GREMLIN Database
DUF2240 - Uncharacterized protein conserved in archaea (DUF2240)
PFAM: PF09999 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 144 (141)
Sequences: 1060 (727)
Seq/√Len: 61.2
META: 0.876

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
93_R139_D3.3491.00
43_L59_L3.3311.00
85_D88_E3.0881.00
64_D67_E3.0691.00
109_I126_A2.8051.00
112_K132_E2.7241.00
108_E132_E2.6421.00
20_E54_R2.6221.00
101_E104_E2.4911.00
93_R140_L2.3811.00
53_E62_T2.2721.00
17_R58_D2.1401.00
120_V125_A2.1211.00
106_V110_N2.0771.00
6_V46_A2.0481.00
110_N113_Q2.0361.00
17_R60_R2.0351.00
49_E84_E2.0241.00
89_R143_E1.9691.00
35_S38_Q1.9221.00
91_L106_V1.8921.00
23_F43_L1.8541.00
8_A12_R1.8101.00
34_F39_A1.7650.99
45_V48_E1.7030.99
7_A10_F1.6660.99
107_A110_N1.6250.99
87_F110_N1.5830.99
47_L59_L1.5760.99
98_T105_V1.5700.99
26_A30_D1.5690.99
100_L104_E1.5680.99
130_A137_V1.5350.98
4_I73_G1.5140.98
30_D33_W1.5060.98
33_W76_P1.5020.98
61_P65_P1.4460.98
18_L61_P1.4000.97
116_L120_V1.3820.97
91_L105_V1.3110.96
90_L94_I1.3100.96
102_K106_V1.2600.95
30_D76_P1.2530.95
46_A74_F1.2270.94
113_Q122_I1.2140.94
6_V9_P1.2090.94
30_D110_N1.2060.94
87_F122_I1.1760.93
16_D60_R1.1690.92
45_V49_E1.1550.92
25_V29_L1.1380.91
54_R57_G1.1190.91
6_V39_A1.1090.90
86_L89_R1.1090.90
129_V133_Q1.0990.90
47_L52_L1.0880.89
5_A27_L1.0850.89
15_K61_P1.0650.88
27_L42_L1.0600.88
95_A105_V1.0400.87
5_A13_K1.0370.87
23_F79_S1.0300.87
52_L109_I1.0300.87
105_V130_A1.0290.87
42_L45_V1.0250.86
108_E111_R1.0230.86
5_A42_L1.0210.86
53_E95_A1.0090.86
86_L131_R1.0070.85
14_G40_K0.9920.85
103_Q106_V0.9740.84
48_E85_D0.9650.83
10_F76_P0.9330.81
35_S125_A0.9260.80
91_L126_A0.9220.80
12_R26_A0.9210.80
84_E92_D0.9200.80
5_A9_P0.9170.80
46_A52_L0.9150.79
94_I130_A0.9120.79
34_F76_P0.9060.79
46_A51_L0.9040.79
94_I98_T0.8980.78
85_D91_L0.8900.78
96_A111_R0.8890.77
32_K92_D0.8810.77
9_P23_F0.8690.76
3_R49_E0.8580.75
123_E126_A0.8570.75
102_K110_N0.8430.74
120_V124_A0.8380.73
120_V133_Q0.8320.73
32_K74_F0.8250.72
34_F109_I0.8110.71
119_L126_A0.7920.69
52_L69_E0.7920.69
20_E40_K0.7900.69
8_A13_K0.7900.69
67_E79_S0.7840.68
128_L140_L0.7780.68
68_V96_A0.7750.67
18_L47_L0.7750.67
38_Q46_A0.7710.67
124_A127_L0.7680.67
51_L63_F0.7650.66
4_I8_A0.7650.66
2_L45_V0.7640.66
27_L115_E0.7560.65
13_K23_F0.7560.65
29_L76_P0.7550.65
13_K19_S0.7530.65
52_L99_G0.7490.65
92_D95_A0.7450.64
