GREMLIN Database
LPTD - LPS-assembly protein LptD
UniProt: P31554 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11569
Length: 784 (685)
Sequences: 2155 (1612)
Seq/√Len: 61.6

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_S247_Y7.4161.00
372_V394_L5.3091.00
85_D109_N5.2671.00
234_K242_E5.1601.00
251_I255_M4.9881.00
185_S200_N4.6751.00
512_A560_T4.6211.00
122_P137_E4.5911.00
152_D167_N4.4891.00
228_F247_Y4.1731.00
310_R336_D3.8091.00
456_T480_R3.7901.00
90_H93_E3.7661.00
57_D72_S3.7191.00
255_M276_F3.7181.00
278_Y285_G3.6611.00
244_Y260_T3.5381.00
455_A481_V3.4821.00
514_Y556_N3.4751.00
730_V752_I3.4221.00
173_C725_C3.3331.00
447_I489_G3.2811.00
70_T86_E3.2041.00
181_S204_K3.1181.00
249_W259_I3.0881.00
228_F245_L3.0421.00
226_S249_W3.0121.00
257_A274_N2.9751.00
242_E262_H2.9641.00
706_D709_A2.9611.00
488_D511_R2.9131.00
453_L481_V2.8591.00
256_D277_R2.8411.00
147_G170_F2.8341.00
85_D108_G2.8291.00
127_N130_T2.8251.00
291_Y309_R2.8131.00
183_V204_K2.7571.00
57_D71_G2.7291.00
287_M315_W2.7111.00
106_A110_V2.6341.00
558_V585_F2.6301.00
728_I754_F2.5601.00
700_V718_G2.5531.00
259_I274_N2.5351.00
328_N360_S2.5241.00
153_L166_D2.4951.00
198_I218_L2.4361.00
86_E107_L2.4291.00
165_L168_G2.4291.00
226_S250_N2.4201.00
103_T125_W2.4171.00
58_H70_T2.4051.00
123_K136_W2.3931.00
478_V525_I2.3871.00
278_Y317_H2.3771.00
653_Q688_V2.3401.00
151_A165_L2.3091.00
73_V87_V2.2731.00
190_D193_E2.2521.00
184_G187_I2.2501.00
68_V88_Q2.2041.00
370_A396_V2.1871.00
274_N289_L2.1651.00
107_L123_K2.1601.00
252_A255_M2.1541.00
315_W329_V2.1351.00
205_V210_I2.1351.00
333_K357_Q2.1271.00
564_S577_I2.1201.00
200_N212_Y2.0961.00
450_E486_K2.0891.00
289_L313_F2.0621.00
390_A393_Q2.0521.00
431_H454_L2.0061.00
722_S759_R1.9821.00
74_D83_Q1.9721.00
62_D65_D1.9681.00
405_P438_L1.9531.00
84_A87_V1.9471.00
102_R129_N1.9411.00
185_S202_R1.9381.00
429_R550_D1.9271.00
254_N278_Y1.9111.00
56_A69_F1.8871.00
77_Q80_S1.8731.00
370_A394_L1.8651.00
179_T724_C1.8641.00
246_P261_P1.8511.00
194_Q221_G1.8411.00
331_Y357_Q1.8411.00
183_V202_R1.8281.00
258_T275_E1.8281.00
260_T273_E1.8281.00
446_S490_K1.8181.00
229_L256_D1.8141.00
273_E290_D1.7941.00
227_G256_D1.7740.99
148_R171_T1.7660.99
226_S248_Y1.7660.99
66_D92_K1.7550.99
194_Q223_K1.7350.99
275_E288_E1.7270.99
447_I487_V1.6960.99
610_G626_I1.6920.99
55_N74_D1.6920.99
81_R113_D1.6890.99
140_Y149_G1.6840.99
325_W361_V1.6740.99
431_H456_T1.6720.99
414_A428_T1.6610.99
457_H479_N1.6600.99
416_H428_T1.6590.99
515_L557_Q1.6560.99
195_V225_R1.6540.99
326_R362_G1.6540.99
285_G317_H1.6530.99
433_E452_K1.6510.99
689_A701_G1.6470.99
322_D325_W1.6430.99
560_T583_Y1.6350.99
217_Q225_R1.6300.99
311_W335_S1.6280.99
484_Q517_V1.6250.99
262_H271_M1.6230.99
80_S114_D1.6160.99
368_F396_V1.6100.99
76_M81_R1.6090.99
475_D524_D1.6080.99
325_W363_Y1.6020.99
235_Y241_F1.6000.99
87_V106_A1.5870.99
319_G327_F1.5780.99
451_A485_F1.5670.99
