GREMLIN Database
ThylakoidFormat - Thylakoid formation protein
PFAM: PF11264 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 216 (215)
Sequences: 670 (359)
Seq/√Len: 24.5
META: 0.721

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
56_D87_R4.2441.00
43_Y89_D3.7921.00
91_Q95_A3.5881.00
43_Y48_A3.5531.00
32_L47_F3.4621.00
2_V25_V3.3481.00
8_A12_A3.0131.00
202_E206_I3.0071.00
23_R26_D2.5960.99
81_F86_Y2.5360.99
211_K214_E2.5350.99
98_K150_N2.4890.99
52_V72_F2.4250.98
77_S83_P2.3730.98
208_E211_K2.3370.98
47_F86_Y2.1160.96
46_L140_F2.1010.96
53_T57_R2.0870.96
10_Y14_P2.0650.95
201_M204_L2.0600.95
134_F140_F2.0190.95
93_L147_L2.0030.95
148_L209_K1.9940.95
148_L151_A1.9910.94
47_F205_L1.9870.94
69_D99_G1.9240.93
170_A180_A1.8270.91
200_L203_E1.7570.90
46_L147_L1.7400.89
47_F51_L1.6960.88
208_E214_E1.6910.88
187_Y193_K1.6490.86
31_E35_L1.6300.86
10_Y13_F1.6210.86
164_K167_E1.5990.85
201_M208_E1.5900.84
126_K174_G1.5510.83
82_D85_E1.5420.82
1_T9_F1.5300.82
194_M202_E1.5260.82
44_D140_F1.5160.81
118_D122_A1.5110.81
1_T5_T1.5060.81
8_A80_G1.5010.81
100_K104_D1.4900.80
5_T16_P1.4900.80
12_A54_T1.4740.79
96_E108_W1.4610.79
134_F203_E1.4420.78
1_T4_D1.4390.78
209_K213_E1.4390.78
103_E106_L1.4350.78
72_F76_C1.4190.77
5_T26_D1.4190.77
99_G151_A1.4180.77
27_E30_V1.4000.76
206_I213_E1.3950.76
161_E164_K1.3940.75
152_D161_E1.3720.74
195_A199_E1.3620.74
207_A213_E1.3330.72
28_L54_T1.3250.72
13_F18_N1.3190.71
192_E199_E1.3160.71
102_S151_A1.3150.71
98_K144_L1.3150.71
187_Y191_L1.3020.70
65_E68_L1.2550.67
66_K69_D1.2460.67
198_K202_E1.2390.66
109_L169_I1.2190.65
94_Q98_K1.2080.64
22_R41_F1.2060.64
209_K212_R1.1980.64
14_P29_L1.1950.63
72_F83_P1.1860.63
48_A89_D1.1830.63
190_N196_Q1.1780.62
149_E215_R1.1750.62
67_D210_K1.1710.62
90_A215_R1.1700.62
198_K215_R1.1380.60
103_E150_N1.1290.59
35_L76_C1.1250.59
91_Q109_L1.1030.57
43_Y85_E1.0970.57
81_F85_E1.0920.56
156_V160_S1.0910.56
182_K186_L1.0870.56
111_E114_E1.0830.56
5_T10_Y1.0830.56
6_K30_V1.0600.54
41_F47_F1.0550.54
91_Q121_L1.0490.53
107_K158_D1.0460.53
69_D84_K1.0450.53
110_S172_A1.0270.52
38_N52_V1.0250.52
161_E206_I1.0190.51
185_D188_R1.0070.50
24_V59_M0.9950.49
154_E157_K0.9910.49
49_L187_Y0.9850.49
72_F196_Q0.9850.49
91_Q94_Q0.9710.48
57_R149_E0.9690.48
107_K205_L0.9610.47
203_E207_A0.9600.47
204_L214_E0.9520.46
169_I174_G0.9510.46
90_A166_L0.9490.46
195_A208_E0.9460.46
84_K91_Q0.9430.46
7_R23_R0.9410.46
182_K207_A0.9300.45
106_L113_G0.9270.45
167_E177_A0.9270.45
44_D137_S0.9250.44
92_K120_D0.9230.44
47_F81_F0.9160.44
19_S168_D0.9130.44
169_I194_M0.9130.44
82_D95_A0.9110.43
149_E194_M0.8980.43
55_F59_M0.8940.42
126_K195_A0.8850.42
36_S46_L0.8830.42
39_A144_L0.8820.41
4_D7_R0.8810.41
54_T194_M0.8770.41
74_A99_G0.8760.41
6_K9_F0.8760.41
170_A177_A0.8660.40
141_A180_A0.8600.40
200_L204_L0.8590.40
59_M71_I0.8570.40
13_F47_F0.8550.40
44_D134_F0.8540.40
31_E75_L0.8520.39
82_D88_E0.8520.39
140_F173_L0.8490.39
62_Y137_S0.8470.39
136_Y141_A0.8410.39
77_S92_K0.8410.39
31_E64_P0.8390.38
45_P168_D0.8320.38
16_P37_V0.8320.38
10_Y15_R0.8290.38
35_L139_L0.8260.38
13_F26_D0.8250.38
95_A150_N0.8240.37
29_L215_R0.8220.37
198_K203_E0.8160.37
94_Q147_L0.8150.37
20_L46_L0.8130.37
10_Y16_P0.8110.37
110_S171_E0.8090.36
156_V159_E0.8080.36
23_R31_E0.8080.36
179_K185_D0.8070.36
183_D187_Y0.8070.36
63_R80_G0.8070.36
198_K206_I0.7970.36
109_L124_I0.7970.36
97_A148_L0.7960.36
41_F44_D0.7960.36
16_P38_N0.7940.35
43_Y78_A0.7920.35
