GREMLIN Database
DPO42 - DNA polymerase IV 2
UniProt: P54560 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 412 (357)
Sequences: 8804 (6297)
Seq/√Len: 333.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
96_E133_R3.9421.00
133_R137_E2.9991.00
186_G196_K2.9341.00
270_K330_R2.9081.00
96_E137_E2.8051.00
33_I73_A2.7641.00
264_H268_E2.6761.00
291_G349_L2.6431.00
23_E82_R2.6051.00
200_N205_S2.3511.00
253_G348_N2.3491.00
135_M166_N2.3191.00
86_V89_Q2.3141.00
12_M142_A2.3041.00
63_L75_V2.2901.00
129_S133_R2.2561.00
270_K334_L2.2191.00
205_S209_G2.1941.00
79_R82_R2.1911.00
186_G200_N2.1671.00
29_N51_L2.1621.00
97_Y133_R2.1441.00
202_M221_K2.0991.00
208_G212_A2.0851.00
102_E150_K2.0731.00
132_G136_R2.0631.00
134_I142_A2.0621.00
231_M236_I2.0391.00
21_K49_C2.0321.00
230_W234_N2.0051.00
30_R74_V2.0021.00
98_T111_M1.9941.00
204_I210_L1.9771.00
181_W208_G1.9771.00
265_F334_L1.9671.00
219_K227_H1.9611.00
181_W211_A1.9491.00
8_F113_I1.9171.00
204_I213_F1.8861.00
12_M90_I1.8811.00
280_V349_L1.8671.00
23_E79_R1.8541.00
65_E69_K1.8431.00
12_M140_V1.8231.00
293_T351_Q1.8201.00
215_L227_H1.8031.00
284_S349_L1.7621.00
131_Q166_N1.7471.00
91_T109_Q1.7391.00
228_V232_T1.7101.00
172_T175_N1.6991.00
321_S324_D1.6591.00
361_N364_Q1.6511.00
274_L326_Y1.6411.00
295_S350_S1.6301.00
95_E101_V1.6261.00
33_I75_V1.6211.00
82_R85_D1.6181.00
320_N355_D1.6151.00
277_S325_V1.6061.00
313_V331_R1.5881.00
51_L54_Q1.5851.00
33_I45_V1.5731.00
17_A32_V1.5701.00
297_S346_G1.5661.00
104_Y110_F1.5661.00
61_S69_K1.5441.00
124_M128_K1.5381.00
177_K181_W1.5241.00
313_V335_T1.5241.00
22_A86_V1.5201.00
122_T125_E1.5191.00
24_N27_L1.5131.00
131_Q168_I1.5131.00
85_D89_Q1.5061.00
254_H280_V1.4971.00
97_Y129_S1.4891.00
152_L171_L1.4811.00
197_H201_R1.4811.00
215_L231_M1.4631.00
213_F217_L1.4611.00
206_T209_G1.4381.00
202_M222_W1.4351.00
281_C322_T1.4341.00
226_G230_W1.4321.00
293_T350_S1.4241.00
127_A146_I1.4211.00
126_I130_I1.4201.00
175_N178_T1.4071.00
262_Y269_I1.4061.00
10_V142_A1.4051.00
148_P176_M1.4051.00
265_F270_K1.3991.00
8_F144_V1.3931.00
329_V347_V1.3931.00
55_K72_E1.3901.00
146_I168_I1.3781.00
21_K28_K1.3751.00
196_K200_N1.3741.00
33_I57_V1.3711.00
264_H267_K1.3701.00
127_A144_V1.3671.00
128_K132_G1.3631.00
227_H231_M1.3601.00
94_L111_M1.3591.00
124_M170_T1.3581.00
62_R65_E1.3551.00
277_S347_V1.3521.00
215_L230_W1.3511.00
20_E83_Y1.3511.00
19_V86_V1.3491.00
147_G152_L1.3351.00
19_V82_R1.3311.00
281_C325_V1.3171.00
284_S291_G1.3161.00
263_E341_P1.3131.00
299_R305_W1.3051.00
255_G346_G1.2991.00
213_F218_L1.2981.00
93_I137_E1.2951.00
260_R268_E1.2861.00
65_E68_E1.2861.00
32_V76_L1.2801.00
14_S18_S1.2771.00
278_E322_T1.2731.00
177_K211_A1.2681.00
110_F189_F1.2681.00
290_M353_S1.2671.00
292_Q351_Q1.2661.00
50_P54_Q1.2641.00
315_L328_A1.2611.00
27_L32_V1.2451.00
