45
13_R16_N0.7550.45
76_W79_I0.7530.44
34_G43_L0.7520.44
70_L153_G0.7470.44
69_L149_L0.7420.43
48_D110_R0.7420.43
47_S176_L0.7370.43
62_G66_T0.7370.43
17_Y70_L0.7330.43
22_I144_R0.7310.42
67_A70_L0.7300.42
124_R158_L0.7260.42
6_Q164_Q0.7250.42
42_N49_P0.7230.42
10_G133_P0.7220.42
103_G109_R0.7180.41
11_S80_L0.7160.41
39_L43_L0.7150.41
98_R114_T0.7120.41
81_W109_R0.7100.41
21_F93_K0.7090.41
91_N98_R0.7050.40
31_L147_I0.7020.40
18_F28_L0.6950.39
158_L162_E0.6930.39
19_W46_F0.6900.39
26_G122_S0.6850.39
5_R113_L0.6840.39
32_L47_S0.6840.39
157_T169_A0.6800.38
80_L91_N0.6780.38
46_F125_V0.6740.38
29_G36_S0.6730.38
100_F138_Y0.6730.38
11_S78_T0.6720.38
114_T146_D0.6690.37
12_R32_L0.6690.37
30_F162_E0.6590.37
160_E167_E0.6570.36
74_Y136_A0.6530.36
13_R154_Q0.6520.36
89_E106_G0.6520.36
41_I47_S0.6510.36
52_L173_G0.6500.36
83_V167_E0.6480.36
55_I87_Y0.6470.36
166_A169_A0.6470.36
61_M143_G0.6460.35
72_S79_I0.6440.35
68_G114_T0.6430.35
40_G60_V0.6400.35
8_I92_K0.6380.35
129_E158_L0.6360.35
98_R124_R0.6290.34
28_L31_L0.6260.34
4_L170_R0.6240.34
67_A71_L0.6220.34
119_D135_R0.6220.34
51_Q83_V0.6210.34
5_R114_T0.6190.33
138_Y151_R0.6180.33
127_I138_Y0.6090.33
25_L28_L0.6090.33
23_L49_P0.6090.33
88_N158_L0.6080.33
33_A55_I0.6080.33
52_L55_I0.6070.32
41_I154_Q0.6070.32
66_T96_I0.6040.32
9_L72_S0.6010.32
28_L72_S0.6000.32
38_Y163_E0.5990.32
123_I169_A0.5990.32
2_N5_R0.5970.32
107_K121_Q0.5940.31
63_F83_V0.5930.31
36_S45_P0.5900.31
19_W135_R0.5870.31
124_R136_A0.5830.31
31_L59_I0.5800.30
13_R135_R0.5780.30
8_I34_G0.5780.30
95_G142_K0.5780.30
19_W22_I0.5750.30
117_L122_S0.5720.30
7_K161_L0.5720.30
67_A158_L0.5720.30
91_N170_R0.5700.30
99_I115_Y0.5670.29
42_N128_K0.5670.29
97_V145_R0.5630.29
166_A175_P0.5540.29
23_L68_G0.5480.28
39_L114_T0.5460.28
33_A176_L0.5460.28
90_F171_F0.5450.28
135_R152_V0.5450.28
141_L145_R0.5440.28
37_S54_F0.5420.28
87_Y159_S0.5400.28
35_L78_T0.5390.27
4_L128_K0.5390.27
10_G177_E0.5380.27
61_M69_L0.5340.27
118_K121_Q0.5330.27
83_V106_G0.5330.27
26_G68_G0.5330.27
115_Y127_I0.5310.27
33_A49_P0.5300.27
116_P119_D0.5300.27
40_G89_E0.5290.27
95_G120_I0.5270.27
3_I72_S0.5260.27
80_L154_Q0.5250.27
74_Y103_G0.5250.27
3_I50_T0.5240.26
78_T104_F0.5210.26
88_N162_E0.5210.26
27_G119_D0.5200.26
3_I137_I0.5200.26
39_L51_Q0.5130.26
99_I158_L0.5090.25
120_I136_A0.5080.25
141_L144_R0.5070.25
102_W118_K0.5070.25
16_N75_L0.5060.25
123_I144_R0.5020.25
74_Y124_R0.5010.25
117_L120_I0.5000.25
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  
1ny4A 1 0.3933 16.1 0.963 Contact Map
4rb5J 1 0.1854 9.6 0.967 Contact Map
3w1yC 1 0.191 8.6 0.967 Contact Map
1p7bA 3 0.7865 8.3 0.968 Contact Map
3j20L 1 0.2022 7.4 0.968 Contact Map
4bpe1 1 0.3652 6.6 0.969 Contact Map
2jovA 1 0.264 6.3 0.969 Contact Map
4ujpV 1 0.2191 5.7 0.97 Contact Map
3j7aN 1 0.1742 5.6 0.97 Contact Map
2mewA 1 0.2191 5.5 0.97 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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