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OPENSEQ.org

pista3 -force run

ID: 1440490253 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 488 (451)
Sequences: 361 (223.7)
Seq/Len: 0.800
Nf(neff/√len): 10.5

HHblits Results: (2015_06)
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: 0.800).

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
241_C246_C3.2011.00
265_I332_I2.8981.00
80_F84_Y2.3690.98
118_G121_C2.1990.96
413_D419_S1.8730.90
157_L160_N1.7980.87
86_D89_Q1.7540.85
151_C157_L1.7040.83
112_C121_C1.7010.83
81_W84_Y1.6990.83
413_D421_G1.6760.82
273_T278_L1.6670.81
364_F431_Y1.6570.81
108_Y120_N1.6330.79
155_Y164_C1.5700.75
87_G103_D1.5670.75
365_G406_G1.5570.74
365_G418_D1.5510.74
25_F31_A1.5370.73
31_A40_R1.5260.72
440_G452_Y1.5260.72
383_P406_G1.5140.72
60_E69_E1.5070.71
321_F458_F1.5070.71
406_G418_D1.5070.71
108_Y121_C1.5070.71
422_P443_C1.5020.71
301_A364_F1.5020.71
344_P349_A1.4960.70
266_L271_I1.4880.70
56_E69_E1.4880.70
110_C121_C1.4870.70
151_C155_Y1.4790.69
56_E60_E1.4540.67
235_I238_G1.4530.67
364_F433_V1.4390.66
418_D450_G1.4370.66
369_E445_R1.4350.66
108_Y118_G1.4200.64
90_C101_C1.4140.64
160_N164_C1.4050.63
53_L70_V1.3900.62
365_G450_G1.3860.62
403_F447_G1.3860.62
414_A441_E1.3830.61
369_E442_G1.3810.61
413_D418_D1.3790.61
157_L164_C1.3730.61
90_C95_C1.3700.60
90_C110_C1.3690.60
55_R69_E1.3650.60
46_E60_E1.3630.60
168_G171_P1.3500.59
140_C151_C1.3490.58
270_Y364_F1.3480.58
413_D450_G1.3460.58
140_C164_C1.3420.58
365_G383_P1.3390.58
365_G417_G1.3380.58
112_C118_G1.3270.57
406_G450_G1.3260.57
365_G413_D1.3230.56
426_R429_D1.3230.56
101_C110_C1.3220.56
329_K332_I1.3170.56
149_C154_G1.3130.55
46_E69_E1.3070.55
140_C149_C1.3020.54
383_P452_Y1.3020.54
415_C422_P1.3020.54
55_R60_E1.2980.54
320_D458_F1.2920.54
259_G293_T1.2910.53
417_G450_G1.2870.53
406_G413_D1.2830.53
99_G118_G1.2820.53
383_P417_G1.2800.53
46_E56_E1.2750.52
136_C149_C1.2690.52
64_Y78_N1.2690.52
210_P213_N1.2680.51
101_C121_C1.2680.51
103_D115_G1.2670.51
419_S422_P1.2580.51
136_C151_C1.2550.50
138_Q170_Y1.2530.50
204_D207_D1.2520.50
265_I400_Q1.2480.50
320_D401_N1.2480.50
406_G417_G1.2460.50
95_C101_C1.2440.49
272_L344_P1.2430.49
309_I313_R1.2280.48
31_A35_L1.2260.48
149_C155_Y1.2230.48
130_S454_K1.2120.47
116_F297_E1.2080.46
417_G452_Y1.2050.46
116_F120_N1.2050.46
418_D452_Y1.2020.46
320_D399_T1.2010.46
107_E119_K1.1970.45
90_C112_C1.1960.45
322_D415_C1.1950.45
365_G443_C1.1900.45
406_G452_Y1.1880.45
383_P418_D1.1860.44
52_H76_K1.1850.44
136_C160_N1.1750.43
68_R72_E1.1750.43
415_C438_S1.1740.43
49_K73_D1.1740.43
50_K72_E1.1710.43
264_T341_A1.1700.43
154_G157_L1.1700.43
419_S450_G1.1670.43
136_C155_Y1.1660.43
276_H452_Y1.1600.42
264_T314_F1.1590.42
136_C157_L1.1570.42
418_D421_G1.1570.42
166_P271_I1.1540.42
359_G394_S1.1530.42
26_I116_F1.1530.42
