GREMLIN Database
DPO4 - DNA polymerase IV
UniProt: Q97W02 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 352 (335)
Sequences: 8883 (6330)
Seq/√Len: 345.8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
94_E131_K3.8961.00
181_A191_A2.9481.00
257_N260_E2.8481.00
131_K135_K2.8171.00
94_E135_K2.7611.00
29_V71_A2.7141.00
19_L80_V2.6611.00
262_K316_V2.6321.00
281_P337_F2.5921.00
246_G336_R2.3511.00
195_K200_N2.3421.00
84_V87_R2.3231.00
61_I73_Y2.3041.00
8_F140_V2.2951.00
127_E131_K2.2481.00
77_R80_V2.2061.00
181_A195_K2.1731.00
200_N204_D2.1491.00
130_N134_E2.1451.00
133_L161_N2.1451.00
25_G49_E2.1371.00
95_Y131_K2.1031.00
262_K320_Q2.1001.00
197_L216_M2.0671.00
203_V207_S2.0641.00
226_I230_R2.0581.00
132_I140_V2.0471.00
100_E148_K2.0401.00
227_S232_E2.0251.00
96_S109_L2.0121.00
17_E47_N2.0071.00
214_K223_K1.9981.00
176_R206_L1.9521.00
176_R203_V1.9161.00
4_L111_I1.8991.00
26_K72_V1.8911.00
8_F88_I1.8701.00
129_K161_N1.8561.00
199_I208_I1.8501.00
272_S337_F1.8451.00
199_I205_T1.8371.00
8_F138_I1.8361.00
167_D170_E1.8311.00
19_L77_R1.8251.00
258_L320_Q1.8191.00
63_E67_I1.7921.00
210_F223_K1.7741.00
224_Y228_L1.7511.00
89_M107_A1.7351.00
276_L337_F1.7221.00
283_A339_K1.7211.00
93_R99_I1.6841.00
172_K176_R1.6331.00
49_E52_K1.6271.00
122_Y126_L1.5821.00
29_V43_V1.5801.00
80_V83_Q1.5801.00
13_A28_V1.5721.00
285_H338_S1.5711.00
102_A108_Y1.5471.00
129_K163_I1.5231.00
287_V334_G1.5191.00
59_I67_I1.5141.00
247_R272_S1.4961.00
83_Q87_R1.4811.00
18_V84_V1.4801.00
124_L128_I1.4761.00
266_F312_Y1.4701.00
120_E123_N1.4701.00
300_R317_K1.4631.00
146_K171_V1.4601.00
197_L217_I1.4501.00
191_A195_K1.4491.00
223_K227_S1.4481.00
307_S343_A1.4391.00
192_E196_K1.4331.00
255_S261_I1.4331.00
125_G144_I1.4331.00
125_G142_V1.4261.00
29_V73_Y1.4221.00
20_N23_L1.4151.00
201_K204_D1.4131.00
210_F226_I1.4061.00
300_R321_K1.4021.00
276_L281_P1.3971.00
208_I212_K1.3951.00
283_A338_S1.3931.00
222_A226_I1.3901.00
4_L142_V1.3891.00
170_E173_R1.3881.00
16_E81_Y1.3811.00
269_I311_A1.3811.00
95_Y127_E1.3691.00
258_L262_K1.3681.00
150_F166_I1.3671.00
210_F227_S1.3601.00
92_L109_L1.3601.00
6_V140_V1.3571.00
15_V80_V1.3481.00
60_P63_E1.3411.00
269_I335_V1.3331.00
213_L226_I1.3271.00
256_R329_K1.3271.00
15_V84_V1.3251.00
63_E66_K1.3221.00
17_E24_K1.3211.00
91_L135_K1.3161.00
145_S150_F1.3131.00
126_L130_N1.3121.00
208_I213_L1.3121.00
53_F70_N1.3111.00
29_V55_V1.3051.00
289_V295_I1.3011.00
315_S335_V1.2821.00
210_F214_K1.2751.00
10_Y14_Q1.2741.00
282_K339_K1.2621.00
23_L28_V1.2581.00
90_N93_R1.2541.00
111_I124_L1.2481.00
247_R275_K1.2471.00
108_Y184_P1.2461.00
91_L131_K1.2441.00
172_K206_L1.2421.00
