GREMLIN Database
DPO4 - DNA polymerase IV
UniProt: Q47155 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13141
Length: 351 (337)
Sequences: 8904 (6326)
Seq/√Len: 344.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
92_R129_T3.8571.00
179_A189_A2.9131.00
260_E317_R2.8761.00
129_T133_E2.8031.00
92_R133_E2.7291.00
30_A69_L2.7081.00
255_H258_E2.6841.00
20_D78_A2.6181.00
283_I336_V2.5941.00
193_E198_R2.3231.00
244_G335_H2.3171.00
9_M138_A2.3001.00
131_F159_N2.2601.00
82_A85_H2.2551.00
59_T71_L2.2341.00
260_E321_D2.2201.00
198_R202_D2.2061.00
125_E129_T2.1951.00
75_R78_A2.1911.00
93_Y129_T2.1091.00
179_A193_E2.1061.00
26_D47_P2.0621.00
195_M214_R2.0411.00
201_G205_K2.0391.00
94_T107_L2.0131.00
130_I138_A2.0021.00
98_E146_K1.9991.00
224_E229_I1.9951.00
18_M45_N1.9861.00
128_Q132_N1.9741.00
256_W321_D1.9591.00
223_W227_Q1.9571.00
212_L220_R1.9141.00
174_Q204_Q1.9061.00
127_R159_N1.9031.00
174_Q201_G1.8901.00
27_I70_T1.8841.00
5_I109_V1.8781.00
9_M86_I1.8691.00
197_L203_V1.8521.00
308_N311_D1.8501.00
270_L336_V1.8341.00
197_L206_C1.8111.00
9_M136_L1.7921.00
165_T168_E1.7841.00
61_M65_L1.7701.00
20_D75_R1.7671.00
274_L336_V1.7571.00
208_L220_R1.7251.00
87_R105_A1.7241.00
285_R338_L1.7201.00
91_S97_I1.6761.00
221_I225_R1.6471.00
47_P50_K1.6221.00
170_P174_Q1.5811.00
190_A194_A1.5791.00
30_A41_I1.5661.00
78_A81_E1.5631.00
14_A29_I1.5571.00
287_G337_T1.5511.00
57_M65_L1.5351.00
100_L106_Y1.5271.00
127_R161_Q1.5251.00
120_T124_Q1.4991.00
30_A71_L1.4991.00
81_E85_H1.4881.00
19_R82_A1.4801.00
289_K333_G1.4781.00
21_N24_L1.4711.00
118_S121_L1.4701.00
264_E313_I1.4671.00
302_H318_K1.4641.00
316_A334_L1.4521.00
122_I126_I1.4481.00
245_V270_L1.4451.00
144_P169_V1.4441.00
189_A193_E1.4371.00
199_T202_D1.4321.00
307_L342_Q1.4301.00
195_M215_F1.4261.00
148_L164_I1.4241.00
206_C210_M1.4231.00
208_L224_E1.4181.00
307_L313_I1.4111.00
123_A142_V1.3931.00
285_R337_T1.3911.00
219_G223_W1.3851.00
253_I259_C1.3831.00
17_E79_Y1.3781.00
93_Y125_E1.3721.00
220_R224_E1.3591.00
208_L223_W1.3551.00
268_P309_K1.3511.00
7_V138_A1.3481.00
256_W260_E1.3481.00
168_E171_A1.3451.00
90_F107_L1.3421.00
5_I140_A1.3401.00
120_T163_V1.3351.00
124_Q128_Q1.3351.00
142_V161_Q1.3341.00
16_V78_A1.3261.00
58_P61_M1.3231.00
123_A140_A1.3221.00
61_M64_K1.3191.00
271_E309_K1.3181.00
143_A148_L1.3141.00
16_V82_A1.3111.00
274_L283_I1.3041.00
206_C211_L1.3001.00
267_Y334_L1.2871.00
18_M25_R1.2871.00
11_C15_A1.2871.00
249_M262_I1.2871.00
30_A53_V1.2871.00
51_F68_H1.2841.00
211_L223_W1.2781.00
282_L340_D1.2731.00
208_L212_L1.2681.00
254_H328_G1.2671.00
109_V122_I1.2491.00
106_Y182_P1.2451.00
89_I133_E1.2421.00
46_Y50_K1.2411.00
