GREMLIN Database
HOLB - DNA polymerase III subunit delta'
UniProt: P28631 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11500
Length: 334 (293)
Sequences: 14316 (9312)
Seq/√Len: 544.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
168_P171_Y3.6421.00
173_V188_L3.6131.00
8_R171_Y3.5901.00
40_L164_L2.6731.00
172_A191_L2.6691.00
173_V187_L2.5921.00
169_E191_L2.4751.00
90_V94_R2.4621.00
46_R69_Q2.3551.00
295_H299_Q2.3441.00
169_E192_R2.3301.00
29_I164_L2.2721.00
4_Y40_L2.2481.00
240_Q243_A2.2431.00
183_S186_A2.1441.00
271_P275_A2.0641.00
241_A244_R2.0601.00
4_Y43_A2.0541.00
175_W198_P2.0281.00
173_V191_L1.9881.00
42_Y78_T1.9331.00
2_R15_V1.9111.00
24_H27_L1.9071.00
15_V19_Q1.8671.00
208_D211_Q1.8641.00
95_E99_K1.8591.00
210_W214_E1.8501.00
167_P198_P1.8271.00
48_L140_W1.8101.00
176_L201_A1.8051.00
76_Y113_W1.7981.00
234_A238_H1.7921.00
288_A292_D1.7921.00
269_D272_G1.7301.00
171_Y174_T1.7071.00
194_S201_A1.7051.00
88_L92_A1.7021.00
257_K261_G1.6951.00
182_M187_L1.6781.00
275_A279_N1.6741.00
109_A140_W1.6461.00
8_R174_T1.6451.00
230_Y234_A1.6321.00
211_Q214_E1.6231.00
276_E280_H1.6211.00
249_A253_M1.6191.00
255_A258_R1.6181.00
250_T254_D1.6051.00
210_W213_R1.5961.00
214_E218_Q1.5841.00
4_Y11_F1.5701.00
102_E105_R1.5501.00
88_L121_T1.5461.00
172_A201_A1.5441.00
176_L187_L1.5291.00
233_L236_L1.5241.00
169_E188_L1.5201.00
272_G276_E1.5111.00
28_L117_A1.5071.00
272_G275_A1.4941.00
267_N270_V1.4821.00
241_A245_L1.4761.00
285_R288_A1.4681.00
30_Q161_L1.4671.00
253_M257_K1.4621.00
91_D95_E1.4551.00
28_L159_C1.4431.00
113_W144_A1.4411.00
181_T211_Q1.4371.00
134_E138_E1.4361.00
230_Y233_L1.4351.00
209_N213_R1.4321.00
117_A143_L1.4271.00
184_Q188_L1.4251.00
282_S285_R1.4121.00
95_E98_E1.4071.00
9_P165_A1.4061.00
267_N271_P1.4051.00
208_D214_E1.3971.00
270_V273_L1.3961.00
213_R216_L1.3371.00
259_H263_A1.3281.00
298_E302_S1.3221.00
177_S187_L1.3131.00
77_Y80_A1.3061.00
309_E313_T1.3061.00
242_P246_H1.3041.00
217_C220_L1.2911.00
75_D80_A1.2831.00
255_A259_H1.2751.00
88_L123_A1.2701.00
74_P81_P1.2681.00
69_Q72_T1.2611.00
225_P228_D1.2511.00
166_P195_A1.2501.00
75_D81_P1.2451.00
227_G231_S1.2431.00
232_L236_L1.2411.00
247_W251_L1.2401.00
69_Q80_A1.2391.00
262_A266_T1.2301.00
290_L294_C1.2251.00
296_I315_L1.2181.00
91_D94_R1.2131.00
283_P287_Q1.2091.00
10_D162_H1.2081.00
98_E102_E1.2071.00
218_Q222_Y1.2061.00
216_L219_A1.2051.00
188_L192_R1.2021.00
117_A151_L1.1921.00
120_L124_A1.1871.00
256_L260_H1.1811.00
273_L276_E1.1791.00
258_R262_A1.1781.00
191_L201_A1.1711.00
209_N212_A1.1631.00
260_H264_Q1.1621.00
215_T219_A1.1601.00
231_S234_A1.1591.00
295_H298_E1.1561.00
73_H81_P1.1561.00
82_E86_N1.1551.00
255_A261_G1.1501.00
208_D213_R1.1491.00
256_L259_H1.1481.00
258_R261_G1.1461.00
172_A198_P1.1461.00
173_V184_Q1.1461.00
46_R50_C1.1441.00
90_V123_A1.1431.00
285_R289_I1.1421.00
16_A19_Q1.1421.00
30_Q163_Y1.1351.00
278_A283_P1.1231.00
208_D212_A1.1221.00
169_E173_V1.1131.00
98_E101_N1.1111.00
232_L235_A1.1021.00
78_T82_E1.1001.00
248_L252_L1.0971.00
253_M256_L1.0911.00
279_N282_S1.0901.00
90_V127_A1.0871.00
218_Q221_A1.0871.00
257_K262_A1.0821.00
215_T218_Q1.0821.00