527_N530_S1.5600.99
93_E103_T1.5510.99
329_V359_F1.5500.99
204_K207_P1.5480.99
529_D548_G1.5400.99
296_K299_E1.5400.99
182_V201_A1.5390.99
275_E286_L1.5340.98
397_N411_Y1.5330.98
110_V124_G1.5310.98
224_R256_D1.5250.98
227_G725_C1.5240.98
201_A213_S1.5050.98
654_L687_A1.5030.98
686_G702_A1.5020.98
198_I201_A1.5010.98
106_A124_G1.4990.98
646_R650_R1.4990.98
512_A558_V1.4970.98
449_T487_V1.4940.98
75_I87_V1.4870.98
271_M292_L1.4830.98
321_M327_F1.4750.98
647_D650_R1.4690.98
355_A380_F1.4670.98
568_D574_R1.4650.98
157_R163_T1.4650.98
258_T277_R1.4590.98
280_S285_G1.4540.98
158_G161_R1.4500.98
226_S252_A1.4360.98
540_L580_G1.4340.98
729_R755_N1.4270.98
431_H549_L1.4260.98
516_Y556_N1.4260.98
244_Y262_H1.4220.98
227_G248_Y1.4160.97
271_M290_D1.4080.97
68_V86_E1.4060.97
311_W333_K1.4060.97
150_K169_S1.4040.97
310_R342_D1.3990.97
368_F398_Y1.3980.97
314_Y332_T1.3810.97
506_Q564_S1.3790.97
121_G135_V1.3790.97
733_E751_A1.3780.97
224_R250_N1.3720.97
227_G231_P1.3710.97
255_M278_Y1.3700.97
103_T127_N1.3660.97
699_I719_V1.3630.97
84_A106_A1.3630.97
83_Q111_H1.3610.97
113_D118_I1.3470.97
407_D437_N1.3420.96
513_Q559_T1.3420.96
703_Y712_Q1.3390.96
508_L562_V1.3380.96
327_F361_V1.3380.96
213_S216_L1.3370.96
241_F265_H1.3360.96
685_V707_T1.3350.96
179_T726_Y1.3320.96
249_W257_A1.3240.96
227_G277_R1.3230.96
529_D550_D1.3170.96
247_Y251_I1.3170.96
179_T723_S1.3150.96
280_S283_G1.3130.96
155_K166_D1.3040.96
624_G640_S1.3030.96
393_Q413_Q1.2960.96
251_I257_A1.2950.96
607_V627_Q1.2920.96
224_R277_R1.2910.96
168_G187_I1.2900.96
224_R227_G1.2860.95
317_H329_V1.2830.95
509_E565_R1.2810.95
186_E199_W1.2800.95
636_A641_S1.2770.95
248_Y256_D1.2750.95
189_H220_V1.2750.95
694_A697_W1.2720.95
545_T553_A1.2710.95
50_L78_G1.2570.95
111_H118_I1.2540.95
324_V365_V1.2520.95
608_W630_T1.2450.95
409_R435_T1.2390.94
577_I612_T1.2380.94
483_P518_P1.2360.94
54_I69_F1.2350.94
519_Y589_R1.2340.94
616_I622_L1.2300.94
720_Q729_R1.2280.94
650_R660_S1.2220.94
429_R458_Y1.2190.94
410_I432_L1.2120.94
292_L343_F1.2080.94
336_D342_D1.2050.94
406_F419_N1.1920.93
727_A757_E1.1910.93
514_Y558_V1.1860.93
734_R750_N1.1840.93
227_G246_P1.1820.93
158_G162_Y1.1750.93
732_Y750_N1.1730.93
482_M520_R1.1710.93
429_R529_D1.1680.93
406_F438_L1.1680.93
122_P355_A1.1660.92
650_R691_W1.1650.92
284_A318_S1.1610.92
455_A479_N1.1600.92
233_A241_F1.1510.92
333_K378_Q1.1490.92
418_V426_E1.1490.92
231_P248_Y1.1450.92
177_S207_P1.1410.92
229_L277_R1.1390.92
642_I646_R1.1390.92
51_P77_Q1.1390.92
628_Y633_D1.1370.91
79_N114_D1.1320.91
46_D49_D1.1300.91
509_E563_T1.1250.91
173_C227_G1.1170.91
734_R748_Y1.1170.91
194_Q220_V1.1120.91
310_R335_S1.1100.90
89_L102_R1.1080.90
190_D195_V1.1080.90
625_G639_N1.1050.90
239_N264_M1.0970.90
156_Q160_N1.0960.90
495_R506_Q1.0960.90
139_D150_K1.0920.90
693_I699_I1.0900.90
271_M339_Y1.0880.90
180_W231_P1.0880.90
250_N253_P1.0850.89
527_N593_D1.0840.89