89_I129_T1.2371.00
24_L29_I1.2351.00
284_A338_L1.2321.00
245_V269_E1.2271.00
14_A18_M1.2231.00
291_K297_Q1.2211.00
245_V273_R1.2211.00
302_H322_E1.2211.00
18_M47_P1.2161.00
51_F66_C1.2161.00
29_I72_L1.2151.00
243_V279_P1.2141.00
5_I123_A1.2101.00
267_Y312_L1.2101.00
170_P204_Q1.2001.00
7_V90_F1.1981.00
251_E258_E1.1981.00
90_F105_A1.1971.00
246_E333_G1.1961.00
88_E91_S1.1891.00
152_A164_I1.1741.00
89_I134_L1.1731.00
124_Q127_R1.1711.00
77_D81_E1.1631.00
191_K214_R1.1551.00
187_V190_A1.1471.00
78_A82_A1.1461.00
315_T318_K1.1411.00
304_W315_T1.1351.00
41_I53_V1.1321.00
17_E75_R1.1251.00
207_D210_M1.1211.00
267_Y271_E1.1191.00
21_N72_L1.1191.00
202_D205_K1.1131.00
210_M214_R1.1091.00
155_M162_F1.1051.00
309_K313_I1.1031.00
19_R78_A1.1001.00
252_D293_D1.0971.00
253_I258_E1.0851.00
6_H153_S1.0821.00
249_M253_I1.0781.00
246_E289_K1.0731.00
291_K331_L1.0721.00
271_E275_A1.0721.00
317_R321_D1.0641.00
96_R236_S1.0591.00
216_G219_G1.0561.00
32_G59_T1.0531.00
204_Q227_Q1.0481.00
271_E312_L1.0461.00
267_Y313_I1.0461.00
284_A340_D1.0441.00
87_R99_P1.0401.00
44_A55_S1.0401.00
285_R301_E1.0371.00
37_R63_L1.0371.00
41_I44_A1.0321.00
121_L125_E1.0251.00
93_Y126_I1.0221.00
314_A318_K1.0191.00
262_I265_R1.0171.00
259_C320_W1.0161.00
181_I200_C1.0011.00
318_K322_E0.9981.00
252_D330_R0.9981.00
190_A193_E0.9941.00
41_I62_A0.9851.00
151_I176_L0.9831.00
86_I134_L0.9821.00
7_V107_L0.9781.00
87_R91_S0.9761.00
60_G64_K0.9751.00
313_I317_R0.9731.00
143_A149_A0.9711.00
14_A43_T0.9681.00
288_V319_T0.9681.00
112_S116_H0.9651.00
53_V69_L0.9631.00
112_S122_I0.9561.00
17_E21_N0.9551.00
19_R135_Q0.9521.00
311_D315_T0.9511.00
32_G39_G0.9511.00
20_D82_A0.9461.00
11_C46_Y0.9431.00
252_D328_G0.9411.00
156_N162_F0.9391.00
42_S74_G0.9381.00
131_F135_Q0.9371.00
154_D180_K0.9321.00
281_L341_P0.9311.00
12_F16_V0.9311.00
302_H315_T0.9291.00
287_G301_E0.9221.00
287_G335_H0.9191.00
263_I288_V0.9171.00
124_Q161_Q0.9171.00
267_Y316_A0.9151.00
112_S117_G0.9131.00
146_K234_V0.9121.00
123_A161_Q0.9071.00
57_M61_M0.9051.00
292_F327_R0.9051.00
285_R303_V0.9001.00
18_M29_I0.8981.00
90_F126_I0.8981.00
76_F80_K0.8941.00
247_R262_I0.8901.00
282_L342_Q0.8901.00
100_L182_P0.8871.00
191_K194_A0.8851.00
263_I332_V0.8811.00
218_F221_I0.8781.00
284_A303_V0.8781.00
290_L332_V0.8751.00
147_F225_R0.8621.00
210_M213_K0.8601.00
303_V338_L0.8581.00
224_E231_E0.8571.00
215_F219_G0.8541.00
85_H88_E0.8531.00
57_M62_A0.8501.00
204_Q226_S0.8501.00
217_K221_I0.8501.00
30_A66_C0.8481.00
263_I316_A0.8471.00
54_R57_M0.8401.00
11_C18_M0.8401.00
27_I68_H0.8391.00
307_L310_A0.8331.00
300_Q322_E0.8331.00
270_L334_L0.8281.00
203_V211_L0.8251.00
13_F76_F0.8221.00
184_V219_G0.8201.00
