GREMLIN Database
HOLB - DNA polymerase III subunit delta'
UniProt: P37540 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 329 (296)
Sequences: 16117 (10249)
Seq/√Len: 595.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
175_E189_R3.6581.00
13_P173_A3.4471.00
170_Q173_A3.3901.00
179_I185_P3.2081.00
179_I188_A2.6911.00
174_I192_A2.6641.00
175_E179_I2.6031.00
171_P193_N2.5631.00
45_A166_F2.5431.00
171_P192_A2.5341.00
175_E188_A2.4941.00
92_K96_Q2.3061.00
280_F284_K2.1561.00
249_Q253_L2.1511.00
231_A234_F2.1251.00
34_F166_F2.0591.00
90_I94_Q2.0361.00
72_I80_L2.0311.00
51_K73_E2.0171.00
72_I79_D2.0001.00
237_D241_P1.9941.00
8_M45_A1.9821.00
278_D281_Q1.9811.00
177_R198_V1.9391.00
246_K249_Q1.9181.00
184_S187_M1.9161.00
8_M48_L1.8721.00
215_A219_K1.8491.00
20_Y24_E1.8411.00
233_F236_Q1.8171.00
175_E192_A1.8021.00
29_S32_Y1.8011.00
178_L201_A1.7971.00
304_E308_R1.7521.00
169_L198_V1.7221.00
176_D179_I1.7101.00
71_R108_E1.7011.00
13_P176_D1.6831.00
6_K20_Y1.6831.00
33_L119_A1.6671.00
279_L282_S1.6651.00
53_F142_M1.6461.00
83_V129_S1.6411.00
173_A176_D1.6391.00
72_I77_H1.6201.00
70_K79_D1.6081.00
249_Q252_G1.5911.00
233_F237_D1.5391.00
297_N301_A1.5341.00
236_Q240_M1.5331.00
253_L257_L1.5311.00
171_P189_R1.5281.00
281_Q284_K1.5021.00
100_E104_K1.4931.00
35_E163_T1.4711.00
174_I201_A1.4651.00
195_T201_A1.4601.00
216_K219_K1.4591.00
285_Q289_Q1.4491.00
183_V188_A1.4441.00
4_S7_E1.4441.00
284_K288_L1.4421.00
265_S269_G1.4351.00
71_R77_H1.4301.00
74_S77_H1.4301.00
93_A97_A1.4261.00
225_H228_K1.4051.00
239_W242_F1.4011.00
280_F283_I1.3951.00
33_L161_C1.3861.00
97_A101_E1.3761.00
178_L188_A1.3731.00
278_D283_I1.3711.00
250_E254_D1.3671.00
221_Y224_L1.3641.00
72_I75_G1.3631.00
75_G79_D1.3561.00
119_A153_L1.3531.00
189_R193_N1.3531.00
74_S79_D1.3471.00
230_H234_F1.3461.00
248_H251_M1.3341.00
237_D240_M1.3331.00
76_N79_D1.3301.00
100_E103_S1.3261.00
8_M16_M1.3241.00
281_Q285_Q1.3221.00
278_D282_S1.3141.00
15_V164_L1.3141.00
221_Y227_R1.2961.00
70_K75_G1.2951.00
262_D266_I1.2871.00
253_L256_L1.2841.00
103_S107_L1.2771.00
90_I123_T1.2761.00
234_F238_Q1.2761.00
93_A96_Q1.2751.00
218_I221_Y1.2731.00
217_V221_Y1.2581.00
263_V267_Q1.2561.00
294_S297_N1.2561.00
238_Q242_F1.2541.00
231_A235_I1.2501.00
236_Q239_W1.2391.00
35_E165_P1.2381.00
264_L267_Q1.2381.00
232_F236_Q1.2321.00
185_P189_R1.2201.00
291_T294_S1.2161.00
