GREMLIN Database
YHDP - UPF0053 protein YhdP
UniProt: O07585 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 444 (411)
Sequences: 7853 (5090)
Seq/√Len: 251.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
226_I327_L4.0951.00
398_D403_D3.8571.00
363_L427_V3.7781.00
406_I411_E3.2531.00
254_E259_N3.2101.00
404_S411_E3.1541.00
294_V303_L3.1521.00
404_S413_I3.1111.00
392_F425_I2.9711.00
234_K237_E2.9521.00
362_I415_N2.8651.00
233_I237_E2.8551.00
268_E289_N2.7941.00
228_S253_E2.7581.00
254_E285_S2.7491.00
357_G360_H2.7381.00
413_I428_K2.6741.00
411_E428_K2.6071.00
130_K133_A2.5971.00
216_A303_L2.5661.00
283_T286_Q2.5261.00
362_I424_Y2.4731.00
252_V288_V2.4711.00
143_I147_R2.4441.00
154_W158_N2.4251.00
316_I327_L2.3621.00
298_A306_K2.3481.00
113_F159_S2.3301.00
411_E430_L2.3191.00
231_H254_E2.2961.00
372_V376_L2.2811.00
226_I324_T2.2301.00
34_I48_V2.2301.00
391_W407_E2.1651.00
16_T70_S2.1231.00
228_S257_K2.1001.00
18_F141_P2.0931.00
316_I324_T2.0851.00
229_L238_M2.0801.00
47_A143_I2.0781.00
415_N426_E2.0551.00
162_L166_A2.0541.00
388_I425_I2.0311.00
356_I360_H2.0211.00
303_L328_V1.9861.00
263_V291_I1.9751.00
47_A140_K1.9701.00
231_H261_I1.9541.00
33_R132_E1.9451.00
416_E424_Y1.9341.00
231_H285_S1.9241.00
360_H426_E1.9171.00
372_V427_V1.9001.00
38_I49_K1.8981.00
57_E150_F1.8801.00
353_I367_V1.8761.00
367_V372_V1.8691.00
219_I328_V1.8641.00
219_I300_I1.8391.00
37_L136_M1.8031.00
188_L205_V1.7901.00
229_L252_V1.7701.00
137_L141_P1.7681.00
418_D423_A1.7631.00
240_D244_I1.7461.00
253_E260_I1.7331.00
360_H428_K1.7131.00
233_I238_M1.7051.00
416_E423_A1.6751.00
42_N136_M1.6751.00
331_E335_E1.6721.00
50_K143_I1.6691.00
355_K361_Y1.6661.00
214_R218_E1.6351.00
314_M327_L1.6261.00
158_N162_L1.5941.00
367_V388_I1.5841.00
372_V388_I1.5671.00
413_I426_E1.5641.00
373_N378_I1.5611.00
362_I426_E1.5551.00
208_I337_I1.5521.00
305_V308_Q1.5391.00
22_S138_F1.5381.00
227_V241_I1.5361.00
204_Y208_I1.5311.00
248_T265_N1.5271.00
232_D254_E1.5231.00
363_L388_I1.5161.00
356_I426_E1.4991.00
412_F425_I1.4941.00
16_T66_I1.4911.00
409_G430_L1.4891.00
47_A139_A1.4891.00
224_T323_G1.4831.00
392_F412_F1.4731.00
227_V247_Y1.4661.00
355_K358_E1.4631.00
230_P233_I1.4611.00
256_D259_N1.4561.00
296_E325_A1.4531.00
393_L422_V1.4511.00
298_A303_L1.4341.00
133_A137_L1.4261.00
407_E412_F1.4181.00
48_V139_A1.4121.00
258_D323_G1.4081.00
8_L76_L1.4061.00
300_I333_I1.3991.00
204_Y337_I1.3921.00
35_D49_K1.3841.00
334_I338_V1.3831.00
356_I359_G1.3821.00
61_A145_F1.3681.00
7_I11_V1.3611.00
105_I109_A1.3541.00
406_I430_L1.3541.00
263_V314_M1.3531.00
