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OPENSEQ.org

RpoD

ID: 1508180496 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 666 (626)
Sequences: 945 (445.9)
Seq/Len: 1.510
Nf(neff/√len): 17.8

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.510).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
361_Q364_D3.9171.00
523_M527_I2.6941.00
186_D267_A2.2200.99
516_I540_L2.1630.99
186_D190_D2.1620.99
432_M441_I2.1580.99
332_R403_E2.1510.99
163_G421_G2.1200.99
519_T540_L2.0900.99
266_I312_L2.0820.99
372_G380_K2.0200.98
272_K300_E1.9840.98
259_V263_F1.9140.97
159_R431_E1.8660.97
125_K128_T1.8050.96
653_H656_R1.7920.95
34_M38_A1.7490.95
395_E399_S1.7470.95
336_Q393_L1.7400.94
243_E246_V1.7380.94
303_S307_A1.6790.93
269_N301_L1.6740.93
627_E636_T1.6700.93
636_T646_K1.6690.93
529_R535_E1.6580.92
151_E564_I1.6450.92
649_R654_P1.6420.92
162_A424_E1.6330.92
243_E247_S1.6270.91
32_K657_S1.6080.91
633_F646_K1.5880.90
341_M362_E1.5780.90
301_L304_R1.5700.89
387_Q391_K1.5620.89
635_V646_K1.5480.88
434_E441_I1.5450.88
570_S575_F1.5430.88
441_I566_D1.5290.88
177_T181_I1.5250.87
369_E387_Q1.5220.87
395_E398_M1.5040.86
639_R642_Q1.4640.84
353_E371_V1.4460.83
386_G390_I1.4410.83
526_E539_K1.4390.83
337_E412_R1.4170.82
272_K279_Q1.4160.82
146_E495_S1.3990.81
630_G636_T1.3980.80
512_T552_K1.3950.80
537_A542_M1.3920.80
23_L26_L1.3880.80
261_E665_D1.3820.79
536_L547_V1.3800.79
432_M566_D1.3770.79
466_M505_I1.3720.79
627_E646_K1.3650.78
598_T619_G1.3620.78
588_A622_T1.3560.78
640_I648_L1.3540.77
356_R371_V1.3430.77
633_F636_T1.3270.75
620_M632_Q1.3250.75
555_K623_D1.3230.75
188_L193_V1.3190.75
359_Q362_E1.3160.75
532_T535_E1.3140.74
562_T572_L1.3100.74
159_R350_A1.3090.74
163_G556_E1.3080.74
500_A510_I1.3010.73
612_L618_I1.2910.73
441_I495_S1.2900.73
633_F640_I1.2880.72
421_G561_E1.2870.72
305_I348_G1.2860.72
529_R550_V1.2850.72
448_T510_I1.2820.72
610_R655_S1.2790.72
420_K423_R1.2710.71
47_D545_E1.2710.71
620_M623_D1.2700.71
564_I568_E1.2670.71
336_Q339_R1.2670.71
351_R362_E1.2650.70
142_M150_R1.2630.70
38_A129_D1.2560.70
523_M529_R1.2550.70
625_T636_T1.2530.69
122_E568_E1.2530.69
529_R532_T1.2530.69
242_L247_S1.2480.69
416_H420_K1.2470.69
186_D189_V1.2460.69
258_R261_E1.2410.68
415_V419_Q1.2400.68
505_I549_K1.2380.68
474_Y478_Y1.2360.68
109_A122_E1.2320.67
34_M44_V1.2290.67
187_E192_R1.2260.67
81_E545_E1.2250.67
38_A51_E1.2230.67
629_V646_K1.2210.66
275_Q300_E1.2210.66
630_G641_R1.2170.66
527_I539_K1.2130.66
144_S370_R1.2120.66
332_R404_T1.2110.66
519_T609_E1.2090.65
625_T641_R1.2080.65
625_T639_R1.2040.65
646_K656_R1.2020.65
627_E630_G1.1980.64
593_L597_T1.1970.64
561_E616_F1.1930.64
139_L544_L1.1890.63
269_N273_L1.1870.63
55_Q80_A1.1870.63
512_T561_E1.1860.63
256_K260_L1.1830.63
473_E510_I1.1830.63
78_V531_P1.1800.63
145_V156_I1.1800.63
131_T422_E1.1790.62
301_L319_I1.1760.62
626_L641_R1.1760.62
510_I514_N1.1750.62
425_A433_I1.1710.62
310_K583_L1.1710.62
32_K70_L1.1690.62
533_P551_L1.1690.62
573_G578_D1.1680.61
359_Q365_P1.1660.61
627_E654_P1.1630.61
166_A424_E1.1600.61
341_M351_R1.1580.60
546_K556_E1.1520.60
521_R613_R1.1490.60
340_L602_A1.1480.59
640_I646_K1.1470.59
638_E642_Q1.1470.59
394_R541_A1.1470.59
163_G521_R1.1450.59
183_I407_E1.1430.59
497_A512_T1.1430.59
521_R561_E1.1420.59
625_T642_Q1.1410.59
588_A632_Q1.1380.58
630_G639_R1.1370.58
173_E417_M1.1360.58
188_L259_V1.1360.58
154_I263_F1.1330.58
545_E613_R1.1310.58
564_I595_E1.1290.58
126_E313_S1.1280.57
139_L441_I1.1250.57
448_T558_I1.1230.57
40_K44_V1.1230.57
171_L313_S1.1230.57
269_N302_K1.1210.57
626_L639_R1.1210.57
140_R558_I1.1200.57
155_A531_P1.1190.57