218_L230_W1.2441.00
113_I126_I1.2411.00
215_L219_K1.2401.00
258_L272_V1.2371.00
254_H283_R1.2371.00
8_F127_A1.2271.00
17_A21_K1.2241.00
93_I133_R1.2221.00
21_K51_L1.2211.00
55_K70_C1.2141.00
10_V94_L1.2051.00
252_I287_A1.2051.00
194_R197_H1.2041.00
313_V328_A1.2031.00
92_A95_E1.2001.00
81_Q85_D1.1891.00
159_N169_F1.1851.00
328_A331_R1.1841.00
326_Y330_R1.1791.00
254_H279_E1.1731.00
258_L262_Y1.1711.00
94_L109_Q1.1711.00
82_R86_V1.1671.00
295_S312_Q1.1521.00
217_L221_K1.1501.00
93_I138_I1.1501.00
24_N76_L1.1471.00
45_V57_V1.1431.00
128_K131_Q1.1371.00
214_P217_L1.1351.00
209_G212_A1.1281.00
299_R344_R1.1271.00
324_D328_A1.1251.00
277_S281_C1.1231.00
100_L243_T1.1221.00
198_H221_K1.1191.00
35_S63_L1.1111.00
9_L157_C1.1091.00
156_A171_L1.1091.00
223_G226_G1.1081.00
315_L319_T1.1071.00
211_A234_N1.0971.00
20_E79_R1.0941.00
262_Y268_E1.0911.00
22_A82_R1.0811.00
330_R334_L1.0781.00
91_T103_P1.0741.00
45_V48_A1.0691.00
41_R67_Q1.0651.00
155_I183_L1.0651.00
10_V111_M1.0641.00
57_V73_A1.0611.00
272_V275_E1.0591.00
372_L375_V1.0561.00
97_Y130_I1.0541.00
293_T312_Q1.0511.00
269_I333_F1.0501.00
116_S120_F1.0481.00
255_G297_S1.0451.00
261_D301_A1.0341.00
292_Q353_S1.0271.00
22_A139_G1.0251.00
45_V66_A1.0241.00
327_E331_R1.0241.00
197_H200_N1.0221.00
277_S326_Y1.0211.00
293_T314_K1.0211.00
296_V332_L1.0151.00
281_C285_R1.0121.00
48_A59_N1.0011.00
277_S329_V0.9981.00
314_K351_Q0.9981.00
188_M207_I0.9971.00
17_A47_A0.9891.00
163_K169_F0.9821.00
290_M320_N0.9821.00
289_V354_S0.9791.00
46_L78_P0.9791.00
125_E129_S0.9781.00
147_G153_A0.9751.00
90_I138_I0.9721.00
116_S126_I0.9721.00
14_S50_P0.9701.00
23_E86_V0.9661.00
15_F19_V0.9621.00
80_M84_I0.9611.00
64_W68_E0.9611.00
292_Q318_P0.9551.00
104_Y189_F0.9431.00
91_T95_E0.9431.00
158_D187_S0.9421.00
273_L345_L0.9411.00
273_L296_V0.9361.00
322_T373_G0.9321.00
298_C345_L0.9301.00
285_R320_N0.9291.00
198_H201_R0.9281.00
261_D343_R0.9271.00
35_S43_G0.9251.00
295_S348_N0.9231.00
290_M355_D0.9131.00
116_S121_G0.9131.00
61_S65_E0.9071.00
280_V347_V0.9071.00
300_G340_K0.9041.00
21_K32_V0.9001.00
222_W226_G0.8991.00
331_R335_T0.8971.00
135_M139_G0.8931.00
182_P208_G0.8931.00
322_T326_Y0.8921.00
94_L130_I0.8921.00
127_A168_I0.8911.00
256_M272_V0.8861.00
217_L220_K0.8801.00
225_N228_V0.8801.00
191_V226_G0.8791.00
128_K168_I0.8781.00
323_Q327_E0.8761.00
318_P353_S0.8741.00
20_E24_N0.8701.00
273_L329_V0.8691.00
292_Q314_K0.8661.00
89_Q92_A0.8551.00
151_A232_T0.8541.00
204_I209_G0.8511.00
210_L218_L0.8511.00
371_S374_Y0.8491.00
261_D341_P0.8481.00
61_S66_A0.8451.00
47_A53_K0.8441.00
319_T324_D0.8431.00
58_V61_S0.8421.00
273_L333_F0.8421.00
16_Y80_M0.8411.00
255_G344_R0.8381.00
323_Q369_K0.8341.00
300_G306_P0.8331.00
211_A233_A0.8321.00
224_I228_V0.8311.00
14_S21_K0.8281.00
150_K241_V0.8271.00
231_M238_Y0.8261.00