310_T314_E1.2391.00
4_L125_G1.2351.00
251_M264_Y1.2311.00
28_V74_L1.2251.00
245_I279_R1.2241.00
144_I163_I1.2231.00
193_K216_M1.2221.00
92_L107_A1.2191.00
53_F68_L1.2181.00
247_R271_E1.2181.00
122_Y165_V1.2151.00
48_Y52_K1.2131.00
285_H299_G1.2121.00
6_V92_L1.2121.00
316_V320_Q1.2121.00
13_A17_E1.2091.00
80_V84_V1.1981.00
126_L129_K1.1971.00
302_F314_E1.1941.00
17_E49_E1.1941.00
157_M164_K1.1861.00
280_I341_I1.1801.00
98_K239_T1.1791.00
91_L136_E1.1771.00
269_I273_Y1.1771.00
79_E83_Q1.1711.00
248_I334_G1.1611.00
189_I192_E1.1531.00
253_R260_E1.1471.00
212_K216_M1.1461.00
283_A299_G1.1421.00
209_E212_K1.1391.00
255_S260_E1.1271.00
154_A166_I1.1261.00
16_E77_R1.1261.00
273_Y277_D1.1171.00
43_V55_V1.1071.00
20_N74_L1.1061.00
251_M255_S1.1011.00
18_V80_V1.0991.00
273_Y311_A1.0981.00
302_F306_I1.0931.00
39_D65_K1.0801.00
248_I287_V1.0791.00
204_D207_S1.0771.00
5_F155_A1.0741.00
218_G222_A1.0731.00
289_V332_R1.0601.00
123_N127_E1.0551.00
269_I312_Y1.0521.00
264_Y267_R1.0441.00
206_L230_R1.0431.00
55_V71_A1.0381.00
89_M101_I1.0371.00
31_C61_I1.0311.00
314_E317_K1.0291.00
145_S151_A1.0231.00
43_V46_A1.0221.00
183_V202_L1.0151.00
283_A301_T1.0081.00
153_I178_L1.0071.00
300_R314_E1.0061.00
95_Y128_I1.0041.00
312_Y316_V1.0041.00
62_V66_K0.9951.00
43_V64_A0.9881.00
158_A164_K0.9881.00
46_A57_A0.9881.00
254_N291_E0.9851.00
89_M93_R0.9731.00
282_K301_T0.9701.00
192_E195_K0.9701.00
126_L163_I0.9671.00
301_T339_K0.9651.00
314_E318_L0.9631.00
88_I136_E0.9591.00
10_Y48_Y0.9591.00
313_S317_K0.9581.00
282_K341_I0.9571.00
44_A76_M0.9571.00
19_L84_V0.9561.00
13_A45_T0.9561.00
317_K321_K0.9521.00
114_K119_R0.9521.00
11_F15_V0.9521.00
156_D182_D0.9391.00
18_V137_K0.9371.00
6_V109_L0.9361.00
254_N331_R0.9331.00
217_I222_A0.9281.00
309_E313_S0.9281.00
114_K124_L0.9221.00
17_E28_V0.9221.00
282_K305_G0.9181.00
285_H336_R0.9171.00
59_I63_E0.9171.00
31_C41_G0.9111.00
92_L128_I0.9031.00
277_D307_S0.9001.00
318_L322_I0.8991.00
254_N329_K0.8981.00
133_L137_K0.8971.00
114_K118_Y0.8951.00
319_L322_I0.8931.00
148_K237_I0.8931.00
265_L286_V0.8871.00
87_R90_N0.8851.00
227_S234_N0.8841.00
249_V264_Y0.8821.00
193_K196_K0.8811.00
78_K82_Q0.8811.00
177_E203_V0.8781.00
212_K215_G0.8761.00
205_T213_L0.8751.00
102_A184_P0.8731.00
59_I64_A0.8701.00
280_I307_S0.8691.00
265_L333_I0.8691.00
305_G341_I0.8611.00
10_Y17_E0.8451.00
315_S318_L0.8391.00
290_T328_R0.8381.00
56_K59_I0.8351.00
29_V68_L0.8251.00
319_L323_L0.8251.00
125_G163_I0.8181.00
265_L319_L0.8171.00
91_L95_Y0.8161.00
288_A333_I0.8151.00
16_E20_N0.8141.00
275_K279_R0.8131.00
82_Q86_S0.8111.00
12_Y78_K0.8111.00
280_I343_A0.8091.00
149_V228_L0.8081.00