406_G422_P1.1520.41
101_C112_C1.1510.41
419_S443_C1.1440.41
139_F152_A1.1430.41
405_A418_D1.1410.41
136_C140_C1.1410.41
442_G445_R1.1380.40
276_H405_A1.1380.40
151_C164_C1.1370.40
29_E335_R1.1360.40
47_E60_E1.1350.40
238_G247_P1.1350.40
140_C155_Y1.1340.40
47_E69_E1.1330.40
421_G450_G1.1310.40
344_P442_G1.1280.39
419_S438_S1.1250.39
251_L259_G1.1230.39
68_R71_F1.1180.39
314_F321_F1.1170.38
417_G439_W1.1170.38
46_E55_R1.1160.38
52_H70_V1.1100.38
266_L384_Y1.1090.38
406_G419_S1.1090.38
136_C154_G1.1090.38
25_F35_L1.1040.37
110_C118_G1.1040.37
47_E56_E1.1030.37
405_A415_C1.1010.37
344_P369_E1.1000.37
365_G419_S1.0980.37
262_G365_G1.0940.37
406_G439_W1.0930.37
348_W434_T1.0930.37
266_L345_E1.0920.36
39_T456_T1.0900.36
303_H332_I1.0900.36
264_T318_T1.0890.36
415_C443_C1.0890.36
94_P112_C1.0880.36
341_A433_V1.0880.36
417_G443_C1.0870.36
88_D103_D1.0840.36
265_I271_I1.0840.36
247_P261_C1.0830.36
149_C157_L1.0830.36
52_H55_R1.0820.36
66_E69_E1.0820.36
24_L31_A1.0800.35
211_T214_P1.0800.35
25_F40_R1.0760.35
261_C277_C1.0750.35
103_D117_E1.0740.35
417_G422_P1.0710.35
418_D440_G1.0670.34
405_A438_S1.0630.34
51_G55_R1.0620.34
151_C154_G1.0600.34
273_T297_E1.0590.34
325_V458_F1.0590.34
112_C116_F1.0560.34
286_V338_V1.0550.34
264_T272_L1.0550.34
155_Y160_N1.0510.33
284_F424_V1.0510.33
64_Y75_D1.0500.33
405_A417_G1.0480.33
401_N442_G1.0460.33
405_A439_W1.0450.33
413_D417_G1.0450.33
393_S448_K1.0420.33
136_C139_F1.0400.32
138_Q152_A1.0380.32
276_H439_W1.0360.32
151_C160_N1.0350.32
30_Q100_K1.0340.32
415_C419_S1.0330.32
246_C362_S1.0330.32
383_P450_G1.0320.32
238_G419_S1.0300.32
421_G438_S1.0300.32
48_M158_A1.0280.31
318_T349_A1.0270.31
150_S334_F1.0270.31
405_A452_Y1.0270.31
252_L353_L1.0270.31
90_C99_G1.0260.31
365_G405_A1.0250.31
54_E59_E1.0230.31
101_C118_G1.0200.31
327_R437_V1.0200.31
99_G112_C1.0200.31
407_Y447_G1.0200.31
41_A344_P1.0190.31
97_N134_G1.0180.31
417_G440_G1.0180.31
365_G377_L1.0170.31
209_D224_Q1.0170.31
422_P450_G1.0160.31
238_G413_D1.0150.30
136_C430_T1.0120.30
377_L413_D1.0120.30
268_E386_D1.0110.30
301_A338_V1.0090.30
438_S452_Y1.0080.30
270_Y314_F1.0080.30
442_G455_V1.0070.30
130_S142_E1.0060.30
348_W457_A1.0060.30
234_R417_G1.0060.30
414_A442_G1.0060.30
90_C94_P1.0050.30
440_G443_C1.0040.30
449_Y452_Y1.0040.30
328_L404_C1.0020.30
271_I429_D1.0010.29
308_V343_L1.0000.29
338_V414_A1.0000.29
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  
4nzqA10.80741000.46Contact Map
4bxwA20.56971000.461Contact Map
3h5cB10.63731000.591Contact Map
3nxpA10.71311000.625Contact Map
3f1sB10.52871000.626Contact Map
4kkdA20.68031000.648Contact Map
1zjkA10.69061000.65Contact Map
4igdA10.68851000.653Contact Map
2bdyA10.53281000.654Contact Map
2xxlA20.66191000.658Contact 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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