306_P311_R0.8221.00
146_I170_T0.8191.00
313_V332_L0.8181.00
370_M374_Y0.8171.00
101_V109_Q0.8161.00
33_I70_C0.8151.00
21_K29_N0.8121.00
84_I88_L0.8091.00
34_V76_L0.8081.00
274_L330_R0.8081.00
311_R336_F0.8041.00
289_V352_L0.8031.00
48_A57_V0.8021.00
195_M198_H0.8001.00
237_D240_P0.7841.00
216_D220_K0.7831.00
93_I97_Y0.7831.00
295_S310_N0.7801.00
144_V168_I0.7791.00
277_S322_T0.7781.00
271_V275_E0.7781.00
89_Q138_I0.7781.00
198_H222_W0.7711.00
177_K212_A0.7701.00
70_C73_A0.7701.00
17_A49_C0.7701.00
100_L112_D0.7681.00
131_Q144_V0.7661.00
135_M141_Y0.7651.00
208_G211_A0.7651.00
355_D370_M0.7631.00
273_L326_Y0.7621.00
98_T101_V0.7591.00
218_L222_W0.7581.00
149_N152_L0.7551.00
164_N167_G0.7551.00
184_P200_N0.7551.00
285_R322_T0.7531.00
294_V328_A0.7521.00
27_L74_V0.7521.00
87_S91_T0.7470.99
113_I127_A0.7470.99
129_S132_G0.7460.99
52_A73_A0.7440.99
195_M222_W0.7440.99
66_A70_C0.7430.99
283_R287_A0.7390.99
279_E282_R0.7390.99
185_V200_N0.7390.99
102_E241_V0.7380.99
184_P187_S0.7360.99
298_C336_F0.7340.99
103_P106_I0.7330.99
91_T101_V0.7300.99
110_F150_K0.7280.99
93_I96_E0.7260.99
317_E324_D0.7210.99
116_S119_L0.7210.99
325_V329_V0.7150.99
271_V274_L0.7130.99
48_A53_K0.7110.99
16_Y78_P0.7100.99
278_E282_R0.7090.99
7_I112_D0.7080.99
125_E128_K0.7020.99
45_V75_V0.7010.99
63_L70_C0.7010.99
270_K274_L0.7000.99
46_L59_N0.7000.99
12_M15_F0.6990.99
50_P53_K0.6970.99
202_M213_F0.6950.99
7_I241_V0.6950.99
67_Q71_P0.6940.99
93_I134_I0.6930.99
118_K121_G0.6870.99
123_P127_A0.6870.99
191_V229_L0.6870.99
132_G135_M0.6850.99
67_Q75_V0.6830.99
202_M217_L0.6830.99
214_P234_N0.6820.99
210_L230_W0.6820.99
36_G43_G0.6810.99
30_R72_E0.6810.99
16_Y106_I0.6810.99
124_M168_I0.6810.99
86_V140_V0.6810.99
97_Y126_I0.6790.99
276_L345_L0.6790.99
185_V204_I0.6780.99
86_V138_I0.6730.99
269_I342_V0.6730.99
294_V325_V0.6710.99
269_I345_L0.6710.99
274_L278_E0.6680.99
265_F333_F0.6680.99
324_D327_E0.6670.99
31_P70_C0.6660.99
13_Q143_R0.6640.99
262_Y272_V0.6640.99
92_A96_E0.6640.99
371_S375_V0.6570.99
175_N179_E0.6550.99
29_N49_C0.6540.99
30_R51_L0.6530.99
256_M279_E0.6510.99
249_Q287_A0.6510.99
298_C342_V0.6480.99
100_L240_P0.6450.98
290_M352_L0.6440.98
257_T344_R0.6420.98
178_T181_W0.6420.98
222_W229_L0.6350.98
268_E271_V0.6350.98
45_V73_A0.6340.98
64_W67_Q0.6340.98
159_N163_K0.6340.98
36_G77_R0.6310.98
185_V196_K0.6300.98
171_L179_E0.6280.98
126_I129_S0.6270.98
100_L115_G0.6250.98
253_G346_G0.6240.98
300_G342_V0.6230.98
81_Q84_I0.6230.98
321_S369_K0.6180.98
44_V59_N0.6160.98
182_P206_T0.6150.98
19_V22_A0.6150.98
141_Y163_K0.6140.98
288_G355_D0.6140.98
35_S75_V0.6110.98
300_G304_D0.6100.98
33_I52_A0.6090.98
325_V349_L0.6080.98
67_Q73_A0.6070.98
311_R335_T0.6070.98
148_P152_L0.6060.98
28_K135_M0.6060.98
21_K30_R0.6050.98
185_V199_L0.6050.98
152_L176_M0.6050.98
66_A73_A0.6040.98
