GREMLIN Database
HOLA - DNA polymerase III subunit delta
UniProt: P28630 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 343 (296)
Sequences: 10838 (6979)
Seq/√Len: 405.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
225_K228_R4.4101.00
152_A164_D3.4391.00
152_A167_N3.3371.00
148_P168_Q3.2121.00
198_T201_R3.2031.00
161_E196_K2.9891.00
143_E146_Q2.8611.00
165_A199_L2.7501.00
199_L203_E2.7221.00
163_D166_A2.6841.00
163_D196_K2.5631.00
10_R14_N2.4101.00
163_D198_T2.3391.00
169_V199_L2.2221.00
221_L253_E2.2181.00
155_A162_L2.2021.00
153_A157_Q2.1741.00
152_A156_K2.1491.00
155_A185_L2.0991.00
148_P167_N2.0911.00
310_L314_Q2.0761.00
307_R311_T2.0671.00
148_P152_A2.0641.00
160_L189_S2.0581.00
162_L167_N2.0491.00
200_P204_Q2.0271.00
60_D63_A2.0231.00
23_L139_C1.9741.00
150_W178_L1.9581.00
261_K295_Q1.9361.00
151_V181_L1.8981.00
147_L181_L1.8931.00
142_P178_L1.8721.00
238_L313_K1.8151.00
220_A228_R1.8101.00
309_E313_K1.7881.00
166_A202_V1.7641.00
63_A66_S1.7171.00
34_S139_C1.6791.00
103_L107_D1.6731.00
148_P171_C1.6621.00
58_N62_N1.6591.00
18_R21_Y1.6571.00
149_R152_A1.6551.00
169_V203_E1.6251.00
77_R109_L1.6191.00
200_P203_E1.6031.00
58_N92_A1.5951.00
220_A232_I1.5861.00
154_R182_A1.5601.00
166_A199_L1.5561.00
262_R295_Q1.5551.00
149_R153_A1.5451.00
260_L287_G1.5431.00
219_D285_M1.5411.00
144_Q172_Y1.5241.00
151_V167_N1.5231.00
147_L171_C1.5161.00
171_C181_L1.5091.00
254_L301_A1.4991.00
59_T63_A1.4871.00
284_G288_E1.4831.00
184_A187_R1.4821.00
144_Q168_Q1.4791.00
63_A67_L1.4771.00
271_A274_D1.4661.00
164_D168_Q1.4561.00
79_T111_I1.4261.00
253_E289_A1.4141.00
294_S297_Q1.4101.00
288_E292_R1.4031.00
174_Y181_L1.4031.00
192_W201_R1.4021.00
218_V254_L1.3981.00
201_R204_Q1.3981.00
72_S107_D1.3921.00
222_L293_L1.3911.00
99_T102_G1.3771.00
173_C206_V1.3671.00
52_T81_L1.3551.00
283_R287_G1.3381.00
219_D223_M1.3331.00
150_W153_A1.3311.00
170_L184_A1.3191.00
24_L136_Q1.3191.00
234_Q238_L1.3111.00
252_R256_L1.3081.00
270_R274_D1.3061.00
145_A149_R1.3011.00
169_V173_C1.2911.00
11_A14_N1.2751.00
151_V185_L1.2701.00
167_N171_C1.2551.00
91_A95_E1.2541.00
163_D199_L1.2451.00
146_Q149_R1.2381.00
148_P164_D1.2271.00
53_F56_D1.2181.00
42_A109_L1.2171.00
151_V171_C1.2161.00
287_G291_N1.2041.00
261_K298_L1.1881.00
302_V306_T1.1841.00
250_L289_A1.1781.00
168_Q172_Y1.1771.00
144_Q171_C1.1761.00
39_R79_T1.1761.00
248_R309_E1.1671.00
