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T0840 1-540

ID: 1404412919 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 540 (507)
Sequences: 587 (325.3)
Seq/Len: 1.158
Nf(neff/√len): 14.4

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: 1.158).

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
96_T99_K3.1151.00
96_T101_L2.9471.00
514_C523_C2.9361.00
514_C525_W2.7021.00
94_G98_T2.5321.00
52_I57_H2.4050.99
299_L326_G2.3760.99
505_C511_C2.3470.99
520_F523_C2.1890.98
505_C514_C2.0500.97
511_C514_C1.9890.96
505_C523_C1.9470.96
514_C520_F1.8850.95
95_D98_T1.8680.94
49_F110_L1.8580.94
520_F525_W1.8230.93
326_G347_F1.8130.93
403_F406_L1.8000.93
511_C523_C1.7930.93
439_V451_Q1.7820.92
114_G121_C1.7250.91
279_R296_Y1.7060.90
98_T101_L1.7030.90
514_C521_M1.6650.89
96_T114_G1.6580.88
56_L124_H1.6520.88
240_L243_Q1.6510.88
258_L261_L1.6490.88
427_T443_G1.6290.87
225_I243_Q1.5970.86
523_C530_C1.5600.84
46_S52_I1.5480.83
241_T259_A1.5130.81
443_G447_G1.5070.81
441_H522_G1.4870.80
116_S119_G1.4810.79
115_S176_Y1.4750.79
57_H326_G1.4650.78
98_T114_G1.4630.78
463_Y479_D1.4510.77
50_V59_L1.4500.77
426_V450_L1.4470.77
111_V347_F1.4450.77
98_T103_L1.4410.77
526_C536_C1.4360.76
505_C525_W1.4170.75
262_S265_E1.4150.75
269_G273_E1.4110.74
350_D354_T1.4050.74
442_M450_L1.3980.74
442_M452_V1.3940.73
296_Y524_G1.3920.73
52_I96_T1.3920.73
119_G273_E1.3900.73
50_V110_L1.3890.73
511_C525_W1.3870.73
385_C400_C1.3820.72
443_G511_C1.3770.72
489_F498_V1.3770.72
451_Q522_G1.3750.72
514_C530_C1.3730.72
514_C524_G1.3710.71
51_A265_E1.3680.71
404_P408_S1.3670.71
323_V500_I1.3660.71
521_M525_W1.3590.70
271_Y428_A1.3590.70
495_V505_C1.3450.69
179_S263_A1.3400.69
102_V329_V1.3330.68
517_A525_W1.3290.68
441_H451_Q1.3290.68
165_T168_E1.3250.68
508_F517_A1.3180.67
427_T431_V1.3160.67
277_D295_P1.3030.66
231_F240_L1.2950.65
169_Q173_S1.2890.65
401_R406_L1.2870.64
488_L508_F1.2830.64
79_C85_C1.2800.64
514_C522_G1.2760.63
104_D347_F1.2730.63
115_S119_G1.2670.63
42_D47_A1.2670.63
243_Q257_R1.2600.62
517_A523_C1.2560.62
33_V36_M1.2530.61
227_Y243_Q1.2490.61
398_T404_P1.2490.61
95_D101_L1.2450.61
243_Q273_E1.2330.59
156_V159_P1.2320.59
268_L273_E1.2210.58
270_D441_H1.2210.58
438_T524_G1.2180.58
177_V297_P1.2160.58
525_W530_C1.2140.58
119_G363_C1.2130.58
426_V442_M1.2120.58
203_A206_F1.2060.57
119_G526_C1.2060.57
399_S403_F1.2040.57
347_F497_Q1.2020.57
250_D352_L1.1820.55
113_C121_C1.1820.55
60_G66_V1.1810.55
203_A208_P1.1800.54
447_G451_Q1.1760.54
161_G164_V1.1760.54
101_L260_R1.1750.54
120_R176_Y1.1740.54
243_Q247_V1.1690.53
364_C499_P1.1670.53
96_T100_V1.1660.53
451_Q521_M1.1630.53
256_T299_L1.1630.53
134_H137_A1.1590.52
180_S193_S1.1560.52
236_F240_L1.1530.52
178_A522_G1.1520.52
312_A315_L1.1520.52
59_L260_R1.1500.52
52_I499_P1.1490.52
208_P211_V1.1480.51