140_A161_Q0.8161.00
43_T49_R0.8161.00
175_T201_G0.8141.00
281_L339_L0.8121.00
230_D233_D0.8101.00
80_K84_N0.8051.00
275_A307_L0.8041.00
178_L193_E0.8031.00
177_P193_E0.8031.00
114_H117_G0.8021.00
145_V148_L0.7981.00
142_V163_V0.7951.00
62_A66_C0.7901.00
83_S87_R0.7901.00
188_S191_K0.7881.00
211_L215_F0.7871.00
98_E234_V0.7851.00
18_M26_D0.7791.00
89_I93_Y0.7771.00
197_L202_D0.7751.00
85_H134_L0.7731.00
263_I320_W0.7731.00
96_R108_D0.7711.00
201_G204_Q0.7691.00
191_K215_F0.7671.00
246_E331_L0.7671.00
96_R111_D0.7651.00
207_D227_Q0.7651.00
177_P180_K0.7651.00
46_Y49_R0.7611.00
24_L70_T0.7591.00
172_F176_L0.7581.00
311_D314_A0.7581.00
256_W320_W0.7571.00
106_Y146_K0.7541.00
286_Q315_T0.7531.00
264_E317_R0.7521.00
63_L67_P0.7511.00
131_F137_T0.7481.00
44_A53_V0.7481.00
66_C69_L0.7481.00
195_M206_C0.7451.00
4_I234_V0.7441.00
97_I105_A0.7391.00
94_T97_I0.7370.99
263_I313_I0.7360.99
168_E172_F0.7360.99
109_V123_A0.7360.99
127_R140_A0.7330.99
87_R97_I0.7290.99
273_R279_P0.7290.99
261_A265_R0.7280.99
89_I130_I0.7270.99
268_P272_R0.7270.99
292_F298_T0.7270.99
48_A69_L0.7270.99
112_S115_C0.7200.99
63_L71_L0.7200.99
209_V213_K0.7170.99
302_H306_R0.7170.99
125_E128_Q0.7170.99
307_L311_D0.7130.99
170_P205_K0.7100.99
89_I92_R0.7080.99
188_S215_F0.7060.99
257_S260_E0.7030.99
306_R311_D0.7030.99
31_I72_L0.7020.99
42_S55_S0.7010.99
290_L323_R0.7010.99
9_M12_F0.7010.99
44_A49_R0.6970.99
14_A45_N0.6910.99
310_A314_A0.6910.99
109_V112_S0.6910.99
215_F222_L0.6880.99
88_E92_R0.6870.99
264_E268_P0.6870.99
4_I108_D0.6850.99
121_L124_Q0.6840.99
290_L329_V0.6820.99
164_I172_F0.6820.99
203_V223_W0.6800.99
59_T66_C0.6790.99
261_A264_E0.6790.99
282_L307_L0.6770.99
275_A309_K0.6760.99
247_R269_E0.6750.99
286_Q312_L0.6750.99
77_D80_K0.6720.99
260_E264_E0.6720.99
82_A134_L0.6630.99
120_T161_Q0.6620.99
13_F74_G0.6610.99
41_I71_L0.6600.99
315_T319_T0.6590.99
269_E272_R0.6580.99
10_D139_S0.6560.99
282_L339_L0.6560.99
244_G333_G0.6560.99
287_G299_T0.6550.99
99_P102_L0.6530.99
258_E261_A0.6530.99
33_G73_P0.6520.99
96_R233_D0.6510.99
137_T156_N0.6510.99
25_R131_F0.6490.99
259_C332_V0.6460.99
27_I47_P0.6450.99
184_V222_L0.6440.99
292_F296_Q0.6440.99
85_H133_E0.6430.99
82_A136_L0.6400.99
276_K279_P0.6390.99
62_A69_L0.6390.99
153_S156_N0.6380.99
267_Y309_K0.6380.99
298_T301_E0.6370.99
32_G71_L0.6310.98
257_S261_A0.6300.98
60_G63_L0.6300.98
195_M210_M0.6270.98
30_A48_A0.6260.98
90_F97_I0.6240.98
128_Q131_F0.6240.98
298_T323_R0.6230.98
43_T55_S0.6220.98
28_P66_C0.6200.98
174_Q205_K0.6190.98
148_L169_V0.6190.98
122_I125_E0.6180.98
156_N160_G0.6170.98
13_F102_L0.6170.98
240_R279_P0.6170.98
178_L189_A0.6160.98
171_A174_Q0.6150.98
