GREMLIN Database
DPO41 - DNA polymerase IV 1
UniProt: P54545 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 414 (363)
Sequences: 8869 (6282)
Seq/√Len: 329.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
97_E133_R3.8831.00
183_G193_A2.9261.00
133_R137_E2.9151.00
266_L323_E2.8841.00
97_E137_E2.7881.00
34_A74_L2.7841.00
261_D264_E2.7581.00
287_A342_G2.5901.00
24_Y83_R2.5871.00
197_K202_H2.3851.00
87_S90_A2.3301.00
250_G341_T2.3261.00
13_M142_S2.3241.00
64_V76_V2.3021.00
135_Q163_L2.2951.00
266_L327_F2.2651.00
80_N83_R2.2181.00
202_H206_E2.2121.00
129_E133_R2.2011.00
30_G52_E2.1811.00
183_G197_K2.1101.00
98_Y133_R2.0811.00
103_E150_K2.0771.00
132_S136_K2.0641.00
205_G209_A2.0621.00
227_K231_N2.0291.00
99_T112_M2.0221.00
134_L142_S2.0211.00
216_K224_P2.0081.00
22_M50_S2.0021.00
228_N233_I1.9981.00
262_E327_F1.9911.00
199_L218_L1.9831.00
178_W208_A1.9741.00
131_Q163_L1.9491.00
178_W205_G1.9241.00
31_K75_I1.9141.00
201_I210_A1.9141.00
9_F114_M1.9131.00
201_I207_L1.8931.00
13_M91_M1.8731.00
276_V342_G1.8541.00
13_M140_L1.8411.00
24_Y80_N1.8371.00
66_Q70_H1.8111.00
169_R172_Q1.8021.00
289_K344_D1.7961.00
280_L342_G1.7951.00
212_E224_P1.7671.00
92_F110_G1.7101.00
225_R229_K1.6871.00
270_R319_L1.6651.00
306_T324_H1.6651.00
83_R86_N1.6571.00
314_Q317_D1.6441.00
96_R102_V1.6401.00
124_L128_K1.6001.00
313_D348_K1.5991.00
18_A33_V1.5971.00
291_F343_T1.5961.00
52_E55_A1.5931.00
174_P178_W1.5931.00
356_D359_S1.5811.00
131_Q165_I1.5691.00
105_V111_Y1.5691.00
293_M339_G1.5591.00
34_A76_V1.5451.00
34_A46_V1.5431.00
62_M70_H1.5401.00
273_A318_I1.5371.00
23_A87_S1.5171.00
306_T328_K1.5121.00
152_L168_L1.4921.00
86_N90_A1.4881.00
203_T206_E1.4861.00
25_D28_L1.4831.00
193_A197_K1.4821.00
194_E198_G1.4751.00
122_R125_E1.4701.00
199_L219_L1.4491.00
274_A315_K1.4421.00
251_N276_V1.4391.00
277_S315_K1.4381.00
98_Y129_E1.4361.00
289_K343_T1.4361.00
172_Q175_D1.4281.00
259_S265_L1.4241.00
322_A340_I1.4201.00
9_F144_I1.4151.00
11_I142_S1.4071.00
223_G227_K1.4061.00
212_E228_N1.4041.00
126_T130_I1.3971.00
56_R73_E1.3931.00
148_P173_V1.3881.00
224_P228_N1.3811.00
127_A144_I1.3791.00
63_P66_Q1.3701.00
20_V87_S1.3691.00
124_L167_I1.3621.00
22_M29_R1.3621.00
210_A214_S1.3561.00
20_V83_R1.3531.00
127_A146_I1.3521.00
308_L321_E1.3511.00
21_E84_Y1.3501.00
210_A215_L1.3491.00
212_E227_K1.3441.00
34_A58_V1.3421.00
277_S318_I1.3341.00
273_A340_I1.3331.00
128_K132_S1.3321.00
262_E266_L1.3281.00
95_L112_M1.3271.00
146_I165_I1.3251.00
260_S334_P1.3241.00
280_L287_A1.3111.00
215_L227_K1.2911.00
28_L33_V1.2871.00
252_S339_G1.2861.00
212_E216_K1.2841.00
66_Q69_R1.2821.00
295_R301_T1.2711.00
15_S19_S1.2691.00
33_V77_L1.2691.00
56_R71_C1.2671.00
51_Y55_A1.2661.00
288_S344_D1.2581.00
9_F127_A1.2571.00
147_A152_L1.2561.00
121_S129_E1.2541.00
94_I137_E1.2481.00
111_Y186_H1.2451.00
174_P208_A1.2431.00
257_H264_E1.2431.00