391_E416_H1.0810.89
414_A430_V1.0760.89
577_I610_G1.0730.89
251_I276_F1.0720.89
573_E576_N1.0670.89
72_S85_D1.0650.89
486_K513_Q1.0580.88
334_V355_A1.0580.88
53_T76_M1.0550.88
138_G154_M1.0520.88
419_N424_M1.0480.88
357_Q376_Q1.0480.88
452_K484_Q1.0480.88
375_K390_A1.0460.88
460_Q526_Y1.0400.87
60_K70_T1.0360.87
293_P309_R1.0340.87
157_R161_R1.0330.87
496_D505_T1.0300.87
199_W215_Y1.0280.87
204_K209_P1.0270.87
169_S181_S1.0250.87
175_P178_D1.0250.87
248_Y257_A1.0240.87
249_W252_A1.0230.86
290_D339_Y1.0210.86
245_L261_P1.0180.86
287_M430_V1.0170.86
515_L555_A1.0110.86
59_A69_F1.0090.86
173_C724_C1.0090.86
529_D552_I1.0050.86
42_L45_G0.9980.85
395_D413_Q0.9950.85
262_H343_F0.9930.85
243_F758_L0.9900.85
105_D125_W0.9890.85
391_E418_V0.9860.84
561_G580_G0.9850.84
276_F285_G0.9850.84
485_F489_G0.9830.84
720_Q727_A0.9810.84
705_Y710_N0.9810.84
209_P212_Y0.9810.84
196_A218_L0.9800.84
333_K376_Q0.9780.84
195_V217_Q0.9760.84
557_Q582_I0.9760.84
641_S655_N0.9750.84
446_S491_M0.9680.83
283_G319_G0.9660.83
458_Y548_G0.9640.83
298_Y308_S0.9560.83
224_R725_C0.9550.82
356_T375_K0.9520.82
533_L547_G0.9510.82
644_Y647_D0.9510.82
406_F417_F0.9500.82
444_W491_M0.9500.82
270_I293_P0.9480.82
313_F331_Y0.9480.82
171_T178_D0.9480.82
330_D358_K0.9470.82
132_D158_G0.9470.82
575_F612_T0.9440.82
82_L142_M0.9430.82
271_M343_F0.9420.82
453_L483_P0.9410.82
758_L765_Y0.9400.81
655_N659_A0.9380.81
74_D81_R0.9350.81
427_A528_Y0.9350.81
526_Y551_R0.9350.81
148_R178_D0.9310.81
219_P231_P0.9310.81
626_I635_V0.9300.81
560_T605_S0.9290.81
188_I199_W0.9290.81
405_P419_N0.9250.80
442_N445_G0.9210.80
497_M566_I0.9190.80
433_E454_L0.9190.80
43_V47_T0.9160.80
685_V703_Y0.9160.80
43_V46_D0.9110.79
229_L725_C0.9090.79
637_T640_S0.9070.79
324_V363_Y0.9060.79
162_Y189_H0.9040.79
244_Y273_E0.9030.79
458_Y529_D0.9030.79
120_K139_D0.9020.79
692_P698_S0.9010.79
231_P256_D0.9000.79
449_T486_K0.9000.79
219_P248_Y0.8960.78
551_R554_S0.8940.78
240_Y265_H0.8920.78
163_T188_I0.8910.78
622_L640_S0.8900.78
435_T450_E0.8900.78
640_S645_R0.8880.78
572_V575_F0.8860.77
429_R551_R0.8850.77
687_A703_Y0.8850.77
173_C180_W0.8840.77
93_E102_R0.8840.77
452_K543_D0.8840.77
180_W725_C0.8800.77
702_A716_M0.8770.77
693_I719_V0.8770.77
371_T395_D0.8760.77
560_T564_S0.8760.77
446_S492_V0.8680.76
278_Y315_W0.8660.76
449_T488_D0.8650.76
454_L480_R0.8620.75
140_Y169_S0.8600.75
439_P448_N0.8580.75
286_L316_N0.8580.75
149_G165_L0.8560.75
334_V340_F0.8530.75
405_P417_F0.8510.75
587_E602_K0.8510.75
643_E647_D0.8510.75
248_Y279_L0.8500.74
482_M552_I0.8490.74
355_A378_Q0.8480.74
458_Y550_D0.8480.74
456_T482_M0.8450.74
612_T624_G0.8430.74
558_V583_Y0.8380.73
229_L246_P0.8380.73
505_T569_D0.8380.73
390_A415_V0.8380.73
256_D725_C0.8370.73
557_Q584_Y0.8360.73
633_D643_E0.8350.73
529_D541_F0.8350.73
197_E217_Q0.8340.73
248_Y277_R0.8340.73
563_T578_S0.8340.73
219_P258_T0.8320.73
69_F87_V0.8320.73
696_R721_Y0.8310.73