35_L64_P0.7910.35
71_I185_D0.7890.35
20_L140_F0.7800.35
173_L211_K0.7760.34
4_D10_Y0.7750.34
125_L128_I0.7750.34
2_V9_F0.7740.34
6_K17_I0.7690.34
22_R35_L0.7680.34
23_R35_L0.7630.33
85_E120_D0.7620.33
52_V87_R0.7590.33
117_G122_A0.7590.33
73_E111_E0.7560.33
125_L144_L0.7550.33
207_A212_R0.7530.33
22_R27_E0.7460.32
17_I104_D0.7430.32
106_L147_L0.7400.32
95_A98_K0.7370.32
74_A78_A0.7310.31
115_G206_I0.7290.31
4_D142_I0.7290.31
83_P89_D0.7280.31
21_Y28_L0.7230.31
36_S160_S0.7200.31
5_T8_A0.7190.31
104_D114_E0.7120.30
79_V150_N0.7080.30
69_D144_L0.7080.30
99_G169_I0.7060.30
58_F190_N0.7050.30
13_F71_I0.6980.29
77_S82_D0.6970.29
16_P19_S0.6970.29
59_M185_D0.6950.29
44_D116_A0.6940.29
63_R194_M0.6930.29
51_L86_Y0.6920.29
111_E151_A0.6900.29
121_L130_S0.6890.29
76_C179_K0.6880.29
87_R167_E0.6870.29
124_I129_A0.6850.29
99_G104_D0.6820.28
104_D132_S0.6820.28
54_T63_R0.6740.28
13_F70_S0.6730.28
92_K126_K0.6730.28
68_L78_A0.6700.28
5_T14_P0.6680.28
2_V5_T0.6620.27
26_D30_V0.6600.27
200_L208_E0.6560.27
30_V148_L0.6530.27
55_F202_E0.6510.27
187_Y196_Q0.6480.27
124_I169_I0.6470.26
97_A111_E0.6470.26
60_K209_K0.6460.26
32_L36_S0.6460.26
92_K173_L0.6430.26
146_T207_A0.6430.26
42_K95_A0.6420.26
66_K156_V0.6420.26
82_D87_R0.6400.26
201_M206_I0.6370.26
9_F17_I0.6340.26
121_L158_D0.6340.26
26_D31_E0.6310.26
73_E83_P0.6300.26
71_I91_Q0.6300.26
111_E171_E0.6290.26
32_L86_Y0.6250.25
43_Y166_L0.6220.25
114_E118_D0.6190.25
126_K200_L0.6170.25
5_T51_L0.6150.25
8_A79_V0.6130.25
115_G118_D0.6120.25
88_E92_K0.6120.25
34_L58_F0.6110.25
49_L90_A0.6110.25
5_T29_L0.6110.25
15_R70_S0.6090.24
26_D32_L0.6080.24
73_E160_S0.6080.24
92_K96_E0.6030.24
81_F147_L0.5940.24
82_D132_S0.5940.24
4_D9_F0.5920.24
141_A205_L0.5910.23
99_G116_A0.5910.23
48_A70_S0.5900.23
29_L199_E0.5890.23
8_A19_S0.5880.23
69_D78_A0.5830.23
96_E204_L0.5810.23
34_L138_R0.5810.23
52_V211_K0.5810.23
148_L169_I0.5800.23
84_K208_E0.5790.23
116_A174_G0.5770.23
49_L52_V0.5740.23
95_A215_R0.5740.23
156_V202_E0.5730.23
30_V35_L0.5730.23
112_K115_G0.5680.22
171_E177_A0.5680.22
167_E208_E0.5660.22
60_K102_S0.5650.22
13_F67_D0.5640.22
66_K91_Q0.5640.22
106_L152_D0.5630.22
117_G120_D0.5630.22
128_I140_F0.5580.22
88_E99_G0.5570.22
69_D103_E0.5550.22
69_D73_E0.5550.22
171_E206_I0.5550.22
94_Q161_E0.5550.22
31_E139_L0.5540.22
24_V215_R0.5490.21
8_A62_Y0.5490.21
62_Y138_R0.5480.21
170_A192_E0.5480.21
206_I209_K0.5480.21
76_C83_P0.5470.21
42_K164_K0.5410.21
40_D60_K0.5400.21
181_E211_K0.5400.21
66_K130_S0.5380.21
35_L135_K0.5380.21
164_K168_D0.5360.21
51_L76_C0.5360.21
15_R23_R0.5340.21
84_K174_G0.5340.21
111_E189_S0.5330.21
121_L137_S0.5320.21
5_T12_A0.5290.20
85_E157_K0.5280.20
160_S164_K0.5220.20
22_R192_E0.5220.20
3_S6_K0.5170.20
102_S176_S0.5140.20
8_A11_E0.5130.20
145_Y206_I0.5110.20
34_L37_V0.5110.20
52_V86_Y0.5100.20
31_E138_R0.5090.20
1_T6_K0.5050.19
100_K105_L0.5040.19
106_L170_A0.5030.19
94_Q107_K0.5000.19
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  
3hoaA 2 0.5185 40.5 0.957 Contact Map
3kw6A 1 0.3472 36.1 0.958 Contact Map
4g3aA 1 0.9028 27.5 0.961 Contact Map
3w3wA 1 0.838 20.7 0.963 Contact Map
2i6xA 1 0.5694 18.6 0.964 Contact Map
2h5nA 5 0.5972 17.1 0.964 Contact Map
2yd0A 1 0.8333 17 0.964 Contact Map
4pj6A 2 0.8148 16.7 0.965 Contact Map
2dznB 1 0.3241 16.5 0.965 Contact Map
2ou3A 2 0.6759 14.4 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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