28_S36_P0.7430.64
4_I15_K0.7400.64
140_L143_E0.7390.64
75_K114_E0.7390.64
138_S142_D0.7380.63
112_K129_V0.7370.63
52_L108_E0.7340.63
25_V30_D0.7240.62
108_E112_K0.7240.62
8_A34_F0.7220.62
24_V35_S0.7170.61
99_G115_E0.7150.61
29_L35_S0.7120.61
19_S58_D0.7100.60
36_P103_Q0.7030.60
97_K120_V0.7010.59
94_I100_L0.6970.59
87_F92_D0.6940.59
116_L122_I0.6910.58
90_L127_L0.6880.58
94_I105_V0.6860.58
77_S80_I0.6800.57
43_L75_K0.6790.57
31_L59_L0.6770.57
21_S49_E0.6760.57
44_D91_L0.6750.57
37_D65_P0.6740.56
108_E129_V0.6710.56
52_L59_L0.6700.56
24_V39_A0.6680.56
54_R89_R0.6670.56
28_S136_D0.6660.56
109_I129_V0.6630.55
9_P27_L0.6580.55
67_E73_G0.6530.54
53_E60_R0.6530.54
55_E60_R0.6490.54
67_E142_D0.6470.53
82_E86_L0.6470.53
112_K115_E0.6470.53
64_D89_R0.6470.53
135_V139_D0.6450.53
64_D110_N0.6430.53
18_L23_F0.6400.53
79_S128_L0.6380.52
26_A137_V0.6380.52
49_E105_V0.6320.52
19_S79_S0.6310.52
29_L36_P0.6290.51
19_S97_K0.6290.51
13_K30_D0.6270.51
67_E96_A0.6250.51
5_A11_K0.6250.51
90_L126_A0.6250.51
35_S94_I0.6210.50
52_L62_T0.6200.50
113_Q116_L0.6110.49
33_W131_R0.6070.49
50_G99_G0.6050.49
10_F33_W0.5990.48
74_F77_S0.5970.48
34_F40_K0.5950.48
101_E138_S0.5920.47
15_K18_L0.5920.47
32_K75_K0.5890.47
70_I105_V0.5850.46
43_L52_L0.5850.46
4_I16_D0.5850.46
7_A11_K0.5800.46
8_A21_S0.5800.46
107_A111_R0.5800.46
6_V51_L0.5710.45
6_V23_F0.5650.44
56_G97_K0.5640.44
20_E57_G0.5640.44
43_L103_Q0.5590.43
9_P18_L0.5590.43
98_T129_V0.5550.43
26_A29_L0.5550.43
20_E24_V0.5530.43
103_Q122_I0.5470.42
108_E133_Q0.5460.42
63_F68_V0.5460.42
39_A45_V0.5440.42
55_E58_D0.5400.41
131_R136_D0.5400.41
50_G120_V0.5400.41
17_R55_E0.5390.41
111_R114_E0.5390.41
112_K125_A0.5360.41
91_L102_K0.5320.41
19_S66_S0.5310.40
34_F43_L0.5250.40
98_T135_V0.5120.38
13_K61_P0.5110.38
87_F95_A0.5070.38
3_R8_A0.5040.37
51_L74_F0.5000.37
58_D142_D0.5000.37
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  
1lvaA 1 0.9444 75.5 0.901 Contact Map
1okrA 2 0.7361 34 0.924 Contact Map
3lmmA 1 0.4167 29.6 0.926 Contact Map
3sy8A 6 0.9444 24.8 0.929 Contact Map
2k4bA 1 0.4097 24.2 0.929 Contact Map
2adlA 2 0.2153 22.3 0.931 Contact Map
4gtnA 2 0.4306 22.2 0.931 Contact Map
4wd9A 2 0.9167 21.8 0.931 Contact Map
3ulqB 1 0.4028 18.7 0.933 Contact Map
1sd4A 2 0.7222 17.3 0.934 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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