GREMLIN Database
DPO3E - DNA polymerase III subunit epsilon
UniProt: P03007 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG10243
Length: 243 (193)
Sequences: 3832 (2578)
Seq/√Len: 185.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
55_D78_T3.6821.00
57_L70_D3.2961.00
63_F69_A3.2671.00
53_K75_D3.0261.00
138_F152_Y2.9801.00
97_I100_A2.8881.00
60_P64_G2.8331.00
109_Y113_L2.3971.00
144_S147_A2.3961.00
47_N169_Q2.2961.00
58_V73_L2.2851.00
142_R147_A2.2771.00
84_D116_R2.2711.00
32_E163_G2.2371.00
98_H130_S2.1941.00
52_L82_V2.1611.00
62_A66_H2.1211.00
50_V85_E2.1081.00
86_F90_I2.0991.00
11_L97_I1.9611.00
34_G168_A1.9471.00
87_M111_F1.9101.00
79_F83_A1.8691.00
58_V70_D1.8531.00
50_V77_P1.8151.00
33_I86_F1.8121.00
78_T81_E1.8011.00
10_V38_V1.7951.00
84_D88_D1.7811.00
7_R39_V1.7531.00
31_I58_V1.7321.00
29_K113_L1.7301.00
131_L143_N1.6171.00
29_K53_K1.6141.00
77_P85_E1.5911.00
72_F75_D1.5651.00
38_V172_A1.5491.00
88_D91_R1.5021.00
72_F76_K1.4981.00
58_V63_F1.4491.00
13_T30_I1.4481.00
35_A86_F1.4461.00
68_I72_F1.4361.00
70_D74_L1.4331.00
7_R37_E1.3921.00
38_V176_L1.3901.00
28_H56_R1.3821.00
77_P82_V1.3731.00
134_A143_N1.3621.00
85_E88_D1.3611.00
54_P73_L1.3501.00
71_E74_L1.3441.00
77_P81_E1.3431.00
149_C170_I1.3281.00
46_N89_Y1.3261.00
32_E49_H1.3221.00
61_E64_G1.3101.00
29_K110_E1.2951.00
48_F86_F1.2931.00
110_E113_L1.2811.00
50_V82_V1.2581.00
154_I174_V1.2531.00
9_I93_A1.2491.00
104_I127_V1.2461.00
69_A72_F1.2291.00
17_G28_H1.2271.00
149_C174_V1.2231.00
47_N89_Y1.2121.00
28_H106_F1.2101.00
31_I68_I1.2021.00
19_N26_E1.1951.00
34_G164_A1.1941.00
15_T102_F1.1931.00
48_F85_E1.1901.00
62_A65_V1.1831.00
149_C154_I1.1741.00
9_I35_A1.1721.00
156_N170_I1.1531.00
28_H59_D1.1481.00
82_V86_F1.1401.00
68_I73_L1.1391.00
138_F181_G1.1341.00
98_H148_L1.1261.00
37_E46_N1.1211.00
29_K55_D1.1081.00
51_Y72_F1.0951.00
55_D80_A1.0851.00
29_K56_R1.0831.00
7_R93_A1.0741.00
60_P63_F1.0691.00
100_A127_V1.0661.00
189_M192_E1.0631.00
50_V76_K1.0361.00
109_Y112_S1.0261.00
156_N161_L1.0221.00
168_A172_A1.0191.00
10_V171_L1.0191.00
138_F178_M1.0171.00
138_F151_R1.0100.99
26_E109_Y1.0080.99
108_D119_P0.9960.99
39_V44_T0.9900.99
18_M28_H0.9840.99
169_Q173_E0.9770.99
38_V43_L0.9700.99
161_L166_L0.9670.99
11_L86_F0.9620.99
49_H165_L0.9620.99
39_V43_L0.9590.99
8_Q175_Y0.9540.99
10_V172_A0.9470.99
119_P125_C0.9330.99
37_E89_Y0.9320.99
206_V210_S0.9310.99
146_D161_L0.9310.99
10_V96_V0.9230.99
61_E65_V0.9210.99
51_Y76_K0.9170.99
86_F89_Y0.9160.99
80_A114_L0.9100.99
59_D62_A0.9080.99
134_A178_M0.9020.99
59_D63_F0.9000.99
99_N102_F0.8990.99
37_E93_A0.8980.99
51_Y163_G0.8970.99
36_V168_A0.8960.99
53_K78_T0.8860.99
108_D118_I0.8840.99
201_T204_R0.8840.99
48_F89_Y0.8820.99
152_Y178_M0.8750.99
206_V209_A0.8710.98
205_I208_Q0.8700.98
90_I111_F0.8700.98
172_A176_L0.8650.98
177_A181_G0.8620.98
33_I52_L0.8610.98
36_V165_L0.8550.98
201_T205_I0.8550.98
39_V42_R0.8500.98
9_I37_E0.8450.98
6_T94_E0.8440.98
137_M178_M0.8430.98
207_R210_S0.8430.98
202_I206_V0.8400.98
13_T107_M0.8350.98
79_F82_V0.8340.98
166_L169_Q0.8230.98
41_R179_T0.8220.98
79_F110_E0.8140.98
59_D73_L0.8080.98
163_G166_L0.8010.97
177_A180_G0.8000.97