437_V443_G1.1480.51
404_P443_G1.1460.51
101_L526_C1.1430.51
427_T430_Y1.1410.51
54_N442_M1.1390.51
401_R407_V1.1370.50
210_F213_L1.1360.50
404_P407_V1.1360.50
508_F513_R1.1250.49
207_A211_V1.1220.49
478_R489_F1.1220.49
164_V301_V1.1210.49
60_G68_S1.1170.48
57_H264_T1.1170.48
402_H406_L1.1150.48
495_V521_M1.1140.48
115_S121_C1.1130.48
514_C526_C1.1130.48
432_T522_G1.1130.48
179_S257_R1.1130.48
119_G271_Y1.1120.48
49_F56_L1.1110.48
508_F511_C1.1090.48
256_T300_Q1.1080.48
437_V513_R1.1080.48
404_P480_V1.1070.47
403_F407_V1.1060.47
402_H408_S1.1060.47
48_V56_L1.1040.47
25_P29_A1.1020.47
511_C526_C1.1000.47
148_R151_D1.0990.47
72_G157_A1.0980.47
274_L325_F1.0940.46
161_G329_V1.0940.46
36_M40_E1.0930.46
430_Y449_I1.0910.46
400_C406_L1.0910.46
500_I522_G1.0900.46
515_L523_C1.0900.46
58_V481_S1.0890.46
276_L326_G1.0880.46
34_Q37_V1.0880.46
495_V508_F1.0880.46
48_V258_L1.0840.45
114_G119_G1.0810.45
451_Q488_L1.0790.45
25_P28_S1.0780.45
207_A212_A1.0760.44
505_C508_F1.0760.44
94_G118_Q1.0750.44
342_S356_I1.0720.44
530_C536_C1.0700.44
437_V453_E1.0700.44
491_S497_Q1.0690.44
374_R377_D1.0690.44
51_A262_S1.0620.43
429_L488_L1.0590.43
54_N95_D1.0580.43
227_Y230_S1.0570.43
448_R476_V1.0560.43
257_R444_T1.0540.42
428_A443_G1.0540.42
111_V297_P1.0540.42
407_V411_F1.0520.42
505_C520_F1.0520.42
150_D153_P1.0510.42
444_T450_L1.0500.42
262_S270_D1.0500.42
56_L122_F1.0480.42
325_F352_L1.0470.42
479_D490_A1.0470.42
301_V357_D1.0450.42
30_G33_V1.0440.41
497_Q508_F1.0430.41
79_C82_C1.0400.41
296_Y356_I1.0400.41
83_A89_P1.0380.41
469_L474_Q1.0330.40
24_V28_S1.0330.40
65_S349_I1.0330.40
165_T364_C1.0310.40
110_L348_P1.0300.40
268_L272_R1.0290.40
43_R103_L1.0280.40
352_L389_P1.0270.40
275_V449_I1.0270.40
516_R519_H1.0270.40
341_N349_I1.0260.40
192_R228_V1.0260.40
189_F192_R1.0250.40
505_C530_C1.0230.39
505_C521_M1.0220.39
48_V257_R1.0210.39
448_R466_N1.0210.39
54_N73_P1.0210.39
329_V500_I1.0150.39
146_H151_D1.0150.39
72_G101_L1.0120.38
275_V295_P1.0120.38
164_V169_Q1.0110.38
36_M39_Y1.0100.38
153_P383_S1.0100.38
394_L400_C1.0080.38
297_P350_D1.0080.38
60_G351_L1.0070.38
109_A124_H1.0050.38
522_G525_W1.0040.38
508_F520_F1.0030.38
299_L328_F1.0030.38
299_L442_M1.0020.38
296_Y339_G1.0020.38
196_I268_L1.0020.38
181_L209_G1.0020.38
271_Y274_L1.0010.37
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: (28Jun14)
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  
4fwwA10.93891000.111Contact Map
2uzxB20.79631000.258Contact Map
3al9A20.86481000.288Contact Map
3okyA10.87041000.303Contact Map
3ol2B10.85371000.33Contact Map
4gz8A20.87411000.355Contact Map
3okyB10.86481000.377Contact Map
1olzA20.85371000.38Contact Map
3nvqA20.83151000.388Contact Map
1q47A20.82961000.424Contact 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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