308_L312_I1.2341.00
93_T96_R1.2261.00
286_M346_V1.2241.00
251_N279_R1.2231.00
94_I133_R1.2221.00
22_M52_E1.2181.00
18_A22_M1.2171.00
281_Q374_E1.2171.00
83_R87_S1.2161.00
255_L268_V1.2131.00
191_K194_E1.2121.00
128_K131_Q1.2091.00
114_M126_T1.2071.00
82_D86_N1.2021.00
11_I95_L1.2011.00
354_Q357_L1.1851.00
94_I138_L1.1851.00
251_N275_S1.1781.00
249_V283_K1.1771.00
259_S264_E1.1761.00
206_E209_A1.1721.00
25_D77_L1.1651.00
101_L240_P1.1621.00
289_K305_S1.1611.00
321_E324_H1.1601.00
291_F305_S1.1571.00
95_L110_G1.1551.00
159_M166_T1.1441.00
10_H157_S1.1431.00
295_R337_L1.1421.00
214_S218_L1.1351.00
46_V58_V1.1351.00
319_L323_E1.1331.00
317_D321_E1.1291.00
211_D214_S1.1281.00
195_K218_L1.1281.00
21_E80_N1.1271.00
156_A168_L1.1151.00
42_R68_K1.1031.00
306_T321_E1.0971.00
92_F104_P1.0901.00
255_L259_S1.0881.00
36_A64_V1.0841.00
23_A83_R1.0741.00
273_A277_S1.0741.00
208_A231_N1.0711.00
268_V271_K1.0581.00
46_V49_C1.0571.00
49_C60_T1.0501.00
252_S293_M1.0451.00
117_T121_S1.0451.00
323_E327_F1.0431.00
125_E129_E1.0421.00
289_K307_T1.0411.00
98_Y130_I1.0401.00
273_A319_L1.0381.00
364_A368_P1.0361.00
58_V74_L1.0361.00
155_M180_L1.0301.00
320_K324_H1.0281.00
288_S307_T1.0271.00
185_M204_I1.0251.00
369_I372_M1.0091.00
23_A139_L1.0091.00
220_G223_G1.0051.00
147_A153_A1.0051.00
307_T344_D1.0031.00
46_V67_A0.9941.00
117_T126_T0.9921.00
292_I325_L0.9861.00
258_D297_A0.9831.00
296_Y302_I0.9831.00
18_A48_T0.9781.00
219_L223_G0.9761.00
265_L326_F0.9761.00
285_V347_E0.9731.00
15_S51_Y0.9711.00
11_I112_M0.9701.00
194_E197_K0.9681.00
65_W69_R0.9671.00
288_S346_V0.9651.00
22_M33_V0.9621.00
160_K166_T0.9611.00
312_I317_D0.9581.00
91_M138_L0.9571.00
286_M313_D0.9571.00
158_D184_E0.9561.00
273_A322_A0.9551.00
16_F20_V0.9541.00
24_Y87_S0.9481.00
92_F96_R0.9481.00
47_V79_P0.9471.00
324_H328_K0.9381.00
105_V186_H0.9361.00
277_S281_Q0.9341.00
315_K370_Q0.9341.00
288_S311_P0.9281.00
269_F292_I0.9251.00
81_F85_R0.9211.00
135_Q139_L0.9171.00
62_M66_Q0.9161.00
253_S268_V0.9151.00
36_A44_G0.9091.00
281_Q313_D0.9091.00
195_K198_G0.9081.00
128_K165_I0.9031.00
291_F303_T0.9011.00
95_L130_I0.8991.00
207_L215_L0.8981.00
269_F322_A0.8961.00
258_D336_R0.8911.00
117_T120_S0.8901.00
222_N225_R0.8861.00
291_F341_T0.8851.00
90_A93_T0.8841.00
21_E25_D0.8791.00
311_P346_V0.8761.00
181_P197_K0.8691.00
188_V223_G0.8691.00
269_F338_L0.8631.00
34_A71_C0.8621.00
179_P205_G0.8611.00
59_K62_M0.8601.00
276_V340_I0.8571.00
286_M348_K0.8531.00
15_S22_M0.8491.00
201_I206_E0.8481.00
208_A230_A0.8481.00
127_A165_I0.8471.00
285_V345_L0.8471.00
315_K319_L0.8451.00
294_I338_L0.8451.00
182_V197_K0.8431.00
348_K367_E0.8431.00
372_M376_L0.8391.00
192_T195_K0.8361.00
62_M67_A0.8361.00
150_K238_V0.8351.00
48_T54_R0.8351.00
258_D334_P0.8331.00
17_Y81_F0.8321.00
151_F229_K0.8291.00
94_I98_Y0.8261.00
269_F326_F0.8251.00
214_S217_R0.8231.00