264_L268_I1.2151.00
111_K142_M1.2101.00
171_P175_E1.2091.00
268_I271_E1.2011.00
266_I270_N1.2001.00
234_F237_D1.1881.00
70_K73_E1.1871.00
252_G256_L1.1821.00
80_L115_I1.1751.00
174_I198_V1.1731.00
279_L283_I1.1721.00
215_A225_H1.1701.00
70_K74_S1.1571.00
256_L260_Y1.1541.00
294_S298_Q1.1531.00
14_R167_Q1.1531.00
221_Y225_H1.1521.00
86_D89_S1.1461.00
72_I76_N1.1361.00
98_L101_E1.1301.00
182_D214_R1.1231.00
251_M255_M1.1211.00
90_I125_N1.1201.00
235_I239_W1.1141.00
229_G233_F1.1141.00
246_K253_L1.1131.00
51_K55_C1.1071.00
77_H80_L1.1051.00
16_M20_Y1.1031.00
85_P89_S1.0991.00
282_S285_Q1.0851.00
286_H289_Q1.0841.00
222_E226_Q1.0831.00
92_K125_N1.0801.00
214_R220_L1.0771.00
190_L193_N1.0731.00
19_L49_L1.0701.00
265_S268_I1.0621.00
71_R74_S1.0621.00
267_Q271_E1.0621.00
101_E105_T1.0621.00
272_D276_Y1.0611.00
287_A291_T1.0581.00
299_I303_L1.0581.00
217_V220_L1.0571.00
75_G78_P1.0531.00
92_K129_S1.0521.00
215_A218_I1.0521.00
273_K276_Y1.0471.00
288_L291_T1.0461.00
71_R79_D1.0371.00
298_Q301_A1.0341.00
21_N24_E1.0341.00
97_A100_E1.0301.00
219_K222_E1.0231.00
222_E225_H1.0211.00
192_A201_A1.0171.00
220_L228_K1.0151.00
219_K223_V1.0121.00
307_K311_S1.0051.00
221_Y228_K1.0031.00
246_K250_E0.9981.00
98_L106_G0.9981.00
287_A292_Q0.9981.00
122_M126_A0.9971.00
158_I163_T0.9961.00
98_L103_S0.9931.00
258_L262_D0.9921.00
301_A305_A0.9891.00
267_Q270_N0.9891.00
288_L292_Q0.9891.00
172_K175_E0.9871.00
255_M259_I0.9821.00
172_K176_D0.9821.00
286_H305_A0.9791.00
188_A192_A0.9711.00
252_G255_M0.9701.00
304_E307_K0.9681.00
215_A221_Y0.9671.00
218_I222_E0.9661.00
238_Q241_P0.9641.00
106_G138_N0.9551.00
214_R221_Y0.9531.00
224_L228_K0.9511.00
175_E185_P0.9501.00
251_M254_D0.9431.00
77_H109_S0.9421.00
257_L261_R0.9411.00
123_T126_A0.9341.00
43_L117_S0.9341.00
70_K77_H0.9301.00
103_S106_G0.9301.00
266_I271_E0.9271.00
242_F246_K0.9251.00
12_Q15_V0.9231.00
70_K76_N0.9191.00
285_Q288_L0.9151.00
5_W51_K0.9141.00
261_R265_S0.9121.00
73_E76_N0.9121.00
276_Y279_L0.9111.00
216_K221_Y0.9101.00
292_Q296_T0.9071.00
191_L201_A0.9011.00
300_L304_E0.8941.00
36_G42_K0.8941.00
91_K94_Q0.8931.00
215_A222_E0.8911.00
71_R76_N0.8851.00
99_Q102_F0.8791.00
83_V86_D0.8771.00
235_I240_M0.8721.00
277_Q281_Q0.8671.00
264_L306_K0.8601.00
91_K123_T0.8551.00
305_A308_R0.8541.00
215_A220_L0.8501.00
98_L105_T0.8451.00
172_K189_R0.8431.00
290_S295_V0.8411.00
284_K287_A0.8371.00