260_L290_L1.1621.00
169_V202_V1.1561.00
236_L246_L1.1521.00
24_L138_T1.1511.00
195_G201_R1.1491.00
54_S83_L1.1481.00
221_L292_R1.1391.00
18_R135_V1.1371.00
82_L112_V1.1341.00
65_F68_C1.1311.00
224_G297_Q1.1281.00
228_R232_I1.1231.00
284_G287_G1.1191.00
102_G133_R1.1141.00
61_W65_F1.1021.00
241_S245_I1.0981.00
66_S69_Q1.0971.00
144_Q148_P1.0951.00
35_Q39_R1.0921.00
81_L113_R1.0871.00
218_V253_E1.0831.00
306_T309_E1.0771.00
271_A275_K1.0761.00
213_T235_Q1.0761.00
258_V298_L1.0751.00
238_L309_E1.0721.00
281_N284_G1.0701.00
186_E190_L1.0691.00
232_I235_Q1.0661.00
36_D54_S1.0611.00
231_H235_Q1.0571.00
153_A156_K1.0481.00
257_L298_L1.0461.00
22_L134_S1.0451.00
21_Y137_V1.0391.00
282_R306_T1.0361.00
95_E99_T1.0351.00
303_Q306_T1.0351.00
45_Q76_S1.0331.00
270_R275_K1.0291.00
19_A109_L1.0261.00
187_R190_L1.0261.00
219_D289_A1.0191.00
53_F78_Q1.0181.00
215_F219_D1.0151.00
255_L287_G1.0131.00
167_N181_L1.0111.00
51_H55_I1.0081.00
170_L202_V1.0071.00
145_A148_P1.0061.00
184_A206_V1.0061.00
280_Q283_R1.0011.00
20_A101_T1.0011.00
237_R243_P0.9991.00
147_L178_L0.9951.00
216_H232_I0.9931.00
273_F281_N0.9921.00
162_L166_A0.9881.00
62_N96_Q0.9881.00
251_Q302_V0.9851.00
169_V172_Y0.9801.00
304_L308_T0.9801.00
242_E320_V0.9761.00
280_Q284_G0.9731.00
216_H228_R0.9701.00
307_R310_L0.9701.00
90_N93_I0.9681.00
155_A160_L0.9661.00
141_T175_E0.9631.00
59_T62_N0.9611.00
282_R309_E0.9561.00
154_R158_L0.9561.00
17_L109_L0.9561.00
98_L129_A0.9511.00
256_L259_N0.9491.00
279_W282_R0.9441.00
59_T64_I0.9381.00
245_I248_R0.9371.00
95_E98_L0.9321.00
297_Q301_A0.9231.00
150_W154_R0.9151.00
85_P110_L0.9121.00
235_Q238_L0.9101.00
312_L315_D0.9091.00
236_L241_S0.9071.00
261_K264_S0.9031.00
242_E245_I0.9001.00
261_K294_S0.8971.00
88_G93_I0.8961.00
68_C80_L0.8951.00
257_L261_K0.8931.00
300_Q304_L0.8811.00
118_S124_A0.8801.00
257_L290_L0.8761.00
255_L259_N0.8761.00
215_F253_E0.8751.00
38_V42_A0.8751.00
220_A225_K0.8751.00
259_N263_Q0.8731.00
191_L205_A0.8721.00
305_L309_E0.8681.00
23_L34_S0.8641.00
129_A133_R0.8631.00
233_L289_A0.8611.00
233_L237_R0.8591.00
260_L286_M0.8531.00
147_L151_V0.8451.00
32_Q36_D0.8421.00
162_L197_L0.8411.00
69_Q103_L0.8381.00
247_L308_T0.8351.00
53_F67_L0.8341.00
216_H235_Q0.8341.00
282_R285_M0.8341.00
251_Q305_L0.8311.00
54_S57_P0.8281.00
209_A212_F0.8271.00
155_A189_S0.8271.00
84_L115_N0.8261.00
299_R303_Q0.8251.00
131_A136_Q0.8241.00