229_L248_Y0.8300.73
642_I645_R0.8290.73
262_H273_E0.8290.73
155_K163_T0.8270.72
160_N192_E0.8270.72
181_S207_P0.8260.72
263_Y270_I0.8250.72
45_G48_N0.8230.72
151_A168_G0.8230.72
510_P561_G0.8230.72
211_F533_L0.8230.72
180_W227_G0.8220.72
173_C277_R0.8200.72
533_L542_R0.8200.72
136_W153_L0.8160.71
458_Y480_R0.8130.71
389_S392_P0.8130.71
329_V357_Q0.8090.71
545_T554_S0.8050.70
212_Y228_F0.8040.70
73_V84_A0.8030.70
179_T206_G0.8020.70
202_R209_P0.8000.70
236_T239_N0.8000.70
180_W246_P0.7960.70
352_D653_Q0.7960.70
174_L724_C0.7960.70
530_S534_Q0.7930.69
410_I434_P0.7920.69
414_A719_V0.7910.69
460_Q528_Y0.7910.69
261_P272_W0.7900.69
636_A660_S0.7900.69
638_S658_Y0.7880.69
540_L609_A0.7870.69
114_D117_V0.7860.69
61_G86_E0.7860.69
219_P227_G0.7800.68
480_R525_I0.7800.68
613_Y623_R0.7780.68
628_Y705_Y0.7770.68
227_G258_T0.7770.68
162_Y165_L0.7770.68
277_R725_C0.7750.67
593_D596_T0.7740.67
154_M628_Y0.7730.67
197_E215_Y0.7720.67
728_I756_I0.7720.67
510_P606_L0.7720.67
69_F724_C0.7690.67
73_V540_L0.7670.67
376_Q506_Q0.7660.67
279_L284_A0.7650.66
211_F453_L0.7640.66
171_T629_D0.7630.66
429_R522_Q0.7620.66
629_D636_A0.7610.66
120_K226_S0.7610.66
61_G67_A0.7570.66
413_Q419_N0.7560.66
312_L332_T0.7560.66
714_D733_E0.7560.66
201_A216_L0.7550.65
82_L124_G0.7540.65
403_V406_F0.7510.65
655_N658_Y0.7510.65
257_A261_P0.7510.65
428_T459_Q0.7500.65
173_C224_R0.7490.65
193_E223_K0.7480.65
459_Q477_S0.7470.65
359_F374_T0.7470.65
124_G135_V0.7460.64
48_N558_V0.7430.64
226_S245_L0.7430.64
126_A133_T0.7430.64
517_V553_A0.7400.64
85_D110_V0.7400.64
592_D596_T0.7380.64
285_G315_W0.7370.64
246_P260_T0.7360.63
182_V203_F0.7350.63
594_N597_W0.7350.63
133_T607_V0.7340.63
224_R229_L0.7330.63
280_S319_G0.7330.63
336_D551_R0.7330.63
602_K752_I0.7320.63
541_F557_Q0.7320.63
638_S656_Y0.7320.63
180_W721_Y0.7310.63
686_G704_Y0.7300.63
66_D90_H0.7290.63
396_V413_Q0.7260.62
224_R231_P0.7260.62
48_N123_K0.7250.62
140_Y723_S0.7210.62
65_D92_K0.7200.62
84_A128_L0.7190.62
250_N256_D0.7180.62
540_L545_T0.7170.61
522_Q551_R0.7170.61
567_Y581_Q0.7160.61
138_G172_S0.7150.61
579_V610_G0.7140.61
497_M500_L0.7120.61
492_V509_E0.7110.61
394_L414_A0.7110.61
246_P258_T0.7100.61
119_L212_Y0.7090.61
84_A187_I0.7090.61
80_S112_Y0.7090.61
691_W699_I0.7080.60
126_A131_K0.7070.60
417_F552_I0.7070.60
540_L550_D0.7070.60
592_D595_I0.7060.60
145_R546_Y0.7050.60
706_D756_I0.7050.60
165_L187_I0.7050.60
212_Y224_R0.7050.60
482_M517_V0.7040.60
655_N686_G0.7030.60
546_Y551_R0.7030.60
683_S707_T0.7030.60
402_D405_P0.7020.60
735_K749_D0.7010.60
226_S256_D0.7000.60
88_Q107_L0.7000.60
629_D652_V0.6990.59
558_V596_T0.6990.59
488_D718_G0.6990.59
48_N211_F0.6980.59
184_G201_A0.6960.59
187_I444_W0.6950.59
480_R529_D0.6940.59
699_I717_L0.6930.59
316_N330_D0.6930.59
330_D356_T0.6930.59
267_R295_D0.6930.59
365_V396_V0.6900.58
328_N358_K0.6890.58
251_I708_N0.6890.58
697_W721_Y0.6890.58