519_T547_V1.1190.57
595_E598_T1.1190.57
53_L73_L1.1180.56
590_Q593_L1.1170.56
630_G642_Q1.1140.56
358_Y362_E1.1120.56
618_I621_N1.1110.56
653_H657_S1.1110.56
625_T637_R1.1110.56
279_Q296_R1.1100.56
629_V656_R1.1090.55
638_E641_R1.1080.55
30_S33_R1.1070.55
415_V418_V1.1070.55
648_L652_K1.1060.55
125_K129_D1.1050.55
156_I558_I1.1040.55
61_E84_D1.1030.55
61_E357_H1.1020.55
432_M632_Q1.1010.55
188_L198_I1.1010.55
521_R553_I1.1000.55
645_A648_L1.1000.55
535_E550_V1.0980.54
334_I358_Y1.0980.54
543_P613_R1.0970.54
45_T50_N1.0950.54
345_E659_K1.0940.54
529_R534_E1.0940.54
392_T396_Q1.0930.54
104_E182_I1.0930.54
453_Q556_E1.0900.54
130_R470_D1.0900.54
448_T564_I1.0890.53
636_T639_R1.0880.53
505_I649_R1.0880.53
342_R345_E1.0870.53
56_E123_T1.0860.53
355_L360_G1.0860.53
448_T562_T1.0860.53
597_T618_I1.0860.53
150_R466_M1.0850.53
629_V633_F1.0850.53
488_I492_I1.0830.53
473_E585_I1.0820.53
340_L352_D1.0800.52
629_V636_T1.0800.52
540_L543_P1.0790.52
178_F347_H1.0790.52
171_L314_L1.0780.52
119_L122_E1.0770.52
186_D541_A1.0770.52
495_S632_Q1.0770.52
172_C184_W1.0770.52
222_E230_V1.0760.52
514_N611_V1.0760.52
351_R595_E1.0750.52
443_I485_T1.0750.52
21_G24_L1.0730.52
156_I431_E1.0720.52
258_R262_T1.0700.51
364_D370_R1.0700.51
368_V410_E1.0690.51
242_L245_N1.0690.51
371_V383_T1.0670.51
67_L631_Q1.0650.51
166_A420_K1.0610.51
178_F202_E1.0610.51
388_D396_Q1.0580.50
646_K663_F1.0580.50
154_I536_L1.0570.50
180_A183_I1.0550.50
547_V550_V1.0530.50
520_S572_L1.0520.50
626_L638_E1.0520.50
626_L642_Q1.0510.49
187_E193_V1.0500.49
137_M142_M1.0500.49
77_V159_R1.0470.49
492_I496_I1.0470.49
513_I562_T1.0470.49
260_L298_Y1.0460.49
404_T407_E1.0460.49
556_E572_L1.0450.49
517_V614_M1.0430.49
558_I600_V1.0420.49
636_T641_R1.0410.48
154_I588_A1.0410.48
594_R598_T1.0410.48
452_L478_Y1.0410.48
616_F648_L1.0410.48
166_A352_D1.0400.48
630_G646_K1.0400.48
208_P661_R1.0390.48
55_Q198_I1.0390.48
368_V390_I1.0380.48
238_D241_D1.0380.48
336_Q390_I1.0370.48
441_I621_N1.0360.48
507_V629_V1.0350.48
217_G237_G1.0340.48
29_A72_E1.0340.48
429_K454_F1.0330.48
397_I400_L1.0330.48
548_R571_H1.0330.48
135_V512_T1.0320.48
453_Q512_T1.0310.47
198_I268_E1.0300.47
647_A651_L1.0290.47
463_I614_M1.0280.47
162_A406_L1.0280.47
572_L578_D1.0270.47
319_I414_I1.0260.47
473_E476_R1.0260.47
326_L405_G1.0250.47
261_E304_R1.0240.47
397_I540_L1.0230.47
125_K399_S1.0230.47
279_Q300_E1.0230.47
473_E569_D1.0230.47
366_H369_E1.0220.46
34_M51_E1.0210.46
164_R581_V1.0200.46
473_E509_M1.0190.46
100_E406_L1.0190.46
240_D247_S1.0180.46
455_L466_M1.0170.46
454_F501_R1.0160.46
549_K597_T1.0160.46
245_N248_L1.0150.46
500_A505_I1.0140.46
609_E619_G1.0140.46
70_L665_D1.0140.46
485_T500_A1.0130.46
144_S564_I1.0120.45
104_E537_A1.0110.45
513_I554_A1.0110.45
397_I609_E1.0100.45
172_C401_A1.0070.45
318_R321_A1.0070.45
636_T642_Q1.0070.45
317_N323_V1.0060.45
618_I623_D1.0060.45
331_K334_I1.0060.45
627_E653_H1.0040.45
233_P237_G1.0040.45
500_A513_I1.0030.45
282_E289_G1.0030.45
270_Y273_L1.0030.45
37_L49_L1.0020.44
453_Q510_I1.0020.44
354_F358_Y1.0020.44
35_I73_L1.0020.44
627_E656_R1.0010.44
36_K83_A1.0010.44
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4yfkF20.70271000.427Contact Map
1l9zH10.4731000.69Contact Map
2a6hF20.5121000.695Contact Map
1sigA10.4551000.74Contact Map
3ugoA10.27031000.82Contact Map
1l0oC10.08561000.862Contact Map
1rp3A40.34381000.865Contact Map
4x8kA1099.80.919Contact Map
4nqwA10.222299.70.929Contact Map
3mzyA10.180299.60.932Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

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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