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PAH

ID: 1481711642 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 452 (424)
Sequences: 512 (307.9)
Seq/Len: 1.208
Nf(neff/√len): 15.0

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: 1.208).

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
192_K221_E3.4121.00
228_E232_Q3.1181.00
195_K214_E2.2980.99
235_Q241_R2.2070.99
324_I399_V1.9580.96
248_L326_W1.9310.96
151_D154_Y1.9100.96
181_E185_K1.9040.96
342_A354_L1.8830.95
319_E376_N1.8800.95
277_Y379_V1.8740.95
257_G264_H1.8640.95
217_C223_N1.8430.94
331_F346_G1.8340.94
191_F214_E1.8150.94
176_R229_D1.7800.93
138_Y143_D1.7790.93
326_W352_G1.7420.92
151_D157_R1.7050.91
154_Y157_R1.6940.90
136_L139_G1.6690.89
364_L388_V1.6570.89
193_T196_S1.6490.89
326_W377_Y1.6170.87
283_I294_F1.6080.87
299_F302_F1.5810.86
144_A150_K1.5670.85
191_F220_H1.5620.85
264_H277_Y1.5150.82
153_V156_A1.5020.82
263_F280_E1.5010.82
271_H275_P1.4850.81
164_I174_I1.4750.80
53_R56_E1.4580.79
282_D285_H1.4430.78
138_Y161_F1.4330.77
306_I341_K1.4310.77
328_T367_L1.4270.77
151_D158_R1.4210.76
377_Y384_P1.4180.76
300_A304_Q1.4170.76
268_Y278_T1.4090.75
365_L385_L1.4030.75
266_T279_P1.3980.75
282_D290_H1.3880.74
148_G151_D1.3840.74
314_P317_Y1.3720.73
330_E344_G1.3590.72
332_G344_G1.3560.71
356_Y362_P1.3550.71
277_Y280_E1.3340.70
46_G52_L1.3270.69
159_K163_D1.3230.69
268_Y271_H1.3130.68
248_L377_Y1.3110.68
194_L198_Y1.3100.68
328_T392_F1.3080.68
268_Y275_P1.3080.68
131_F137_S1.2980.67
345_A349_S1.2940.66
325_Y386_Y1.2920.66
72_L78_E1.2890.66
148_G165_A1.2800.65
257_G277_Y1.2730.64
267_Q271_H1.2650.64
154_Y158_R1.2590.63
277_Y380_T1.2580.63
275_P280_E1.2540.63
174_I356_Y1.2530.63
243_R253_D1.2530.63
150_K161_F1.2510.62
306_I321_L1.2470.62
409_P447_A1.2440.62
64_H68_R1.2440.62
136_L140_A1.2390.61
223_N229_D1.2240.60
283_I287_L1.2210.60
284_C288_L1.2190.59
240_F300_A1.2140.59
190_V206_Y1.2090.59
300_A303_S1.2030.58
285_H290_H1.2030.58
308_L312_G1.2030.58
149_F155_R1.1990.58
291_V325_Y1.1960.57
375_Q385_L1.1940.57
418_T422_E1.1850.56
276_M382_F1.1840.56
39_F51_V1.1780.56
171_G186_T1.1760.55
292_P304_Q1.1730.55
41_L56_E1.1730.55
378_T384_P1.1710.55
344_G353_E1.1650.54
185_K188_G1.1640.54
327_F349_S1.1640.54
344_G349_S1.1630.54
179_Y183_E1.1630.54
263_F271_H1.1630.54
142_L146_H1.1630.54
311_L321_L1.1610.54
267_Q275_P1.1550.53
327_F331_F1.1530.53
394_D398_K1.1520.53
158_R165_A1.1470.53
84_D92_T1.1470.53
156_A169_R1.1440.52
248_L265_C1.1440.52
277_Y346_G1.1430.52
124_T236_T1.1430.52
299_F309_A1.1420.52
131_F264_H1.1400.52
303_S310_S1.1390.52
326_W351_F1.1390.52
351_F377_Y1.1380.52
248_L351_F1.1340.51
244_P253_D1.1330.51
148_G158_R1.1290.51