263_V270_N0.8361.00
218_I225_H0.8361.00
228_K231_A0.8351.00
18_L164_L0.8351.00
231_A240_M0.8331.00
303_L307_K0.8321.00
301_A304_E0.8311.00
290_S298_Q0.8281.00
49_L144_V0.8261.00
229_G232_F0.8231.00
263_V268_I0.8211.00
276_Y312_N0.8211.00
223_V226_Q0.8191.00
230_H233_F0.8161.00
231_A238_Q0.8151.00
264_L271_E0.8141.00
214_R219_K0.8131.00
257_L260_Y0.8091.00
242_F245_E0.8091.00
102_F114_Y0.8091.00
248_H252_G0.8081.00
245_E248_H0.8041.00
13_P17_K0.8011.00
236_Q242_F0.8011.00
235_I238_Q0.7981.00
297_N300_L0.7971.00
286_H290_S0.7941.00
306_K310_H0.7931.00
254_D258_L0.7851.00
191_L204_L0.7811.00
218_I226_Q0.7741.00
94_Q97_A0.7721.00
115_I146_I0.7721.00
99_Q105_T0.7721.00
303_L306_K0.7721.00
191_L205_S0.7691.00
21_N25_K0.7681.00
71_R75_G0.7661.00
13_P16_M0.7641.00
178_L205_S0.7621.00
223_V227_R0.7621.00
99_Q103_S0.7611.00
56_L110_H0.7611.00
250_E253_L0.7601.00
290_S293_Q0.7561.00
262_D268_I0.7421.00
186_H189_R0.7391.00
203_E206_R0.7381.00
253_L260_Y0.7331.00
268_I272_D0.7301.00
92_K123_T0.7301.00
224_L227_R0.7291.00
184_S214_R0.7261.00
249_Q255_M0.7241.00
102_F133_F0.7221.00
229_G236_Q0.7201.00
275_I279_L0.7201.00
22_S29_S0.7191.00
220_L224_L0.7191.00
18_L21_N0.7111.00
84_Q117_S0.7101.00
249_Q256_L0.7091.00
278_D284_K0.7081.00
134_L153_L0.7071.00
246_K252_G0.7071.00
267_Q292_Q0.7061.00
214_R217_V0.7051.00
266_I269_G0.7041.00
19_L164_L0.7031.00
264_L270_N0.7011.00
9_N177_R0.6991.00
35_E150_P0.6991.00
220_L225_H0.6951.00
187_M190_L0.6941.00
246_K260_Y0.6921.00
16_M45_A0.6911.00
37_K40_T0.6891.00
308_R311_S0.6871.00
300_L303_L0.6851.00
40_T166_F0.6831.00
256_L259_I0.6831.00
266_I283_I0.6791.00
28_L142_M0.6791.00
75_G80_L0.6791.00
186_H217_V0.6761.00
187_M208_D0.6741.00
37_K197_N0.6721.00
257_L299_I0.6671.00
183_V186_H0.6581.00
220_L223_V0.6571.00
296_T300_L0.6551.00
46_A144_V0.6471.00
245_E249_Q0.6441.00
233_F240_M0.6431.00
252_G260_Y0.6411.00
101_E104_K0.6391.00
289_Q294_S0.6371.00
26_D53_F0.6371.00
32_Y164_L0.6361.00
135_E159_S0.6321.00
290_S294_S0.6301.00
50_A113_L0.6281.00
254_D306_K0.6251.00
29_S162_Q0.6211.00
76_N80_L0.6211.00
18_L207_N0.6191.00
245_E252_G0.6191.00
233_F239_W0.6191.00
195_T204_L0.6191.00
96_Q129_S0.6181.00
276_Y280_F0.6171.00
221_Y226_Q0.6151.00
21_N211_A0.6131.00
9_N173_A0.6111.00
214_R218_I0.6091.00
277_Q280_F0.6071.00
279_L284_K0.6071.00
263_V266_I0.6051.00
17_K21_N0.6051.00
174_I178_L0.6031.00