151_I182_P0.6130.98
17_E20_D0.6130.98
32_G74_G0.6070.98
11_C49_R0.6050.98
253_I262_I0.6030.98
26_D45_N0.6030.98
74_G79_Y0.6030.98
259_C329_V0.6020.98
176_L180_K0.6020.98
175_T199_T0.6000.98
178_L197_L0.5980.98
300_Q323_R0.5980.98
41_I66_C0.5980.98
264_E309_K0.5950.98
272_R276_K0.5940.98
243_V273_R0.5930.98
33_G39_G0.5920.98
144_P148_L0.5920.98
312_L316_A0.5910.98
84_N88_E0.5910.98
263_I317_R0.5890.98
293_D327_R0.5890.98
171_A175_T0.5880.98
292_F329_V0.5870.97
40_V55_S0.5860.97
266_L332_V0.5830.97
182_P225_R0.5810.97
302_H305_P0.5780.97
16_V20_D0.5770.97
203_V215_F0.5740.97
225_R230_D0.5730.97
80_K102_L0.5720.97
208_L227_Q0.5710.97
186_K190_A0.5710.97
129_T132_N0.5710.97
93_Y122_I0.5700.97
271_E316_A0.5680.97
270_L286_Q0.5670.97
130_I134_L0.5660.97
178_L192_L0.5650.97
340_D344_E0.5630.97
63_L69_L0.5610.97
248_T331_L0.5610.97
243_V281_L0.5610.97
200_C226_S0.5610.97
169_V172_F0.5580.97
90_F94_T0.5570.97
155_M172_F0.5550.97
169_V173_L0.5550.97
117_G122_I0.5550.97
302_H319_T0.5550.97
222_L225_R0.5520.96
16_V19_R0.5510.96
22_P25_R0.5510.96
203_V226_S0.5490.96
147_F151_I0.5480.96
104_E150_K0.5480.96
5_I142_V0.5460.96
280_D342_Q0.5460.96
9_M16_V0.5450.96
184_V189_A0.5450.96
170_P227_Q0.5430.96
94_T122_I0.5420.96
340_D343_M0.5390.96
24_L72_L0.5390.96
283_I286_Q0.5350.96
289_K299_T0.5350.96
293_D330_R0.5340.96
41_I69_L0.5340.96
127_R138_A0.5340.96
245_V266_L0.5340.96
164_I169_V0.5310.96
312_L336_V0.5310.96
10_D46_Y0.5300.95
95_S111_D0.5300.95
30_A59_T0.5290.95
46_Y158_P0.5280.95
212_L219_G0.5260.95
144_P165_T0.5260.95
101_S104_E0.5250.95
300_Q319_T0.5250.95
147_F222_L0.5240.95
336_V339_L0.5240.95
119_A123_A0.5230.95
59_T63_L0.5230.95
19_R85_H0.5230.95
18_M27_I0.5230.95
62_A65_L0.5220.95
5_I119_A0.5220.95
178_L203_V0.5210.95
111_D115_C0.5200.95
10_D156_N0.5190.95
224_E227_Q0.5170.95
15_A43_T0.5160.95
262_I332_V0.5140.95
175_T200_C0.5130.95
258_E262_I0.5120.95
283_I339_L0.5110.95
290_L320_W0.5110.95
54_R65_L0.5110.95
329_V332_V0.5100.94
86_I136_L0.5100.94
271_E336_V0.5100.94
269_E273_R0.5080.94
293_D328_G0.5050.94
310_A313_I0.5040.94
29_I45_N0.5040.94
54_R61_M0.5000.94
23_A27_I0.5000.94
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  
4q45F 1 0.9658 100 0.064 Contact Map
4f50A 1 0.9459 100 0.076 Contact Map
4dezA 2 0.6581 100 0.083 Contact Map
3gqcA 3 0.9715 100 0.091 Contact Map
4tqrA 1 0.9544 100 0.092 Contact Map
3pzpA 1 0.9544 100 0.113 Contact Map
3osnA 1 0.9487 100 0.114 Contact Map
4ecqA 1 0.9715 100 0.117 Contact Map
1t94A 1 0.9373 100 0.118 Contact Map
2aq4A 1 0.9544 100 0.124 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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