328_T334_C1.1280.51
61_N65_I1.1220.50
263_F275_P1.1210.50
198_Y245_V1.1190.50
165_A169_R1.1190.50
243_R266_T1.1180.50
373_A402_F1.1170.50
271_H280_E1.1150.49
216_Y237_C1.1140.49
369_L398_K1.1130.49
179_Y187_W1.1130.49
335_K390_E1.1120.49
186_T213_L1.1100.49
59_D100_H1.1100.49
148_G154_Y1.1090.49
266_T286_E1.1080.49
319_E323_T1.1070.49
133_N166_Y1.1060.49
242_L319_E1.1020.48
317_Y407_P1.0990.48
330_E353_E1.0990.48
352_G382_F1.0990.48
130_R440_E1.0990.48
183_E187_W1.0980.48
369_L414_Y1.0970.48
408_R412_V1.0940.47
349_S353_E1.0920.47
208_H296_D1.0920.47
226_Q267_Q1.0890.47
365_L371_K1.0870.47
64_H78_E1.0860.47
278_T379_V1.0850.47
131_F140_A1.0850.47
259_A280_E1.0830.46
254_F263_F1.0820.46
154_Y165_A1.0820.46
332_G353_E1.0810.46
306_I310_S1.0740.45
135_I265_C1.0740.45
307_G313_A1.0710.45
252_R271_H1.0700.45
137_S140_A1.0690.45
145_D273_S1.0690.45
285_H289_G1.0680.45
238_T263_F1.0680.45
60_V65_I1.0660.45
169_R181_E1.0660.45
332_G349_S1.0630.44
248_L352_G1.0630.44
330_E349_S1.0630.44
270_R281_P1.0610.44
327_F352_G1.0560.44
425_D429_Q1.0560.44
362_P386_Y1.0550.44
59_D90_A1.0500.43
263_F268_Y1.0500.43
134_Q137_S1.0490.43
271_H279_P1.0470.43
136_L264_H1.0460.43
352_G377_Y1.0460.43
268_Y279_P1.0430.42
340_I388_V1.0420.42
214_E220_H1.0390.42
284_C403_A1.0380.42
282_D289_G1.0370.42
325_Y330_E1.0350.42
342_A352_G1.0330.42
188_G192_K1.0320.41
310_S321_L1.0320.41
243_R260_F1.0320.41
254_F280_E1.0310.41
278_T309_A1.0300.41
125_I167_N1.0300.41
212_L237_C1.0290.41
161_F169_R1.0280.41
307_G310_S1.0270.41
330_E345_A1.0260.41
207_N229_D1.0240.41
286_E290_H1.0230.41
262_V266_T1.0220.40
252_R268_Y1.0210.40
350_S353_E1.0190.40
347_L354_L1.0190.40
308_L315_D1.0190.40
276_M324_I1.0170.40
312_G315_D1.0170.40
243_R246_A1.0140.40
327_F330_E1.0130.40
134_Q140_A1.0120.40
345_A353_E1.0120.40
415_D437_I1.0110.39
219_F287_L1.0100.39
205_E336_Q1.0100.39
198_Y230_V1.0080.39
447_A450_K1.0080.39
332_G345_A1.0070.39
420_R427_T1.0070.39
184_K223_N1.0070.39
202_A348_L1.0060.39
67_S79_F1.0060.39
440_E443_I1.0050.39
252_R312_G1.0040.39
226_Q229_D1.0040.39
206_Y228_E1.0030.39
253_D266_T1.0030.39
46_G67_S1.0030.39
323_T327_F1.0020.39
60_V77_Y1.0010.39
213_L291_V1.0010.39
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  
1phzA10.89161000.137Contact Map
1tohA10.7191000.193Contact Map
4v06A20.76111000.197Contact Map
1j8uA10.67921000.224Contact Map
1mlwA10.64161000.253Contact Map
3tk2A10.6041000.421Contact Map
4bptA40.53981000.463Contact Map
2v27A20.57961000.463Contact Map
3mwbA20.316499.90.873Contact Map
2mdaA20.201399.50.915Contact 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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