410_C429_K1.3441.00
147_R150_F1.3411.00
356_I362_I1.3391.00
254_E261_I1.3281.00
392_F414_I1.3281.00
21_A134_V1.3251.00
41_G45_A1.3151.00
35_D39_A1.3101.00
363_L372_V1.3101.00
6_L10_A1.3081.00
223_R258_D1.3041.00
37_L42_N1.3031.00
392_F405_I1.3031.00
249_R313_H1.2991.00
385_V394_T1.2911.00
71_I74_G1.2891.00
415_N424_Y1.2891.00
409_G429_K1.2891.00
15_L69_T1.2851.00
237_E240_D1.2751.00
373_N380_L1.2751.00
61_A153_I1.2721.00
395_Q407_E1.2651.00
150_F154_W1.2601.00
44_A136_M1.2591.00
343_D346_D1.2501.00
77_G111_I1.2401.00
46_I50_K1.2371.00
227_V245_E1.2241.00
138_F141_P1.2231.00
295_I298_A1.2181.00
49_K53_T1.2121.00
101_V105_I1.2081.00
410_C427_V1.2071.00
48_V135_S1.2071.00
19_F65_G1.2011.00
314_M329_T1.1991.00
392_F396_K1.1971.00
245_E250_Y1.1941.00
122_A163_L1.1861.00
42_N45_A1.1821.00
44_A140_K1.1811.00
141_P144_W1.1811.00
233_I241_I1.1791.00
158_N161_R1.1691.00
258_D324_T1.1661.00
306_K310_E1.1611.00
291_I316_I1.1561.00
353_I375_L1.1411.00
86_H90_V1.1401.00
140_K144_W1.1391.00
369_I373_N1.1361.00
227_V250_Y1.1351.00
18_F138_F1.1311.00
66_I70_S1.1311.00
19_F145_F1.1291.00
272_A287_F1.1191.00
216_A294_V1.1161.00
260_I316_I1.1091.00
38_I46_I1.1061.00
359_G429_K1.1061.00
341_I346_D1.1011.00
24_F27_I1.0991.00
223_R323_G1.0971.00
70_S115_H1.0971.00
126_V169_L1.0951.00
354_R362_I1.0871.00
216_A317_L1.0831.00
34_I49_K1.0761.00
376_L410_C1.0631.00
228_S324_T1.0621.00
264_I287_F1.0621.00
9_V73_L1.0621.00
63_Q66_I1.0591.00
11_V15_L1.0571.00
249_R331_E1.0441.00
405_I412_F1.0431.00
50_K54_H1.0381.00
282_S286_Q1.0321.00
191_S195_G1.0291.00
331_E341_I1.0251.00
43_K46_I1.0221.00
9_V111_I1.0191.00
34_I52_T1.0121.00
44_A48_V1.0101.00
225_E421_H1.0071.00
294_V315_A1.0011.00
16_T20_V0.9921.00
389_G393_L0.9861.00
119_G124_K0.9821.00
236_S240_D0.9821.00
23_E124_K0.9781.00
393_L399_V0.9761.00
179_H187_I0.9721.00
352_E364_D0.9701.00
365_G388_I0.9701.00
230_P255_G0.9681.00
406_I409_G0.9681.00
294_V317_L0.9671.00
373_N379_H0.9631.00
353_I363_L0.9601.00
219_I333_I0.9581.00
192_Y202_F0.9541.00
391_W412_F0.9541.00
103_S107_A0.9531.00
144_W147_R0.9531.00
162_L165_K0.9511.00
29_I131_A0.9431.00
51_V58_Y0.9421.00
261_I288_V0.9401.00
412_F427_V0.9381.00
231_H288_V0.9371.00
155_L158_N0.9361.00
353_I361_Y0.9331.00
292_I306_K0.9291.00
307_M315_A0.9231.00
239_M243_Q0.9191.00
364_D424_Y0.9151.00
232_D285_S0.9071.00
161_R171_T0.9071.00
255_G259_N0.9071.00
217_K296_E0.9051.00
9_V80_T0.9021.00
61_A146_Y0.8991.00
29_I34_I0.8951.00
21_A127_A0.8941.00
20_V24_F0.8911.00
226_I257_K0.8881.00
184_L191_S0.8871.00
396_K405_I0.8861.00
389_G421_H0.8851.00
