GREMLIN Database
LIGT - 2'-5'-RNA ligase
UniProt: P37025 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG12330
Length: 176 (168)
Sequences: 2303 (1787)
Seq/√Len: 137.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
80_G89_W3.4451.00
153_T168_P3.4081.00
47_A107_R3.3961.00
151_E171_R3.3341.00
72_F149_V3.1781.00
158_S167_T3.1131.00
12_D155_Y3.0001.00
9_F64_A2.9371.00
34_G129_L2.9351.00
21_I90_L2.8571.00
80_G91_G2.7471.00
60_L110_A2.7071.00
156_A167_T2.6041.00
156_A169_L2.3591.00
10_A155_Y2.3081.00
11_I149_V2.2281.00
9_F49_L2.2231.00
159_F164_T2.1681.00
5_Q51_E2.1221.00
25_R42_L2.1171.00
7_L52_V2.1011.00
77_D93_R2.0441.00
9_F106_L1.9751.00
5_Q156_A1.9681.00
73_T146_S1.9581.00
64_A106_L1.9381.00
73_T148_A1.9281.00
76_L90_L1.8901.00
49_L110_A1.8241.00
14_P147_Y1.8031.00
152_F172_W1.7991.00
47_A117_Q1.7991.00
65_G170_K1.7921.00
155_Y168_P1.7651.00
103_A107_R1.7261.00
75_T146_S1.7131.00
61_S170_K1.6171.00
168_P171_R1.5971.00
53_S56_K1.5901.00
67_I152_F1.5721.00
19_E39_A1.5331.00
69_Q105_M1.4991.00
160_A163_R1.4931.00
7_L154_L1.4861.00
82_W89_W1.4551.00
14_P17_I1.4511.00
37_V164_T1.4341.00
41_N166_Y1.4071.00
153_T171_R1.3861.00
68_R152_F1.3831.00
160_A165_R1.3781.00
94_Q97_R1.3671.00
90_L128_L1.3641.00
46_L152_F1.3011.00
107_R117_Q1.2871.00
34_G131_D1.2661.00
41_N164_T1.2551.00
106_L110_A1.1811.00
13_L155_Y1.1801.00
13_L18_R1.1670.99
36_P129_L1.1630.99
38_A41_N1.1520.99
76_L126_I1.1500.99
82_W91_G1.1010.99
56_K59_A1.0960.99
37_V130_R1.0950.99
111_A117_Q1.0820.99
57_E61_S1.0800.99
64_A152_F1.0770.99
130_R159_F1.0410.99
20_Q145_W1.0400.99
7_L49_L1.0320.99
6_R130_R1.0270.99
159_F166_Y1.0250.99
85_S131_D1.0100.98
115_C118_S1.0050.98
15_A18_R1.0020.98
154_L172_W0.9990.98
69_Q174_L0.9980.98
109_Q113_S0.9910.98
18_R39_A0.9850.98
61_S172_W0.9800.98
6_R48_F0.9670.98
13_L147_Y0.9580.98
64_A154_L0.9440.98
47_A103_A0.9300.97
49_L52_V0.9290.97
103_A124_P0.9240.97
12_D153_T0.9180.97
49_L115_C0.9130.97
49_L106_L0.9030.97
6_R157_S0.9020.97
47_A106_L0.8910.97
5_Q54_A0.8890.97
52_V56_K0.8880.96
130_R157_S0.8830.96
52_V57_E0.8740.96
11_I72_F0.8700.96
38_A163_R0.8550.96
86_R131_D0.8530.96
46_L102_L0.8470.95
170_K173_A0.8430.95
83_L86_R0.8380.95
17_I147_Y0.8360.95
110_A113_S0.8290.95
44_L92_M0.8150.94
88_V129_L0.8110.94
41_N157_S0.7980.94
75_T93_R0.7900.93
76_L92_M0.7880.93
37_V42_L0.7860.93
126_I129_L0.7810.93
46_L103_A0.7800.93
47_A110_A0.7790.93
151_E174_L0.7780.93
48_F130_R0.7750.93
11_I46_L0.7610.92
11_I152_F0.7600.92
94_Q100_I0.7590.92
59_A112_R0.7570.92
74_L99_L0.7490.91
6_R51_E0.7440.91
35_R132_A0.7420.91
101_Q105_M0.7410.91
9_F154_L0.7400.91
35_R130_R0.7270.90
60_L64_A0.7180.90
150_T173_A0.7110.89
87_V130_R0.7050.89
64_A172_W0.6970.88
76_L147_Y0.6950.88
7_L50_G0.6940.88
53_S57_E0.6930.88
34_G132_A0.6920.88