228_N235_H0.8211.00
306_T325_L0.8181.00
215_L219_L0.8161.00
17_Y79_P0.8141.00
85_R89_R0.8131.00
262_E326_F0.8111.00
252_S337_L0.8041.00
368_P371_Q0.8021.00
146_I167_I0.8011.00
270_R323_E0.7991.00
205_G208_A0.7991.00
304_R329_H0.7951.00
181_P184_E0.7951.00
304_R325_L0.7941.00
316_N366_D0.7941.00
49_C58_V0.7941.00
316_N320_K0.7911.00
22_M30_G0.7871.00
102_V110_G0.7861.00
263_E266_L0.7841.00
101_L113_D0.7791.00
99_T102_V0.7791.00
67_A71_C0.7791.00
375_K378_K0.7781.00
144_I165_I0.7761.00
135_Q141_P0.7701.00
371_Q375_K0.7681.00
269_F319_L0.7681.00
302_I329_H0.7621.00
131_Q144_I0.7611.00
92_F102_V0.7591.00
103_E238_V0.7581.00
172_Q176_I0.7561.00
367_E371_Q0.7550.99
114_M127_A0.7520.99
192_T219_L0.7510.99
149_N152_L0.7500.99
213_H217_R0.7500.99
123_A127_A0.7490.99
234_H237_P0.7480.99
290_L321_E0.7480.99
71_C74_L0.7450.99
129_E132_S0.7450.99
90_A138_L0.7450.99
94_I134_L0.7440.99
195_K219_L0.7430.99
53_A74_L0.7430.99
199_L210_A0.7420.99
267_G271_K0.7420.99
8_I113_D0.7390.99
18_A50_S0.7380.99
304_R328_K0.7380.99
88_S92_F0.7380.99
279_R283_K0.7380.99
28_L75_I0.7380.99
282_R378_K0.7360.99
8_I238_V0.7360.99
174_P209_A0.7360.99
207_L227_K0.7340.99
168_L176_I0.7320.99
35_V77_L0.7310.99
294_I329_H0.7300.99
101_L116_D0.7300.99
273_A315_K0.7260.99
111_Y150_K0.7260.99
188_V226_L0.7240.99
176_I180_L0.7230.99
211_D231_N0.7210.99
132_S135_Q0.7150.99
318_I342_G0.7130.99
68_K72_P0.7120.99
318_I322_A0.7120.99
321_E325_L0.7100.99
114_M117_T0.7100.99
275_S278_D0.7080.99
49_C54_R0.7040.99
94_I97_E0.7030.99
47_V60_T0.7020.99
13_M16_F0.7000.99
266_L270_R0.6970.99
87_S138_L0.6960.99
68_K76_V0.6940.99
274_A278_D0.6940.99
51_Y54_R0.6890.99
104_P107_I0.6870.99
157_S160_K0.6870.99
64_V71_C0.6870.99
46_V76_V0.6860.99
125_E128_K0.6850.99
290_L318_I0.6840.99
82_D85_R0.6830.99
124_L165_I0.6800.99
294_I335_V0.6780.99
31_K73_E0.6770.99
310_N317_D0.6750.99
32_P71_C0.6750.99
267_G270_R0.6730.99
182_V193_A0.6700.99
93_T97_E0.6680.99
253_S275_S0.6650.99
286_M345_L0.6630.99
14_N143_S0.6600.99
246_F283_K0.6580.99
87_S140_L0.6570.99
17_Y107_I0.6560.99
29_R135_Q0.6560.99
270_R274_A0.6540.99
219_L226_L0.6530.99
212_E231_N0.6520.99
36_A76_V0.6520.99
37_G78_P0.6510.99
315_K374_E0.6490.98
263_E267_G0.6490.98
68_K74_L0.6470.98
293_M303_T0.6450.98
296_Y335_V0.6450.98
276_V290_L0.6440.98
250_G339_G0.6430.98
262_E330_W0.6430.98
259_S268_V0.6410.98
249_V285_V0.6410.98
308_L311_P0.6410.98
199_L214_S0.6410.98
98_Y126_T0.6400.98
46_V74_L0.6400.98
141_P160_K0.6390.98
182_V201_I0.6380.98
265_L335_V0.6360.98
265_L338_L0.6360.98
326_F330_W0.6350.98
272_L338_L0.6320.98
126_T129_E0.6310.98
375_K379_K0.6310.98
34_A53_A0.6290.98
364_A367_E0.6280.98
148_P152_L0.6260.98
20_V23_A0.6230.98
65_W68_K0.6230.98
354_Q358_F0.6220.98
101_L237_P0.6210.98
121_S126_T0.6210.98
30_G50_S0.6200.98
133_R136_K0.6200.98
37_G44_G0.6160.98
254_T337_L0.6160.98