247_T250_E0.6031.00
287_A290_S0.5981.00
106_G110_H0.5961.00
119_A127_A0.5961.00
233_F242_F0.5951.00
150_P153_L0.5951.00
270_N273_K0.5921.00
295_V299_I0.5921.00
90_I116_I0.5921.00
222_E227_R0.5901.00
260_Y263_V0.5901.00
292_Q295_V0.5901.00
198_V201_A0.5881.00
242_F247_T0.5871.00
219_K225_H0.5861.00
267_Q272_D0.5851.00
231_A236_Q0.5831.00
257_L302_V0.5811.00
241_P245_E0.5791.00
261_R264_L0.5791.00
260_Y295_V0.5791.00
46_A115_I0.5791.00
230_H236_Q0.5781.00
259_I262_D0.5771.00
104_K107_L0.5771.00
242_F252_G0.5751.00
116_I130_L0.5751.00
169_L173_A0.5751.00
217_V224_L0.5681.00
232_F239_W0.5681.00
33_L153_L0.5671.00
214_R224_L0.5671.00
272_D275_I0.5661.00
262_D265_S0.5641.00
183_V209_E0.5641.00
28_L49_L0.5631.00
17_K20_Y0.5631.00
119_A142_M0.5631.00
259_I286_H0.5631.00
95_I99_Q0.5621.00
216_K225_H0.5601.00
47_L136_E0.5591.00
132_K136_E0.5591.00
56_L105_T0.5580.99
215_A223_V0.5570.99
15_V166_F0.5560.99
119_A143_A0.5560.99
71_R78_P0.5560.99
284_K292_Q0.5560.99
98_L114_Y0.5560.99
102_F141_T0.5560.99
296_T299_I0.5560.99
72_I78_P0.5520.99
245_E253_L0.5510.99
265_S270_N0.5510.99
169_L177_R0.5510.99
214_R222_E0.5500.99
280_F286_H0.5500.99
190_L194_M0.5470.99
219_K227_R0.5470.99
106_G109_S0.5460.99
229_G235_I0.5440.99
249_Q257_L0.5440.99
113_L144_V0.5440.99
83_V87_G0.5400.99
128_N154_L0.5380.99
220_L226_Q0.5370.99
14_R17_K0.5370.99
99_Q104_K0.5360.99
134_L161_C0.5320.99
209_E212_E0.5310.99
247_T253_L0.5310.99
169_L174_I0.5300.99
305_A309_L0.5290.99
32_Y142_M0.5270.99
201_A205_S0.5260.99
48_L51_K0.5250.99
102_F106_G0.5240.99
188_A201_A0.5200.99
34_F45_A0.5160.99
113_L142_M0.5150.99
263_V271_E0.5150.99
216_K220_L0.5140.99
52_S55_C0.5140.99
293_Q297_N0.5140.99
122_M127_A0.5130.99
232_F235_I0.5080.99
247_T252_G0.5080.99
248_H253_L0.5070.99
219_K226_Q0.5060.99
217_V222_E0.5050.99
282_S286_H0.5040.99
204_L207_N0.5000.99
127_A154_L0.5000.99
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 0.9392 100 0.359 Contact Map
1jr3A 3 0.9848 100 0.446 Contact Map
2gnoA 1 0.8389 100 0.484 Contact Map
1sxjE 1 0.8906 100 0.485 Contact Map
1iqpA 5 0.8967 100 0.488 Contact Map
2chqA 3 0.8997 100 0.496 Contact Map
3zh9B 1 0.8815 100 0.511 Contact Map
1sxjC 1 0.8967 100 0.511 Contact Map
1jr3D 1 0.8875 100 0.511 Contact Map
1sxjD 1 0.8997 100 0.512 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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