71_I112_T0.8851.00
13_I114_L0.8821.00
395_Q405_I0.8811.00
151_P155_L0.8801.00
47_A50_K0.8741.00
298_A302_D0.8731.00
396_K400_E0.8721.00
22_S142_L0.8701.00
77_G81_I0.8691.00
242_I250_Y0.8670.99
251_P260_I0.8670.99
211_F304_L0.8670.99
342_R349_E0.8660.99
240_D243_Q0.8660.99
165_K170_E0.8570.99
75_V108_Y0.8570.99
285_S288_V0.8550.99
368_L371_Q0.8510.99
335_E340_E0.8500.99
161_R165_K0.8480.99
75_V78_E0.8460.99
137_L140_K0.8430.99
235_I238_M0.8410.99
230_P253_E0.8350.99
120_E124_K0.8350.99
211_F301_Q0.8340.99
54_H57_E0.8310.99
45_A136_M0.8300.99
146_Y150_F0.8290.99
391_W395_Q0.8270.99
21_A25_A0.8210.99
78_E107_A0.8170.99
229_L250_Y0.8160.99
38_I42_N0.8150.99
33_R37_L0.8140.99
303_L333_I0.8110.99
24_F127_A0.8110.99
229_L241_I0.8110.99
211_F333_I0.8050.99
109_A113_F0.8040.99
365_G389_G0.8040.99
67_T112_T0.8000.99
331_E346_D0.8000.99
225_E366_K0.7980.99
381_E385_V0.7950.99
36_Q40_E0.7880.99
18_F65_G0.7880.99
102_I106_F0.7870.99
313_H334_I0.7870.99
62_C142_L0.7860.99
319_D325_A0.7820.99
240_D274_I0.7810.99
63_Q70_S0.7790.99
319_D323_G0.7780.99
319_D322_G0.7760.99
292_I315_A0.7760.99
331_E340_E0.7750.99
331_E336_E0.7730.99
8_L11_V0.7720.99
335_E343_D0.7710.99
73_L111_I0.7700.99
268_E345_F0.7680.99
242_I269_V0.7650.99
66_I120_E0.7640.99
331_E343_D0.7630.99
364_D367_V0.7590.99
235_I282_S0.7590.99
223_R319_D0.7570.99
17_A21_A0.7570.99
385_V391_W0.7560.99
282_S287_F0.7530.99
56_D161_R0.7500.99
229_L284_I0.7500.99
51_V139_A0.7480.99
249_R344_E0.7460.98
16_T115_H0.7450.98
260_I324_T0.7450.98
73_L115_H0.7430.98
261_I285_S0.7430.98
181_E213_D0.7420.98
74_G78_E0.7420.98
304_L338_V0.7410.98
331_E344_E0.7400.98
184_L197_I0.7400.98
67_T124_K0.7400.98
31_G53_T0.7390.98
216_A328_V0.7390.98
140_K143_I0.7360.98
135_S139_A0.7360.98
98_L101_V0.7340.98
248_T267_K0.7330.98
295_I320_E0.7330.98
251_P316_I0.7320.98
313_H331_E0.7290.98
37_L40_E0.7280.98
71_I108_Y0.7250.98
66_I115_H0.7250.98
284_I288_V0.7250.98
231_H238_M0.7230.98
164_T169_L0.7210.98
90_V96_G0.7200.98
320_E390_G0.7200.98
365_G422_V0.7180.98
217_K325_A0.7180.98
216_A298_A0.7150.98
181_E185_R0.7150.98
121_L156_L0.7150.98
265_N268_E0.7140.98
34_I45_A0.7130.98
56_D125_T0.7120.98
399_V417_I0.7120.98
64_L152_F0.7110.98
63_Q74_G0.7110.98
291_I314_M0.7100.98
8_L12_L0.7080.98
354_R424_Y0.7080.98
44_A47_A0.7080.98
66_I121_L0.7080.98
253_E256_D0.7060.98
33_R36_Q0.7040.98
14_A17_A0.7020.98
181_E209_F0.7010.98
249_R265_N0.7000.98
215_L218_E0.6990.98
330_V341_I0.6990.98
75_V104_F0.6990.98
74_G77_G0.6980.98
55_L58_Y0.6960.98
12_L72_G0.6960.98
229_L242_I0.6960.98
355_K359_G0.6960.98