224_R248_Y0.6880.58
186_E200_N0.6880.58
658_Y683_S0.6870.58
163_T186_E0.6870.58
257_A276_F0.6870.58
315_W331_Y0.6870.58
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311_W751_A0.5390.41
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320_V453_L0.5380.41
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511_R563_T0.5360.41
615_R621_G0.5360.41
382_E386_S0.5360.41
506_Q566_I0.5350.41
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107_L432_L0.5330.41
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562_V623_R0.5320.41
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635_V638_S0.5250.40
351_T719_V0.5240.40
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385_T423_D0.5230.40
286_L710_N0.5230.40
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440_L447_I0.5220.40
634_N660_S0.5220.40
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429_R552_I0.5210.39
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366_Q754_F0.5170.39
537_Y578_S0.5170.39
629_D693_I0.5160.39
208_V572_V0.5160.39
310_R343_F0.5160.39
334_V380_F0.5150.39
90_H103_T0.5150.39
142_M449_T0.5150.39
422_D569_D0.5140.39
715_S738_G0.5140.39
135_V236_T0.5140.39
519_Y559_T0.5130.39
536_D540_L0.5130.39
575_F579_V0.5130.39
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190_D246_P0.5130.39
425_P460_Q0.5130.39
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325_W370_A0.5120.39
686_G720_Q0.5120.39
159_E396_V0.5120.39
256_D721_Y0.5120.39
408_T436_I0.5120.39
136_W155_K0.5120.39
448_N488_D0.5110.38
287_M314_Y0.5110.38
131_K572_V0.5110.38
535_S539_G0.5100.38
260_T275_E0.5100.38
215_Y592_D0.5100.38
48_N52_V0.5090.38
43_V185_S0.5090.38
360_S373_S0.5090.38
530_S535_S0.5090.38
154_M551_R0.5090.38
47_T50_L0.5090.38
245_L263_Y0.5080.38
622_L707_T0.5080.38
545_T606_L0.5080.38
529_D551_R0.5080.38
723_S762_S0.5070.38
379_V557_Q0.5070.38
453_L457_H0.5070.38
58_H502_P0.5060.38
195_V221_G0.5060.38
180_W229_L0.5060.38
133_T535_S0.5050.38
45_G160_N0.5050.38
388_Y419_N0.5050.38
619_R685_V0.5050.38
737_N754_F0.5050.38
598_E756_I0.5040.38
104_V126_A0.5040.38
217_Q245_L0.5040.38
217_Q221_G0.5040.38
227_G758_L0.5040.38
205_V756_I0.5030.38
603_T631_R0.5030.38
489_G656_Y0.5020.37
228_F535_S0.5020.37
49_D475_D0.5010.37
225_R275_E0.5010.37
178_D363_Y0.5010.37
430_V453_L0.5000.37
283_G317_H0.5000.37
141_Q147_G0.5000.37
493_F508_L0.5000.37
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  
4q35A 1 0.963 100 0.141 Contact Map
4uu4A 1 0.1696 99.6 0.892 Contact Map
2r19A 3 0.1735 99.1 0.916 Contact Map
3my2A 2 0.1518 97.8 0.943 Contact Map
1kmoA 1 0.7194 93.6 0.962 Contact Map
3qlbA 1 0.7309 87.6 0.967 Contact Map
4fqeA 1 0.2117 69.4 0.973 Contact Map
2wjrA 1 0.2423 68.8 0.973 Contact Map
2x9kA 1 0.3367 58.4 0.974 Contact Map
1ormA 1 0.1837 49 0.976 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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