206_L229_A0.8071.00
290_T296_V0.8051.00
199_I204_D0.8051.00
26_K70_N0.8041.00
265_L312_Y0.7981.00
147_N150_F0.7961.00
186_I222_A0.7931.00
133_L139_T0.7891.00
64_A68_L0.7841.00
272_S335_V0.7841.00
213_L217_I0.7831.00
45_T51_R0.7821.00
170_E174_L0.7821.00
142_V163_I0.7781.00
286_V318_L0.7771.00
220_A224_Y0.7761.00
193_K217_I0.7751.00
48_Y51_R0.7731.00
23_L72_V0.7691.00
203_V206_L0.7681.00
98_K113_D0.7651.00
98_K110_D0.7631.00
163_I166_I0.7621.00
269_I315_S0.7611.00
233_Y236_P0.7601.00
306_I310_T0.7581.00
197_L208_I0.7561.00
87_R136_E0.7551.00
180_I195_K0.7541.00
100_E237_I0.7521.00
96_S99_I0.7521.00
261_I319_L0.7521.00
127_E130_N0.7491.00
17_E25_G0.7451.00
89_M99_I0.7411.00
85_S89_M0.7401.00
190_T193_K0.7381.00
270_E274_Y0.7381.00
68_L71_A0.7360.99
111_I125_G0.7340.99
311_A315_S0.7330.99
263_P267_R0.7330.99
108_Y148_K0.7300.99
179_D195_K0.7260.99
91_L132_I0.7250.99
262_K266_F0.7230.99
298_R322_I0.7220.99
290_T294_D0.7190.99
144_I165_V0.7160.99
190_T217_I0.7150.99
249_V271_E0.7120.99
99_I107_A0.7120.99
302_F305_G0.7100.99
65_K69_P0.7090.99
172_K207_S0.7090.99
3_V110_D0.7090.99
129_K142_V0.7060.99
248_I332_R0.7060.99
65_K73_Y0.7050.99
61_I68_L0.7050.99
258_L319_L0.7040.99
174_L178_L0.7030.99
179_D182_D0.6990.99
46_A55_V0.6970.99
90_N94_E0.6930.99
44_A57_A0.6920.99
46_A51_R0.6920.99
131_K134_E0.6910.99
111_I114_K0.6900.99
121_A125_G0.6900.99
84_V136_E0.6890.99
13_A47_N0.6890.99
312_Y320_Q0.6870.99
300_R318_L0.6860.99
209_E230_R0.6840.99
50_A71_A0.6840.99
30_V74_L0.6830.99
8_F11_F0.6810.99
3_V237_I0.6780.99
259_E263_P0.6770.99
91_L94_E0.6760.99
32_V75_P0.6760.99
263_P266_F0.6760.99
259_E262_K0.6750.99
260_E263_P0.6730.99
217_I225_L0.6720.99
288_A330_I0.6720.99
101_I104_I0.6680.99
116_R119_R0.6670.99
205_T226_I0.6650.99
285_H297_S0.6650.99
123_N126_L0.6630.99
98_K236_P0.6630.99
246_G334_G0.6620.99
12_Y76_M0.6620.99
266_F270_E0.6620.99
79_E82_Q0.6620.99
310_T313_S0.6610.99
211_D215_G0.6590.99
271_E274_Y0.6550.99
9_D141_T0.6550.99
26_K49_E0.6530.99
43_V73_Y0.6530.99
186_I225_L0.6510.99
287_V297_S0.6480.99
242_R279_R0.6420.99
87_R135_K0.6390.99
284_I314_E0.6390.99
173_R176_R0.6390.99
166_I174_L0.6380.99
92_L99_I0.6370.99
261_I330_I0.6330.98
124_L127_E0.6320.98
261_I333_I0.6300.98
197_L212_K0.6280.98
265_L315_S0.6270.98
16_E19_L0.6220.98
298_R321_K0.6210.98
153_I184_P0.6210.98
312_Y318_L0.6210.98
176_R207_S0.6190.98
31_C76_M0.6180.98
155_A158_A0.6170.98
298_R318_L0.6170.98
210_F230_R0.6160.98
178_L182_D0.6140.98
296_V322_I0.6130.98
62_V65_K0.6120.98
122_Y163_I0.6110.98
12_Y104_I0.6100.98
177_E201_K0.6090.98
180_I199_I0.6080.98
84_V138_I0.6070.98
139_T158_A0.6070.98
311_A318_L0.6050.98