202_I207_R0.7990.97
112_S118_I0.7980.97
70_D73_L0.7900.97
202_I205_I0.7860.97
20_Q109_Y0.7860.97
11_L90_I0.7850.97
63_F70_D0.7770.97
53_K74_L0.7720.97
31_I59_D0.7690.97
57_L60_P0.7560.96
190_E193_T0.7530.96
96_V175_Y0.7510.96
58_V68_I0.7480.96
160_T166_L0.7480.96
94_E128_T0.7440.96
142_R150_A0.7400.96
53_K56_R0.7390.96
88_D92_G0.7370.96
118_I125_C0.7370.96
97_I104_I0.7330.96
188_A192_E0.7310.96
66_H163_G0.7210.95
52_L78_T0.7180.95
205_I209_A0.7170.95
83_A111_F0.7160.95
99_N131_L0.7140.95
20_Q106_F0.7140.95
192_E195_Q0.7080.95
197_Q201_T0.7060.95
152_Y174_V0.7050.95
141_K150_A0.7050.95
174_V177_A0.7030.95
80_A84_D0.7020.94
147_A150_A0.7010.94
63_F72_F0.7000.94
72_F163_G0.6980.94
50_V86_F0.6980.94
157_S160_T0.6890.94
101_A132_A0.6880.94
52_L79_F0.6870.94
31_I66_H0.6850.94
203_Q208_Q0.6820.94
31_I62_A0.6810.94
203_Q209_A0.6810.94
134_A138_F0.6790.93
143_N151_R0.6640.93
11_L107_M0.6610.93
116_R119_P0.6540.92
51_Y68_I0.6510.92
193_T197_Q0.6510.92
49_H163_G0.6510.92
61_E66_H0.6480.92
17_G106_F0.6440.92
20_Q27_G0.6420.91
171_L175_Y0.6410.91
201_T208_Q0.6390.91
47_N165_L0.6340.91
52_L86_F0.6310.91
102_F106_F0.6300.91
180_G183_T0.6250.90
20_Q105_G0.6190.90
34_G165_L0.6180.90
32_E165_L0.6160.90
20_Q26_E0.6130.89
79_F84_D0.6090.89
176_L180_G0.6080.89
184_S188_A0.6020.89
130_S175_Y0.6010.89
95_L127_V0.5970.88
191_G199_E0.5970.88
35_A89_Y0.5970.88
186_A189_M0.5960.88
203_Q207_R0.5910.88
76_K82_V0.5880.87
83_A114_L0.5870.87
36_V172_A0.5850.87
134_A148_L0.5830.87
128_T133_V0.5810.87
53_K73_L0.5790.87
86_F95_L0.5720.86
130_S134_A0.5720.86
103_D162_H0.5700.86
154_I173_E0.5690.86
173_E176_L0.5680.86
29_K79_F0.5650.85
11_L95_L0.5640.85
63_F71_E0.5640.85
162_H167_D0.5630.85
83_A87_M0.5620.85
90_I95_L0.5620.85
101_A105_G0.5610.85
138_F143_N0.5590.85
153_E177_A0.5560.84
205_I210_S0.5510.84
36_V169_Q0.5490.84
200_A203_Q0.5490.84
15_T99_N0.5480.84
43_L176_L0.5470.83
133_V175_Y0.5460.83
168_A171_L0.5460.83
17_G102_F0.5410.83
148_L174_V0.5380.82
58_V62_A0.5380.82
8_Q96_V0.5350.82
10_V168_A0.5340.82
197_Q200_A0.5330.82
87_M91_R0.5290.81
17_G62_A0.5290.81
203_Q210_S0.5280.81
149_C156_N0.5280.81
184_S189_M0.5270.81
178_M181_G0.5260.81
68_I74_L0.5260.81
16_T59_D0.5250.81
128_T175_Y0.5250.81
129_D171_L0.5230.81
118_I124_F0.5220.80
130_S148_L0.5220.80
53_K70_D0.5210.80
111_F119_P0.5190.80
166_L171_L0.5170.80
194_Q197_Q0.5150.80
92_G125_C0.5140.79
83_A110_E0.5140.79
203_Q206_V0.5130.79
190_E201_T0.5130.79
84_D115_K0.5130.79
100_A171_L0.5110.79
156_N166_L0.5060.78
195_Q198_G0.5050.78
14_E167_D0.5050.78
18_M59_D0.5030.78
198_G203_Q0.5020.78
105_G109_Y0.5010.78
186_A191_G0.5010.78
32_E152_Y0.5000.78
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  
1w0hA 1 0.7654 100 0.349 Contact Map
2xriA 1 0.7449 100 0.35 Contact Map
1zbuA 1 0.8765 100 0.352 Contact Map
4qozB 1 0.8642 100 0.352 Contact Map
2guiA 1 0.7202 100 0.357 Contact Map
3cg7A 2 0.8848 100 0.361 Contact Map
2p1jA 2 0.7037 100 0.381 Contact Map
3mxmB 2 0.7572 100 0.382 Contact Map
3v9wA 3 0.7531 100 0.387 Contact Map
2qxfA 1 0.8683 100 0.398 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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