158_L189_S0.8231.00
60_D65_F0.8211.00
36_D40_Q0.8211.00
218_V221_L0.8171.00
218_V252_R0.8131.00
62_N65_F0.8101.00
235_Q239_E0.8091.00
35_Q113_R0.8051.00
256_L286_M0.8041.00
214_P245_I0.8031.00
26_N29_L0.8031.00
226_S229_A0.8011.00
102_G129_A0.8011.00
254_L298_L0.7981.00
98_L102_G0.7981.00
273_F283_R0.7961.00
32_Q83_L0.7961.00
228_R231_H0.7941.00
140_Q143_E0.7851.00
213_T216_H0.7841.00
303_Q307_R0.7841.00
259_N262_R0.7821.00
38_V111_I0.7811.00
258_V302_V0.7801.00
285_M288_E0.7781.00
123_N128_T0.7781.00
16_G42_A0.7771.00
278_V282_R0.7761.00
258_V262_R0.7751.00
237_R278_V0.7711.00
242_E246_L0.7671.00
214_P218_V0.7661.00
46_G52_T0.7661.00
68_C100_L0.7621.00
227_K231_H0.7621.00
42_A77_R0.7601.00
217_W246_L0.7601.00
308_T312_L0.7571.00
22_L114_G0.7561.00
254_L305_L0.7561.00
192_W195_G0.7551.00
100_L104_L0.7531.00
61_W64_I0.7451.00
102_G132_N0.7441.00
260_L263_Q0.7431.00
293_L298_L0.7431.00
276_H284_G0.7421.00
223_M292_R0.7411.00
23_L35_Q0.7391.00
79_T109_L0.7391.00
37_A40_Q0.7351.00
158_L186_E0.7341.00
219_D292_R0.7341.00
24_L123_N0.7311.00
253_E257_L0.7301.00
23_L31_L0.7291.00
255_L260_L0.7251.00
255_L258_V0.7171.00
31_L113_R0.7161.00
170_L181_L0.7151.00
65_F100_L0.7151.00
77_R107_D0.7121.00
54_S81_L0.7101.00
85_P112_V0.7101.00
128_T131_A0.7071.00
41_V44_A0.7031.00
210_A241_S0.7031.00
264_S291_N0.7001.00
27_D30_L0.6981.00
304_L307_R0.6981.00
156_K162_L0.6971.00
156_K159_N0.6931.00
39_R81_L0.6911.00
65_F69_Q0.6901.00
261_K290_L0.6901.00
155_A167_N0.6891.00
82_L85_P0.6891.00
58_N90_N0.6861.00
67_L78_Q0.6790.99
58_N96_Q0.6770.99
246_L249_T0.6760.99
226_S230_L0.6760.99
67_L70_A0.6680.99
165_A168_Q0.6670.99
281_N285_M0.6670.99
154_R157_Q0.6670.99
51_H72_S0.6650.99
263_Q287_G0.6640.99
202_V206_V0.6630.99
311_T315_D0.6610.99
174_Y184_A0.6600.99
261_K291_N0.6600.99
293_L301_A0.6590.99
142_P146_Q0.6550.99
175_E181_L0.6540.99
8_Q11_A0.6520.99
293_L297_Q0.6510.99
101_T130_L0.6490.99
254_L293_L0.6490.99
182_A186_E0.6480.99
58_N61_W0.6470.99
28_P179_L0.6450.99
245_I249_T0.6440.99
83_L113_R0.6410.99
258_V295_Q0.6390.99
202_V205_A0.6370.99
308_T311_T0.6340.99
28_P31_L0.6330.99
52_T55_I0.6320.99
253_E256_L0.6320.99
99_T103_L0.6320.99
297_Q300_Q0.6320.99
306_T310_L0.6300.99
285_M289_A0.6290.99
237_R241_S0.6280.99
35_Q83_L0.6260.99
311_T316_Y0.6230.99
185_L189_S0.6220.99
188_L205_A0.6210.99
287_G290_L0.6130.99
216_H219_D0.6110.99