114_K117_D0.6040.98
64_A71_A0.6040.98
316_V319_L0.6040.98
29_V50_A0.6040.98
130_N133_L0.6030.98
27_P68_L0.6030.98
268_A333_I0.6010.98
214_K219_E0.6010.98
150_F171_V0.6000.98
10_Y51_R0.5960.98
341_I345_G0.5960.98
146_K150_F0.5930.98
184_P228_L0.5910.98
42_A57_A0.5910.98
258_L323_L0.5900.98
255_S264_Y0.5900.98
222_A225_L0.5880.98
311_A320_Q0.5870.98
76_M81_Y0.5860.97
180_I191_A0.5860.97
45_T57_A0.5840.97
31_C73_Y0.5840.97
172_K230_R0.5840.97
56_K67_I0.5820.97
25_G47_N0.5820.97
166_I171_V0.5810.97
95_Y124_L0.5780.97
225_L228_L0.5740.97
250_T332_R0.5740.97
287_V295_I0.5730.97
173_R177_E0.5720.97
168_D172_K0.5720.97
280_I340_F0.5710.97
273_Y337_F0.5700.97
157_M174_L0.5700.97
113_D117_D0.5680.97
304_H310_T0.5650.97
146_K167_D0.5650.97
32_V41_G0.5650.97
43_V68_L0.5640.97
132_I136_E0.5630.97
162_G165_V0.5630.97
245_I275_K0.5620.97
314_E320_Q0.5610.97
4_L144_I0.5610.97
288_A322_I0.5610.97
228_L233_Y0.5580.97
274_Y278_K0.5580.97
286_V319_L0.5570.97
247_R268_A0.5570.97
281_P284_I0.5560.97
311_A337_F0.5530.96
158_A162_G0.5530.96
309_E312_Y0.5530.96
290_T330_I0.5510.96
214_K222_A0.5500.96
21_P24_K0.5500.96
205_T229_A0.5490.96
23_L74_L0.5480.96
291_E329_K0.5470.96
86_S90_N0.5470.96
82_Q104_I0.5450.96
180_I194_L0.5450.96
15_V19_L0.5440.96
205_T217_I0.5420.96
266_F316_V0.5410.96
177_E202_L0.5380.96
64_A67_I0.5370.96
56_K63_E0.5370.96
106_E152_K0.5340.96
133_L136_E0.5330.96
311_A314_E0.5320.96
306_I311_A0.5300.96
272_S284_I0.5290.95
65_K71_A0.5260.95
180_I205_T0.5260.95
129_K140_V0.5250.95
291_E328_R0.5230.95
92_L96_S0.5230.95
8_F15_V0.5220.95
50_A55_V0.5220.95
330_I333_I0.5220.95
9_D48_Y0.5210.95
139_T161_N0.5210.95
121_A144_I0.5200.95
18_V87_R0.5190.95
342_E345_G0.5180.95
186_I191_A0.5180.95
28_V47_N0.5160.95
260_E264_Y0.5140.95
315_S319_L0.5140.95
78_K104_I0.5130.95
29_V61_I0.5130.95
103_S106_E0.5120.95
188_N192_E0.5120.95
337_F340_F0.5090.94
266_F313_S0.5090.94
171_V174_L0.5090.94
300_R303_P0.5050.94
149_V153_I0.5050.94
61_I65_K0.5050.94
171_V175_I0.5040.94
291_E331_R0.5040.94
113_D119_R0.5010.94
284_I311_A0.5010.94
313_S316_V0.5000.94
119_R124_L0.5000.94
89_M92_L0.5000.94
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  
4f50A 1 0.9545 100 0.066 Contact Map
4tqrA 1 0.9716 100 0.083 Contact Map
4q45F 1 0.9517 100 0.104 Contact Map
4dezA 2 0.6562 100 0.108 Contact Map
3gqcA 3 0.9716 100 0.108 Contact Map
3pzpA 1 0.9517 100 0.13 Contact Map
1t94A 1 0.9375 100 0.134 Contact Map
3osnA 1 0.946 100 0.135 Contact Map
4ecqA 1 0.9631 100 0.139 Contact Map
3mfiA 1 0.9602 100 0.143 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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