66_I69_T0.6960.98
164_T168_G0.6950.98
134_V138_F0.6930.98
395_Q408_E0.6910.98
99_S103_S0.6910.98
292_I310_E0.6880.97
63_Q67_T0.6880.97
59_L119_G0.6860.97
145_F149_A0.6850.97
16_T67_T0.6840.97
29_I132_E0.6840.97
353_I372_V0.6840.97
369_I380_L0.6810.97
396_K403_D0.6800.97
223_R321_Y0.6790.97
16_T69_T0.6780.97
242_I266_I0.6770.97
204_Y211_F0.6750.97
13_I119_G0.6730.97
181_E212_D0.6730.97
227_V244_I0.6700.97
378_I410_C0.6700.97
369_I385_V0.6700.97
335_E346_D0.6680.97
238_M242_I0.6660.97
221_I342_R0.6660.97
202_F206_N0.6650.97
66_I119_G0.6650.97
241_I244_I0.6640.97
13_I73_L0.6630.97
74_G112_T0.6630.97
341_I344_E0.6630.97
380_L391_W0.6620.97
67_T115_H0.6620.97
207_K337_I0.6610.97
87_P90_V0.6610.97
71_I78_E0.6590.97
118_V163_L0.6590.97
336_E340_E0.6590.97
379_H408_E0.6590.97
249_R314_M0.6560.97
205_V209_F0.6550.97
273_C276_G0.6550.97
306_K309_K0.6540.97
29_I48_V0.6540.97
51_V146_Y0.6530.97
356_I416_E0.6530.97
342_R348_D0.6510.96
355_K360_H0.6500.96
44_A139_A0.6500.96
238_M284_I0.6490.96
44_A137_L0.6490.96
384_E394_T0.6460.96
25_A135_S0.6460.96
13_I16_T0.6460.96
375_L378_I0.6410.96
69_T112_T0.6390.96
238_M283_T0.6340.96
318_S324_T0.6330.96
163_L167_F0.6330.96
381_E395_Q0.6300.96
373_N383_E0.6290.96
38_I44_A0.6260.96
389_G422_V0.6250.96
152_F156_L0.6240.95
20_V115_H0.6230.95
352_E367_V0.6200.95
67_T71_I0.6200.95
243_Q271_T0.6180.95
71_I75_V0.6180.95
229_L233_I0.6170.95
280_V283_T0.6170.95
303_L307_M0.6170.95
16_T63_Q0.6160.95
133_A136_M0.6150.95
391_W405_I0.6150.95
185_R206_N0.6130.95
72_G104_F0.6120.95
223_R322_G0.6120.95
330_V338_V0.6100.95
280_V284_I0.6090.95
48_V52_T0.6090.95
20_V120_E0.6090.95
251_P263_V0.6080.95
10_A14_A0.6080.95
304_L333_I0.6060.95
98_L102_I0.6060.95
104_F108_Y0.6060.95
214_R336_E0.6040.95
6_L80_T0.6030.95
50_K147_R0.6020.95
74_G79_S0.6010.94
210_E213_D0.6000.94
69_T73_L0.5990.94
170_E174_E0.5990.94
63_Q115_H0.5980.94
46_I49_K0.5970.94
157_N160_A0.5960.94
57_E146_Y0.5960.94
75_V111_I0.5940.94
54_H146_Y0.5920.94
249_R343_D0.5910.94
64_L112_T0.5890.94
251_P386_D0.5880.94
331_E345_F0.5880.94
248_T343_D0.5860.94
294_V298_A0.5850.94
219_I336_E0.5850.94
67_T108_Y0.5830.94
372_V375_L0.5830.94
29_I58_Y0.5830.94
23_E67_T0.5830.94
20_V66_I0.5810.93
286_Q290_P0.5810.93
90_V99_S0.5780.93
293_H318_S0.5760.93
81_I107_A0.5750.93
86_H100_H0.5740.93
265_N289_N0.5740.93
52_T55_L0.5720.93
249_R263_V0.5710.93
417_I420_H0.5710.93
292_I312_V0.5700.93
24_F63_Q0.5680.93
23_E120_E0.5680.93
305_V309_K0.5680.93
236_S281_D0.5670.93
212_D301_Q0.5670.93
129_Q169_L0.5650.92
298_A317_L0.5640.92
148_I151_P0.5630.92