279_W286_M0.6100.99
26_N141_T0.6080.99
223_M228_R0.6050.99
124_A128_T0.6050.99
98_L125_A0.6050.99
288_E291_N0.6040.99
188_L191_L0.6030.99
160_L195_G0.6010.99
130_L134_S0.6000.99
29_L178_L0.5980.99
192_W197_L0.5980.99
290_L301_A0.5960.99
278_V281_N0.5950.99
22_L136_Q0.5950.99
68_C108_L0.5930.99
234_Q312_L0.5920.99
123_N138_T0.5900.99
211_H215_F0.5890.99
53_F57_P0.5880.99
156_K161_E0.5800.98
244_V270_R0.5800.98
174_Y177_N0.5780.98
229_A289_A0.5760.98
61_W88_G0.5760.98
257_L293_L0.5730.98
51_H54_S0.5730.98
21_Y109_L0.5720.98
11_A15_E0.5720.98
26_N177_N0.5720.98
257_L286_M0.5720.98
221_L250_L0.5690.98
66_S70_A0.5650.98
177_N180_A0.5650.98
8_Q12_Q0.5640.98
251_Q270_R0.5630.98
154_R186_E0.5620.98
43_A52_T0.5620.98
247_L305_L0.5590.98
244_V274_D0.5570.98
212_F216_H0.5560.98
247_L270_R0.5560.98
32_Q179_L0.5550.98
44_A77_R0.5550.98
279_W283_R0.5550.98
37_A41_V0.5540.98
29_L139_C0.5520.98
100_L103_L0.5520.98
279_W285_M0.5510.98
166_A170_L0.5510.98
33_E154_R0.5500.98
219_D288_E0.5500.98
188_L197_L0.5480.98
245_I252_R0.5470.98
17_L42_A0.5430.98
210_A213_T0.5410.98
247_L251_Q0.5410.98
188_L202_V0.5390.97
257_L289_A0.5380.97
215_F218_V0.5370.97
230_L304_L0.5360.97
31_L139_C0.5350.97
90_N127_F0.5330.97
36_D103_L0.5320.97
256_L278_V0.5290.97
243_P246_L0.5290.97
80_L108_L0.5290.97
197_L204_Q0.5280.97
184_A188_L0.5270.97
167_N170_L0.5260.97
130_L136_Q0.5260.97
70_A73_L0.5260.97
58_N65_F0.5240.97
149_R164_D0.5230.97
237_R309_E0.5230.97
311_T314_Q0.5160.97
55_I60_D0.5150.97
225_K231_H0.5150.97
272_L284_G0.5140.97
60_D92_A0.5140.97
251_Q255_L0.5130.97
250_L305_L0.5110.97
217_W229_A0.5090.96
231_H234_Q0.5080.96
85_P126_W0.5080.96
273_F278_V0.5080.96
252_R282_R0.5070.96
166_A197_L0.5060.96
300_Q303_Q0.5050.96
33_E36_D0.5040.96
44_A47_F0.5030.96
217_W221_L0.5020.96
33_E37_A0.5020.96
166_A188_L0.5000.96
150_W182_A0.5000.96
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  
1jr3D 1 0.9825 100 0.228 Contact Map
3zh9B 1 0.9534 100 0.298 Contact Map
1jr3A 3 0.9446 100 0.426 Contact Map
1a5tA 2 0.8484 100 0.471 Contact Map
2chqA 3 0.8455 100 0.516 Contact Map
1iqpA 5 0.8484 100 0.522 Contact Map
1sxjD 1 0.8513 100 0.524 Contact Map
1sxjB 1 0.8426 100 0.538 Contact Map
3u61B 3 0.8163 100 0.544 Contact Map
1sxjC 1 0.8542 100 0.555 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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