GREMLIN Database
Ycf34 - Hypothetical chloroplast protein Ycf34
PFAM: PF10718 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 78 (77)
Sequences: 559 (227)
Seq/√Len: 25.9
META: 0.78

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
69_E75_K5.1521.00
12_R33_D4.0071.00
38_E64_E3.2491.00
27_H32_P2.1850.97
37_K65_S2.1800.97
69_E72_K2.1200.97
42_H61_V1.8020.92
37_K64_E1.7850.92
1_M4_C1.7690.91
44_N62_G1.7250.90
24_G42_H1.6690.89
4_C7_C1.6470.88
28_L32_P1.5180.83
20_E32_P1.4750.81
3_I7_C1.4630.81
31_T77_R1.4510.80
43_V58_W1.4410.80
19_V57_E1.3960.78
6_N71_G1.3840.77
6_N68_E1.2790.71
72_K78_P1.2340.68
20_E27_H1.2310.68
32_P39_P1.2180.67
7_C13_C1.2110.67
21_T24_G1.1740.64
50_K53_D1.1710.64
45_I56_M1.1660.64
44_N65_S1.1660.64
15_T36_P1.0960.59
13_C16_Y1.0660.57
64_E75_K1.0640.57
57_E60_V1.0420.55
19_V39_P1.0340.54
66_F71_G1.0300.54
25_V32_P1.0290.54
23_H39_P1.0070.52
18_A22_Q0.9700.50
4_C13_C0.9650.49
31_T67_L0.9600.49
45_I50_K0.9590.49
49_D55_E0.9560.49
44_N61_V0.9450.48
22_Q58_W0.9450.48
37_K67_L0.9430.48
73_W78_P0.9420.48
63_C66_F0.9310.47
2_C7_C0.9210.46
9_W12_R0.9180.46
71_G78_P0.9150.46
46_R54_I0.8940.44
6_N70_P0.8920.44
18_A28_L0.8910.44
44_N54_I0.8720.43
17_H20_E0.8620.42
3_I13_C0.8520.41
14_I36_P0.8500.41
27_H39_P0.8500.41
58_W65_S0.8380.40
68_E74_S0.8350.40
26_P37_K0.8310.40
17_H32_P0.8300.40
65_S77_R0.8120.38
3_I6_N0.7830.36
18_A29_T0.7670.35
39_P60_V0.7610.35
25_V61_V0.7580.35
9_W61_V0.7540.34
7_C16_Y0.7540.34
30_E75_K0.7440.34
11_D32_P0.7420.34
9_W62_G0.7340.33
41_I66_F0.7320.33
8_H67_L0.7310.33
34_F44_N0.7030.31
64_E77_R0.7030.31
5_V8_H0.6900.30
68_E73_W0.6760.29
10_V15_T0.6740.29
38_E74_S0.6640.29
68_E77_R0.6590.28
40_T51_N0.6540.28
12_R28_L0.6530.28
63_C73_W0.6500.28
9_W60_V0.6490.28
70_P77_R0.6490.28
23_H32_P0.6420.27
31_T37_K0.6270.26
1_M7_C0.6210.26
8_H49_D0.6150.26
20_E25_V0.6150.26
22_Q36_P0.6110.26
19_V62_G0.6050.25
40_T64_E0.6030.25
34_F43_V0.6010.25
30_E45_I0.5990.25
20_E60_V0.5860.24
29_T43_V0.5850.24
20_E23_H0.5770.24
30_E68_E0.5740.24
24_G61_V0.5700.23
64_E69_E0.5690.23
14_I35_E0.5670.23
50_K55_E0.5560.23
11_D17_H0.5550.23
43_V47_D0.5550.23
20_E39_P0.5470.22
65_S76_L0.5450.22
21_T37_K0.5450.22
19_V23_H0.5400.22
62_G77_R0.5390.22
18_A62_G0.5380.22
14_I17_H0.5340.21
17_H27_H0.5330.21
40_T74_S0.5300.21
43_V50_K0.5150.21
22_Q41_I0.5000.20
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  
3oh8A 1 0.3846 13.9 0.922 Contact Map
2azjA 2 0.5897 3.7 0.94 Contact Map
1zgkA 1 0.4615 2.3 0.946 Contact Map
3pkoA 2 0.7051 1.8 0.949 Contact Map
2rc5A 1 0.6667 1.7 0.95 Contact Map
1usyA 3 0.5513 1.5 0.952 Contact Map
3jqqA 2 0.6154 1.3 0.953 Contact Map
2j1pA 2 0.5769 1.3 0.954 Contact Map
2lcoA 1 0.1026 1.2 0.954 Contact Map
4c68A 1 0.8077 1.1 0.955 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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