273_L330_R0.6030.98
252_I289_V0.6010.98
19_V23_E0.5990.98
78_P83_Y0.5970.97
252_I283_R0.5940.97
198_H223_G0.5930.97
328_A332_L0.5930.97
37_D41_R0.5900.97
113_I116_S0.5900.97
210_L222_W0.5880.97
311_R332_L0.5870.97
349_L352_L0.5870.97
274_L322_T0.5870.97
361_N366_Y0.5870.97
94_L101_V0.5860.97
84_I106_I0.5850.97
14_S53_K0.5840.97
8_F146_I0.5800.97
89_Q137_E0.5790.97
18_S47_A0.5780.97
282_R286_N0.5770.97
47_A59_N0.5770.97
333_F337_W0.5760.97
321_S373_G0.5760.97
134_I138_I0.5750.97
232_T237_D0.5730.97
163_K167_G0.5720.97
155_I189_F0.5700.97
272_V345_L0.5700.97
229_L232_T0.5680.97
108_E154_K0.5680.97
45_V70_C0.5680.97
296_V333_F0.5680.97
280_V294_V0.5670.97
25_P28_K0.5670.97
219_K226_G0.5670.97
20_E23_E0.5650.97
183_L187_S0.5650.97
291_G294_V0.5630.96
133_R136_R0.5630.96
181_W212_A0.5620.96
301_A340_K0.5620.96
319_T325_V0.5610.96
189_F232_T0.5610.96
281_C329_V0.5600.96
306_P336_F0.5570.96
35_S78_P0.5570.96
94_L98_T0.5550.96
215_L226_G0.5550.96
269_I337_W0.5520.96
177_K234_N0.5490.96
88_L92_A0.5470.96
193_S197_H0.5470.96
301_A343_R0.5470.96
178_T182_P0.5460.96
63_L67_Q0.5440.96
265_F337_W0.5440.96
207_I233_A0.5430.96
58_V65_E0.5430.96
210_L233_A0.5420.96
151_A155_I0.5420.96
176_M180_M0.5410.96
99_D115_G0.5390.95
105_S108_E0.5380.95
227_H230_W0.5380.95
159_N179_E0.5370.95
215_L234_N0.5360.95
80_M106_I0.5350.95
27_L76_L0.5350.95
150_K240_P0.5350.95
8_F126_I0.5320.95
270_K326_Y0.5320.95
131_Q142_A0.5320.95
37_D77_R0.5310.95
33_I63_L0.5310.95
353_S356_D0.5300.95
163_K168_I0.5290.95
267_K271_V0.5280.95
69_K72_E0.5270.95
91_T94_L0.5270.95
298_C333_F0.5260.95
115_G119_L0.5260.95
254_H276_L0.5260.95
313_V316_A0.5240.95
225_N229_L0.5220.95
13_Q50_P0.5220.95
279_E283_R0.5220.95
179_E183_L0.5210.95
333_F336_F0.5200.95
323_Q326_Y0.5200.95
199_L222_W0.5180.94
22_A89_Q0.5180.94
159_N187_S0.5170.94
315_L318_P0.5170.94
268_E272_V0.5170.94
252_I284_S0.5150.94
34_V47_A0.5150.94
45_V63_L0.5140.94
66_A69_K0.5140.94
224_I227_H0.5120.94
127_A130_I0.5110.94
148_P172_T0.5100.94
167_G170_T0.5100.94
297_S310_N0.5090.94
171_L176_M0.5090.94
32_V49_C0.5080.94
297_S348_N0.5070.94
291_G352_L0.5060.94
21_K27_L0.5050.94
90_I140_V0.5040.94
231_M234_N0.5030.93
98_T126_I0.5020.93
46_L80_M0.5020.93
121_G126_I0.5010.93
281_C349_L0.5010.93
10_V144_V0.5000.93
301_A341_P0.5000.93
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 0.8083 100 0.136 Contact Map
4dezA 2 0.5607 100 0.145 Contact Map
3gqcA 3 0.8422 100 0.154 Contact Map
4q45F 1 0.8252 100 0.155 Contact Map
4tqrA 1 0.818 100 0.164 Contact Map
3pzpA 1 0.8252 100 0.175 Contact Map
3osnA 1 0.8252 100 0.183 Contact Map
1t94A 1 0.8107 100 0.184 Contact Map
4ecqA 1 0.8398 100 0.185 Contact Map
2aq4A 1 0.8325 100 0.187 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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