GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Welcome: casp11@openseq.org My Submissions
T0826

ID: 1403198838 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 544 (532)
Sequences: 652 (472.4)
Seq/Len: 1.226
Nf(neff/√len): 20.5

HHblits Results: (2013_03)
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: 1.226).

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
237_V430_I4.5181.00
382_S422_T4.1501.00
517_T537_L3.8661.00
307_L518_V3.8101.00
250_N269_N3.7081.00
248_G257_T3.7041.00
327_C331_C3.4901.00
433_V447_V2.8101.00
450_V511_H2.7791.00
392_T425_Y2.7131.00
397_K424_L2.6671.00
363_D436_K2.6241.00
516_S534_M2.4811.00
242_T423_V2.2730.99
435_R438_E2.1910.99
103_M106_N2.1610.98
396_R401_T2.1210.98
259_L428_Q2.1110.98
520_G535_D2.0860.98
530_Y535_D2.0650.98
242_T426_V2.0500.97
499_C540_C2.0250.97
311_V522_M2.0240.97
131_G135_A2.0090.97
276_C286_C1.9720.97
273_V509_Y1.9420.96
489_F517_T1.9070.96
245_A475_G1.8280.94
429_F433_V1.8010.94
242_T382_S1.8000.94
234_V374_V1.8000.94
395_E428_Q1.7620.93
263_R431_D1.6880.90
216_Q219_M1.6690.90
242_T247_W1.6530.89
218_D221_V1.6260.88
247_W379_T1.6160.88
242_T451_S1.5950.87
429_F536_I1.5930.87
20_S27_L1.5800.86
259_L431_D1.5730.86
348_C353_C1.5690.85
22_Y27_L1.5630.85
318_V334_V1.5590.85
248_G255_Q1.5440.84
236_L374_V1.5440.84
233_F443_L1.5400.84
274_R477_T1.5230.83
87_A127_I1.5070.82
356_N425_Y1.5030.82
234_V446_V1.5000.82
230_L444_E1.4720.80
392_T429_F1.4710.80
79_P139_I1.4660.80
462_M467_A1.4600.79
214_Y305_D1.4600.79
246_N420_D1.4530.79
31_F35_V1.4430.78
173_Q177_Y1.4420.78
446_V489_F1.4410.78
59_F165_C1.4400.78
255_Q424_L1.4340.78
256_T420_D1.4220.77
52_T177_Y1.4030.75
519_L527_S1.4030.75
450_V514_Y1.3990.75
402_C410_C1.3860.74
455_E476_Q1.3830.74
62_N162_S1.3770.74
195_N327_C1.3640.73
214_Y333_K1.3570.72
255_Q261_A1.3570.72
236_L450_V1.3550.72
287_M514_Y1.3550.72
520_G530_Y1.3520.72
309_D333_K1.3480.71
401_T418_T1.3450.71
236_L514_Y1.3370.70
249_L260_L1.3360.70
359_L363_D1.3340.70
387_Y455_E1.3340.70
79_P135_A1.3310.70
117_R380_I1.3290.70
79_P138_Y1.3260.69
233_F366_L1.3230.69
243_R283_S1.3200.69
104_L203_K1.3170.69
117_R386_T1.3140.68
82_L138_Y1.3120.68
283_S464_L1.3080.68
244_A269_N1.3040.68
243_R437_L1.3030.68
403_D418_T1.2990.67
296_Y423_V1.2990.67
241_T464_L1.2990.67
248_G261_A1.2980.67
48_I51_Y1.2970.67
396_R399_T1.2940.67
509_Y536_I1.2910.66
254_R417_N1.2900.66
290_T304_Q1.2890.66
246_N475_G1.2750.65
474_S477_T1.2620.64
456_S476_Q1.2610.64
420_D484_W1.2530.63
254_R420_D1.2510.63
193_P417_N1.2500.63
252_Y420_D1.2450.62
411_T414_T1.2430.62
392_T395_E1.2300.61
195_N331_C1.2290.61
218_D527_S1.2280.61
91_Q118_L1.2210.60
129_C136_L1.2090.59
252_Y256_T1.2060.59
306_N330_V1.1990.58
312_Q335_P1.1960.58
246_N416_V1.1940.58