254_D258_R1.0821.00
292_D296_I1.0811.00
11_F15_V1.0741.00
255_A262_A1.0741.00
289_I292_D1.0721.00
279_N283_P1.0711.00
296_I311_L1.0681.00
221_A225_P1.0671.00
217_C221_A1.0661.00
89_G121_T1.0621.00
228_D232_L1.0621.00
222_Y226_S1.0601.00
99_K103_H1.0561.00
189_A192_R1.0541.00
229_W233_L1.0501.00
212_A215_T1.0431.00
14_L44_L1.0321.00
208_D218_Q1.0321.00
8_R12_E1.0311.00
222_Y225_P1.0251.00
209_N214_E1.0181.00
231_S235_A1.0161.00
256_L262_A1.0151.00
292_D315_L1.0061.00
251_L255_A1.0061.00
41_I142_F1.0051.00
87_T121_T1.0001.00
267_N305_G0.9921.00
73_H107_G0.9901.00
291_G295_H0.9831.00
259_H262_A0.9831.00
216_L220_L0.9741.00
257_K264_Q0.9721.00
77_Y81_P0.9701.00
156_R161_L0.9651.00
229_W232_L0.9641.00
77_Y99_K0.9611.00
190_A201_A0.9611.00
287_Q291_G0.9601.00
234_A237_N0.9591.00
31_A37_D0.9521.00
293_V315_L0.9441.00
16_A20_A0.9431.00
227_G230_Y0.9421.00
312_I316_L0.9371.00
187_L191_L0.9331.00
223_S227_G0.9301.00
294_C298_E0.9301.00
290_L316_L0.9281.00
71_G78_T0.9271.00
170_Q174_T0.9261.00
73_H80_A0.9251.00
268_V271_P0.9231.00
211_Q218_Q0.9231.00
275_A278_A0.9181.00
243_A247_W0.9121.00
287_Q290_L0.9071.00
292_D295_H0.9071.00
246_H250_T0.9031.00
13_K16_A0.8971.00
261_G264_Q0.8951.00
72_T80_A0.8881.00
269_D274_V0.8871.00
38_D115_T0.8831.00
242_P245_L0.8801.00
288_A291_G0.8791.00
73_H76_Y0.8761.00
8_R11_F0.8741.00
281_L289_I0.8731.00
228_D231_S0.8721.00
213_R220_L0.8641.00
69_Q73_H0.8631.00
278_A282_S0.8581.00
117_A141_F0.8531.00
75_D78_T0.8501.00
69_Q81_P0.8451.00
170_Q173_V0.8431.00
190_A205_F0.8391.00
7_L10_D0.8361.00
71_G82_E0.8341.00
294_C297_R0.8311.00
247_W250_T0.8271.00
11_F40_L0.8241.00
220_L223_S0.8191.00
286_L290_L0.8131.00
268_V272_G0.8121.00
276_E279_N0.8111.00
75_D103_H0.8081.00
297_R301_M0.8051.00
210_W218_Q0.8041.00
190_A204_L0.8011.00
70_A73_H0.8001.00
132_L151_L0.7961.00
244_R247_W0.7951.00
183_S211_Q0.7911.00
121_T124_A0.7901.00
13_K162_H0.7841.00
89_G92_A0.7821.00
71_G80_A0.7821.00
223_S226_S0.7801.00
88_L114_V0.7731.00
296_I299_Q0.7701.00
74_P77_Y0.7681.00
213_R221_A0.7671.00
185_D214_E0.7661.00
252_L256_L0.7651.00
74_P80_A0.7621.00
73_H77_Y0.7601.00
243_A246_H0.7571.00
251_L254_D0.7551.00
313_T316_L0.7531.00
5_P175_W0.7531.00
80_A115_T0.7521.00
270_V274_V0.7501.00
76_Y80_A0.7491.00
271_P274_V0.7481.00
260_H263_A0.7481.00
72_T77_Y0.7441.00
111_V142_F0.7421.00
216_L221_A0.7381.00
224_V227_G0.7371.00
244_R316_L0.7371.00
194_S204_L0.7361.00
112_V139_T0.7351.00
212_A220_L0.7341.00
212_A219_A0.7321.00
277_L296_I0.7321.00
281_L286_L0.7311.00
220_L226_S0.7301.00
239_E242_P0.7291.00
13_K207_G0.7281.00
100_L112_V0.7271.00
14_L162_H0.7251.00
233_L237_N0.7251.00
281_L284_S0.7231.00
249_A257_K0.7191.00
203_A206_Q0.7181.00
114_V128_L0.7171.00
170_Q188_L0.7171.00
81_P86_N0.7141.00
100_L131_T0.7131.00
283_P290_L0.7121.00
30_Q148_P0.7111.00
299_Q302_S0.7111.00
245_L252_L0.7071.00
148_P151_L0.7061.00
93_V97_T0.7061.00
69_Q78_T0.7051.00
254_D257_K0.7041.00
250_T253_M0.7031.00
104_A108_G0.7021.00
44_L142_F0.7011.00
252_L255_A0.7001.00
261_G265_V0.7001.00
265_V297_R0.6981.00
99_K102_E0.6981.00
49_L76_Y0.6951.00
71_G76_Y0.6951.00
291_G294_C0.6951.00
245_L249_A0.6951.00
