GREMLIN Database
RNaseH_like - Ribonuclease H-like
PFAM: PF04308 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_10
Length: 145 (138)
Sequences: 4497 (2860)
Seq/√Len: 243.4
META: 0.927

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_N73_L3.1151.00
64_R115_E3.0731.00
55_E73_L3.0661.00
50_Y143_H2.9481.00
37_T77_L2.7191.00
24_T74_S2.6291.00
62_S65_E2.6081.00
101_L120_I2.3511.00
104_N107_G2.3431.00
108_K111_E2.3231.00
76_E80_E2.3051.00
113_I129_I2.1351.00
69_N72_S2.0761.00
24_T37_T2.0761.00
79_L125_F2.0291.00
67_I109_S1.9401.00
7_K11_K1.8201.00
13_E16_P1.8191.00
67_I112_L1.7731.00
72_S76_E1.7191.00
128_K132_D1.6871.00
19_K44_V1.6771.00
19_K98_E1.6291.00
5_E49_R1.6141.00
21_Y135_A1.6111.00
117_V129_I1.5481.00
32_E56_K1.5301.00
67_I116_A1.5261.00
98_E128_K1.5231.00
22_I74_S1.5221.00
34_D56_K1.4781.00
71_V101_L1.4511.00
8_E12_E1.4451.00
133_A137_S1.4391.00
4_E8_E1.4361.00
109_S112_L1.4251.00
74_S99_I1.4181.00
17_E44_V1.3921.00
34_D54_K1.3651.00
71_V116_A1.3471.00
75_L120_I1.3371.00
72_S119_Y1.3351.00
78_A125_F1.3131.00
4_E88_R1.3011.00
40_V135_A1.2651.00
118_G122_G1.2601.00
28_V31_K1.2601.00
5_E51_F1.2441.00
103_I116_A1.2431.00
75_L119_Y1.2241.00
57_E60_I1.2211.00
9_F41_V1.2131.00
8_E11_K1.2091.00
42_H48_G1.1891.00
67_I103_I1.1851.00
35_F69_N1.1831.00
16_P46_K1.1591.00
100_H128_K1.1491.00
27_Q144_T1.1341.00
101_L116_A1.1171.00
37_T55_E1.0851.00
99_I102_D1.0851.00
26_S66_R1.0731.00
35_F61_Y1.0581.00
74_S120_I1.0511.00
19_K96_D1.0421.00
104_N110_N1.0171.00
60_I66_R1.0141.00
36_V52_Y0.9991.00
117_V127_A0.9891.00
14_P17_E0.9801.00
121_R127_A0.9661.00
113_I117_V0.9591.00
39_I77_L0.9571.00
67_I70_E0.9531.00
78_A99_I0.9501.00
31_K56_K0.9431.00
18_Y43_R0.9381.00
75_L123_M0.9351.00
79_L83_E0.9321.00
33_T66_R0.9301.00
68_L72_S0.9281.00
35_F73_L0.9251.00
20_I41_V0.9251.00
5_E8_E0.9191.00
40_V139_V0.9161.00
68_L115_E0.9141.00
88_R93_A0.9071.00
112_L116_A0.8991.00
41_V51_F0.8760.99
100_H134_F0.8740.99
48_G139_V0.8690.99
50_Y139_V0.8680.99
84_L87_K0.8580.99
57_E69_N0.8560.99
117_V121_R0.8560.99
79_L82_C0.8500.99
81_L85_L0.8370.99
4_E15_G0.8310.99
68_L116_A0.8260.99
110_N113_I0.8210.99
21_Y134_F0.8170.99
114_K121_R0.8150.99
103_I113_I0.8050.99
21_Y42_H0.7920.99
63_L108_K0.7870.99
135_A138_S0.7740.99
104_N109_S0.7740.99
121_R126_E0.7740.99
9_F13_E0.7740.99
14_P18_Y0.7720.99
64_R111_E0.7670.99
28_V33_T0.7630.99
136_A139_V0.7620.99
134_F138_S0.7610.99
22_I78_A0.7550.98
34_D144_T0.7520.98
4_E7_K0.7480.98
68_L119_Y0.7470.98
72_S123_M0.7430.98
33_T61_Y0.7330.98
13_E18_Y0.7320.98
101_L127_A0.7230.98
68_L71_V0.7220.98
72_S79_L0.7180.98
98_E102_D0.7130.98
77_L80_E0.7090.98
66_R71_V0.7040.98
60_I65_E0.6980.97
53_R76_E0.6970.97
73_L76_E0.6940.97
29_K32_E0.6940.97
133_A138_S0.6850.97
76_E79_L0.6840.97
9_F12_E0.6800.97
87_K93_A0.6770.97
96_D126_E0.6760.97
13_E43_R0.6710.97
59_K62_S0.6700.97
119_Y123_M0.6700.97
74_S78_A0.6670.97
64_R68_L0.6540.96
66_R70_E0.6540.96
80_E84_L0.6430.96
137_S144_T0.6430.96
21_Y40_V0.6420.96
75_L125_F0.6420.96
40_V48_G0.6410.96
107_G110_N0.6400.96
65_E69_N0.6370.96
40_V116_A0.6340.95
21_Y44_V0.6330.95
105_P110_N0.6320.95
99_I120_I0.6310.95
13_E46_K0.6310.95
82_C125_F0.6300.95
131_P136_A0.6230.95
100_H133_A0.6190.95
10_I13_E0.6170.95
17_E96_D0.6150.95
9_F49_R0.6130.95
36_V54_K0.6080.94
22_I81_L0.6060.94
109_S116_A0.6000.94
32_E58_R0.5990.94
57_E73_L0.5960.94
37_T73_L0.5960.94
23_G26_S0.5940.94
52_Y120_I0.5940.94
11_K15_G0.5780.93
27_Q33_T0.5710.92
53_R80_E0.5700.92
68_L112_L0.5650.92
52_Y143_H0.5640.92
134_F139_V0.5630.92
10_I95_V0.5630.92
106_N110_N0.5580.91
46_K123_M0.5560.91
4_E11_K0.5550.91
99_I104_N0.5540.91
33_T57_E0.5500.91
64_R122_G0.5460.91
10_I14_P0.5440.90
45_G48_G0.5420.90
134_F137_S0.5420.90
33_T59_K0.5400.90
34_D66_R0.5390.90
70_E74_S0.5380.90
7_K10_I0.5360.90
32_E92_L0.5360.90
28_V32_E0.5360.90
86_E95_V0.5310.89
11_K17_E0.5240.89
112_L115_E0.5230.89
27_Q142_R0.5230.89
9_F14_P0.5190.88
67_I71_V0.5150.88
131_P135_A0.5140.88
117_V132_D0.5120.88
9_F18_Y0.5100.87
114_K118_G0.5100.87
64_R99_I0.5090.87
33_T60_I0.5080.87
58_R62_S0.5050.87
98_E118_G0.5020.86
104_N144_T0.5020.86
49_R127_A0.5000.86
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  
1xovA 1 0.5724 54.1 0.92 Contact Map
1rblM 3 0.2828 34.6 0.929 Contact Map
4ol8A 2 0.8621 32 0.93 Contact Map
1svdM 3 0.2759 21 0.936 Contact Map
3czxA 2 0.6 16.5 0.939 Contact Map
3m89A 1 0.4345 13.6 0.941 Contact Map
1gk8I 3 0.269 13 0.942 Contact Map
3o59X 1 0.2414 10.5 0.944 Contact Map
1wddS 3 0.2897 10.4 0.944 Contact Map
1jwqA 1 0.6069 8.3 0.947 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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