67_A74_L0.6140.98
249_V279_R0.6130.98
179_P203_T0.6120.98
20_V24_Y0.6120.98
45_I60_T0.6100.98
317_D320_K0.6090.98
95_L102_V0.6090.98
31_K52_E0.6080.98
175_D178_W0.6060.98
264_E267_G0.6050.98
79_P84_Y0.6050.98
180_L184_E0.6040.98
342_G345_L0.6020.98
182_V196_L0.6020.98
15_S54_R0.6010.98
48_T60_T0.5990.97
90_A137_E0.5950.97
326_F329_H0.5940.97
368_P372_M0.5940.97
186_H229_K0.5930.97
85_R107_I0.5930.97
195_K220_G0.5930.97
296_Y300_R0.5910.97
152_L173_V0.5910.97
155_M186_H0.5890.97
207_L230_A0.5880.97
278_D282_R0.5870.97
190_K194_E0.5860.97
22_M31_K0.5860.97
314_Q370_Q0.5850.97
281_Q315_K0.5850.97
270_R315_K0.5820.97
168_L173_V0.5820.97
38_N42_R0.5820.97
268_V338_L0.5780.97
314_Q366_D0.5770.97
109_E154_K0.5740.97
106_S109_E0.5730.97
316_N319_L0.5730.97
229_K234_H0.5710.97
373_M377_N0.5690.97
287_A290_L0.5680.97
163_L166_T0.5680.97
226_L229_K0.5670.96
21_E24_Y0.5650.96
294_I326_F0.5650.96
277_S322_A0.5640.96
9_F146_I0.5620.96
134_L138_L0.5610.96
207_L219_L0.5590.96
38_N78_P0.5570.96
46_V71_C0.5570.96
269_F323_E0.5560.96
216_K221_I0.5550.96
264_E268_V0.5540.96
170_K174_P0.5540.96
312_I318_I0.5530.96
123_A146_I0.5530.96
175_D179_P0.5530.96
297_A336_R0.5520.96
95_L99_T0.5500.96
160_K164_G0.5490.96
14_N160_K0.5480.96
89_R93_T0.5470.96
372_M375_K0.5470.96
59_K66_Q0.5460.96
352_Y355_L0.5460.96
34_A64_V0.5440.96
174_P231_N0.5440.96
26_P29_R0.5430.96
148_P169_R0.5420.95
121_S125_E0.5410.95
9_F123_A0.5400.95
173_V176_I0.5400.95
92_F95_L0.5370.95
249_V280_L0.5360.95
14_N51_Y0.5350.95
151_F155_M0.5340.95
23_A90_A0.5340.95
188_V193_A0.5340.95
19_S48_T0.5320.95
204_I230_A0.5320.95
251_N272_L0.5310.95
99_T126_T0.5310.95
306_T309_R0.5300.95
81_F107_I0.5300.95
224_P227_K0.5290.95
221_I225_R0.5290.95
178_W209_A0.5270.95
64_V68_K0.5270.95
150_K237_P0.5270.95
100_D116_D0.5270.95
173_V177_L0.5270.95
59_K70_H0.5250.95
151_F226_L0.5240.95
11_I144_I0.5240.95
95_L104_P0.5230.95
33_V50_S0.5190.94
275_S279_R0.5180.94
159_M176_I0.5180.94
265_L330_W0.5170.94
228_N231_N0.5140.94
216_K223_G0.5140.94
35_V48_T0.5090.94
22_M25_D0.5090.94
212_E223_G0.5090.94
335_V338_L0.5080.94
277_S342_G0.5080.94
67_A70_H0.5070.94
28_L77_L0.5070.94
13_M20_V0.5070.94
353_K356_D0.5070.94
297_A334_P0.5070.94
349_E353_K0.5050.93
196_L201_I0.5040.93
118_P122_R0.5030.93
293_M341_T0.5010.93
374_E377_N0.5010.93
22_M28_L0.5000.93
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  
4f50A 1 0.8019 100 0.159 Contact Map
4dezA 2 0.558 100 0.164 Contact Map
3gqcA 3 0.8285 100 0.177 Contact Map
4q45F 1 0.8188 100 0.18 Contact Map
4tqrA 1 0.8116 100 0.187 Contact Map
1t94A 1 0.8068 100 0.191 Contact Map
3pzpA 1 0.8213 100 0.192 Contact Map
3osnA 1 0.8116 100 0.201 Contact Map
2aq4A 1 0.8237 100 0.201 Contact Map
4ecqA 1 0.8333 100 0.202 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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