169_E195_A0.6941.00
114_V141_F0.6941.00
76_Y81_P0.6901.00
21_G48_L0.6811.00
9_P12_E0.6781.00
217_C225_P0.6761.00
23_G140_W0.6731.00
210_W220_L0.6711.00
92_A95_E0.6701.00
51_Q54_Q0.6681.00
104_A138_E0.6681.00
262_A265_V0.6641.00
5_P171_Y0.6601.00
12_E16_A0.6581.00
100_L139_T0.6581.00
32_L197_S0.6571.00
256_L261_G0.6551.00
87_T92_A0.6541.00
69_Q76_Y0.6531.00
117_A125_A0.6531.00
251_L261_G0.6521.00
214_E217_C0.6511.00
77_Y127_A0.6491.00
307_N310_L0.6481.00
130_K134_E0.6471.00
282_S287_Q0.6461.00
29_I40_L0.6441.00
10_D164_L0.6431.00
176_L205_F0.6421.00
220_L224_V0.6381.00
133_E157_S0.6371.00
229_W236_L0.6331.00
167_P175_W0.6321.00
252_L258_R0.6321.00
213_R218_Q0.6281.00
244_R248_L0.6281.00
269_D273_L0.6271.00
187_L201_A0.6241.00
216_L222_Y0.6241.00
212_A218_Q0.6241.00
101_N131_T0.6221.00
224_V228_D0.6221.00
235_A243_A0.6211.00
273_L277_L0.6211.00
131_T141_F0.6171.00
109_A138_E0.6171.00
78_T81_P0.6161.00
185_D188_L0.6161.00
87_T90_V0.6141.00
219_A223_S0.6131.00
82_E127_A0.6051.00
239_E243_A0.6041.00
97_T100_L0.5991.00
211_Q220_L0.5971.00
194_S197_S0.5961.00
219_A222_Y0.5961.00
116_D146_R0.5951.00
27_L162_H0.5921.00
35_M164_L0.5921.00
217_C222_Y0.5901.00
70_A81_P0.5901.00
286_L289_I0.5881.00
218_Q223_S0.5840.99
210_W216_L0.5830.99
43_A46_R0.5820.99
79_L92_A0.5820.99
32_L35_M0.5810.99
245_L248_L0.5790.99
238_H241_A0.5770.99
214_E220_L0.5740.99
131_T134_E0.5740.99
213_R217_C0.5700.99
96_V104_A0.5690.99
277_L281_L0.5680.99
75_D82_E0.5680.99
280_H284_S0.5670.99
240_Q244_R0.5670.99
23_G44_L0.5660.99
306_I311_L0.5640.99
210_W221_A0.5640.99
104_A107_G0.5620.99
72_T75_D0.5580.99
70_A80_A0.5580.99
132_L159_C0.5550.99
18_Y44_L0.5540.99
284_S288_A0.5520.99
208_D215_T0.5510.99
281_L285_R0.5510.99
90_V121_T0.5490.99
118_A146_R0.5480.99
258_R266_T0.5480.99
249_A252_L0.5470.99
217_C224_V0.5450.99
41_I113_W0.5440.99
75_D104_A0.5440.99
172_A176_L0.5440.99
247_W257_K0.5400.99
76_Y82_E0.5400.99
221_A224_V0.5390.99
272_G279_N0.5390.99
249_A256_L0.5370.99
94_R127_A0.5370.99
221_A226_S0.5370.99
173_V177_S0.5350.99
106_L110_K0.5310.99
241_A252_L0.5310.99
267_N274_V0.5300.99
75_D108_G0.5290.99
15_V47_Y0.5280.99
126_N152_L0.5280.99
174_T178_R0.5260.99
45_S111_V0.5250.99
27_L164_L0.5240.99
258_R264_Q0.5230.99
218_Q226_S0.5220.99
96_V112_V0.5200.99
18_Y47_Y0.5170.99
174_T177_S0.5160.99
208_D220_L0.5160.99
305_G311_L0.5140.99
17_S24_H0.5140.99
249_A262_A0.5110.99
167_P172_A0.5110.99
27_L44_L0.5080.99
167_P171_Y0.5080.99
69_Q75_D0.5060.99
247_W255_A0.5050.99
235_A247_W0.5030.98
47_Y50_C0.5030.98
120_L125_A0.5020.98
278_A281_L0.5020.98
247_W254_D0.5010.98
77_Y96_V0.5000.98
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  
1a5tA 2 0.9701 100 0.333 Contact Map
1jr3A 3 0.976 100 0.452 Contact Map
1iqpA 5 0.8802 100 0.458 Contact Map
1sxjE 1 0.8862 100 0.46 Contact Map
2chqA 3 0.8772 100 0.469 Contact Map
1sxjD 1 0.8743 100 0.478 Contact Map
1sxjC 1 0.8802 100 0.479 Contact Map
2gnoA 1 0.8323 100 0.502 Contact Map
3zh9B 1 0.8563 100 0.524 Contact Map
1jr3D 1 0.8743 100 0.532 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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