393_E396_R1.1940.58
68_I77_L1.1900.57
311_V518_V1.1850.57
278_T320_W1.1840.57
247_W257_T1.1800.56
395_E425_Y1.1780.56
359_L436_K1.1760.56
244_A478_H1.1680.55
311_V320_W1.1660.55
58_F460_N1.1630.55
306_N332_G1.1600.54
118_L379_T1.1590.54
314_A522_M1.1580.54
391_Y422_T1.1570.54
243_R515_F1.1560.54
363_D367_N1.1530.54
286_C402_C1.1460.53
356_N392_T1.1450.53
243_R464_L1.1450.53
18_F500_L1.1400.52
327_C336_N1.1390.52
162_S194_S1.1280.51
92_E99_F1.1270.51
55_V168_G1.1270.51
382_S423_V1.1250.51
354_L392_T1.1240.51
260_L404_T1.1230.51
235_V433_V1.1210.50
468_P476_Q1.1200.50
276_C410_C1.1190.50
333_K478_H1.1170.50
247_W333_K1.1160.50
234_V518_V1.1150.50
241_T283_S1.1110.49
110_T114_E1.1110.49
77_L82_L1.1060.49
31_F53_M1.1050.49
420_D455_E1.1030.49
425_Y428_Q1.0980.48
331_C336_N1.0980.48
473_P476_Q1.0980.48
287_M450_V1.0960.48
321_L337_T1.0940.48
293_R329_G1.0890.47
483_M537_L1.0890.47
391_Y396_R1.0870.47
256_T260_L1.0860.47
241_T451_S1.0830.47
292_D534_M1.0810.47
286_C410_C1.0800.46
23_S65_F1.0790.46
21_L58_F1.0760.46
285_P289_S1.0750.46
274_R474_S1.0690.45
97_I467_A1.0690.45
329_G481_M1.0670.45
309_D512_D1.0660.45
32_F35_V1.0640.45
31_F185_K1.0600.45
417_N420_D1.0590.44
243_R426_V1.0550.44
392_T428_Q1.0540.44
24_S57_L1.0530.44
305_D313_R1.0520.44
243_R476_Q1.0510.44
391_Y395_E1.0500.44
243_R400_P1.0490.43
19_L22_Y1.0480.43
26_V147_V1.0480.43
276_C348_C1.0440.43
62_N158_L1.0420.43
402_C456_S1.0410.43
234_V316_V1.0390.42
410_C456_S1.0380.42
306_N331_C1.0360.42
220_A313_R1.0350.42
426_V430_I1.0350.42
456_S473_P1.0350.42
281_A301_A1.0350.42
457_L461_G1.0350.42
456_S472_A1.0330.42
49_F177_Y1.0320.42
417_N468_P1.0310.42
247_W422_T1.0310.42
188_T198_G1.0300.42
16_I38_L1.0300.42
241_T244_A1.0290.42
437_L447_V1.0290.42
400_P417_N1.0290.42
257_T261_A1.0280.41
247_W260_L1.0270.41
220_A527_S1.0270.41
242_T257_T1.0270.41
45_G48_I1.0260.41
104_L175_Q1.0250.41
249_L267_I1.0230.41
460_N475_G1.0220.41
20_S24_S1.0200.41
519_L524_I1.0190.41
29_Y35_V1.0190.41
414_T418_T1.0180.40
63_F163_F1.0180.40
235_V377_L1.0170.40
483_M517_T1.0170.40
244_A376_I1.0110.40
11_G14_A1.0090.40
218_D314_A1.0060.39
117_R389_E1.0050.39
263_R435_R1.0040.39
326_G466_A1.0030.39
277_G285_P1.0020.39
286_C456_S1.0000.39
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: (14Jun14)
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  
4kavA10.61031000.697Contact Map
3b5qA20.5461000.82Contact Map
2vqrA10.54781000.822Contact Map
2qzuA10.56431000.822Contact Map
2w5qA10.57351000.83Contact Map
4mhxA20.53491000.83Contact Map
2w8dA20.58091000.831Contact Map
1fsuA10.52941000.833Contact Map
3lxqA20.57171000.833Contact Map
1aukA10.51651000.835Contact 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.

Page generated in 0.0445 seconds.