100_I124_P0.6880.88
103_A121_P0.6870.88
20_Q23_H0.6860.87
63_L106_L0.6840.87
65_G172_W0.6800.87
29_F64_A0.6750.87
63_L109_Q0.6680.86
35_R38_A0.6680.86
132_A165_R0.6670.86
11_I99_L0.6650.86
77_D141_P0.6640.86
51_E159_F0.6620.86
136_V139_P0.6620.86
77_D143_F0.6600.85
21_I128_L0.6560.85
67_I105_M0.6550.85
21_I42_L0.6530.85
9_F47_A0.6490.84
9_F152_F0.6470.84
58_K61_S0.6430.84
130_R164_T0.6420.84
68_R71_G0.6370.83
12_D18_R0.6360.83
63_L110_A0.6360.83
33_A135_A0.6310.83
56_K115_C0.6290.83
161_R164_T0.6150.81
9_F60_L0.6130.81
72_F99_L0.6130.81
66_R109_Q0.6110.81
34_G126_I0.6100.81
21_I76_L0.6070.80
74_L92_M0.6060.80
22_I42_L0.6060.80
68_R105_M0.6060.80
109_Q112_R0.6040.80
103_A122_F0.6000.79
44_L126_I0.5970.79
77_D144_N0.5960.79
23_H104_N0.5930.79
52_V60_L0.5920.79
74_L147_Y0.5910.78
9_F110_A0.5880.78
97_R100_I0.5870.78
55_E59_A0.5830.78
19_E23_H0.5820.77
97_R101_Q0.5810.77
78_D145_W0.5810.77
33_A157_S0.5780.77
47_A115_C0.5780.77
72_F102_L0.5770.77
61_S65_G0.5750.77
23_H27_T0.5740.76
9_F172_W0.5720.76
59_A62_L0.5720.76
12_D168_P0.5710.76
88_V126_I0.5700.76
59_A63_L0.5670.76
159_F162_G0.5600.75
24_W143_F0.5580.74
66_R112_R0.5550.74
149_V152_F0.5550.74
77_D97_R0.5550.74
76_L144_N0.5550.74
79_A142_G0.5520.74
160_A164_T0.5510.74
20_Q142_G0.5510.74
74_L96_P0.5500.73
70_P98_G0.5500.73
98_G101_Q0.5500.73
158_S165_R0.5500.73
105_M109_Q0.5490.73
15_A39_A0.5490.73
32_E129_L0.5480.73
132_A157_S0.5460.73
100_I104_N0.5460.73
13_L126_I0.5440.73
22_I25_R0.5430.72
35_R164_T0.5430.72
36_P88_V0.5420.72
11_I147_Y0.5350.71
37_V41_N0.5340.71
135_A138_I0.5330.71
106_L109_Q0.5300.71
110_A116_F0.5290.71
37_V127_T0.5280.70
92_M145_W0.5280.70
62_L173_A0.5270.70
77_D90_L0.5260.70
103_A110_A0.5260.70
16_E20_Q0.5250.70
61_S64_A0.5240.70
56_K116_F0.5210.69
131_D164_T0.5200.69
10_A153_T0.5190.69
52_V115_C0.5190.69
63_L112_R0.5170.69
122_F164_T0.5170.69
110_A115_C0.5160.69
49_L60_L0.5160.69
79_A90_L0.5160.69
34_G42_L0.5130.68
135_A140_P0.5130.68
152_F174_L0.5130.68
5_Q57_E0.5130.68
151_E173_A0.5130.68
7_L169_L0.5120.68
34_G41_N0.5090.68
75_T173_A0.5080.67
132_A163_R0.5080.67
49_L172_W0.5070.67
17_I76_L0.5060.67
66_R105_M0.5060.67
57_E169_L0.5050.67
102_L152_F0.5040.67
69_Q101_Q0.5030.67
48_F166_Y0.5010.66
84_R133_S0.5000.66
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  
4qakA 1 0.9886 100 0.202 Contact Map
1iuhA 1 0.9659 100 0.252 Contact Map
1vgjA 1 0.9659 100 0.272 Contact Map
3j4qA 1 0.9773 100 0.301 Contact Map
2vfkA 1 0.983 100 0.331 Contact Map
1jh6A 5 0.9375 100 0.394 Contact Map
4h7wA 1 0.9261 100 0.394 Contact Map
2d4gA 2 0.9034 100 0.396 Contact Map
2fsqA 1 0.8864 96.9 0.848 Contact Map
2xmiA 1 0.8864 49.9 0.923 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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