211_F299_P0.5600.92
70_S120_E0.5580.92
191_S196_E0.5580.92
156_L160_A0.5580.92
369_I372_V0.5570.92
31_G49_K0.5570.92
15_L19_F0.5560.92
231_H234_K0.5560.92
260_I293_H0.5560.92
236_S280_V0.5560.92
20_V70_S0.5550.92
313_H341_I0.5550.92
237_E241_I0.5550.92
28_R58_Y0.5540.92
185_R210_E0.5540.92
42_N46_I0.5540.92
367_V371_Q0.5540.92
38_I41_G0.5520.92
131_A134_V0.5520.92
37_L41_G0.5520.92
218_E386_D0.5510.92
281_D285_S0.5510.92
217_K386_D0.5510.92
35_D38_I0.5500.91
71_I107_A0.5500.91
78_E116_V0.5490.91
81_I109_A0.5470.91
43_K140_K0.5450.91
20_V62_C0.5440.91
45_A135_S0.5440.91
12_L69_T0.5430.91
70_S121_L0.5410.91
253_E257_K0.5410.91
151_P154_W0.5410.91
265_N313_H0.5410.91
231_H283_T0.5400.91
396_K404_S0.5390.91
189_S206_N0.5380.91
313_H330_V0.5380.91
112_T116_V0.5380.91
257_K324_T0.5380.91
144_W148_I0.5350.90
180_S184_L0.5350.90
223_R320_E0.5340.90
295_I318_S0.5330.90
12_L17_A0.5330.90
363_L376_L0.5320.90
376_L427_V0.5320.90
331_E338_V0.5320.90
157_N161_R0.5320.90
69_T108_Y0.5310.90
406_I428_K0.5310.90
289_N312_V0.5300.90
67_T70_S0.5300.90
165_K171_T0.5290.90
243_Q275_S0.5290.90
45_A132_E0.5280.90
58_Y64_L0.5270.90
393_L403_D0.5260.90
211_F337_I0.5260.90
50_K53_T0.5260.90
216_A299_P0.5240.89
363_L375_L0.5240.89
72_G75_V0.5220.89
203_K207_K0.5220.89
27_I60_S0.5220.89
351_S354_R0.5220.89
69_T119_G0.5210.89
63_Q121_L0.5200.89
411_E415_N0.5200.89
78_E108_Y0.5190.89
70_S73_L0.5190.89
59_L63_Q0.5180.89
359_G428_K0.5180.89
29_I136_M0.5170.89
296_E322_G0.5160.89
242_I270_L0.5160.89
48_V136_M0.5150.89
59_L66_I0.5150.89
37_L45_A0.5140.89
422_V425_I0.5140.89
222_P225_E0.5130.88
96_G99_S0.5120.88
423_A426_E0.5120.88
218_E393_L0.5110.88
185_R205_V0.5100.88
361_Y375_L0.5090.88
96_G100_H0.5070.88
299_P302_D0.5060.88
417_I422_V0.5050.88
29_I37_L0.5050.88
60_S67_T0.5040.88
26_I135_S0.5040.88
125_T128_I0.5040.88
272_A276_G0.5030.87
74_G108_Y0.5030.87
272_A282_S0.5020.87
252_V284_I0.5020.87
86_H105_I0.5020.87
33_R45_A0.5010.87
56_D60_S0.5010.87
22_S26_I0.5010.87
248_T313_H0.5000.87
391_W408_E0.5000.87
382_N394_T0.5000.87
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  
4hg0A 2 0.5203 100 0.507 Contact Map
3lhhA 1 0.2815 100 0.767 Contact Map
3ocoA 2 0.3041 99.9 0.782 Contact Map
3oi8A 2 0.3514 99.9 0.783 Contact Map
3ocmA 5 0.3356 99.9 0.789 Contact Map
3kxrA 3 0.3626 99.9 0.793 Contact Map
2v8qE 1 0.5315 99.9 0.794 Contact Map
3lv9A 2 0.2928 99.9 0.798 Contact Map
4iysA 2 0.3198 99.9 0.804 Contact Map
3t4nC 1 0.5338 99.9 0.813 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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