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OPENSEQ.org

1BIFA

ID: 1411599738 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 432 (412)
Sequences: 434 (258.2)
Seq/Len: 1.053
Nf(neff/√len): 12.7

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: 1.053).

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
41_Y76_D2.4270.99
218_C244_F2.2170.98
73_A76_D1.9880.96
39_G43_R1.9630.95
298_M306_H1.9580.95
11_P15_K1.9310.95
142_Y153_D1.8900.94
39_G42_R1.8850.94
183_D186_Q1.8770.94
319_Y333_V1.8660.93
9_G15_K1.8080.92
322_R331_D1.7730.91
16_T325_K1.7570.90
300_Y314_R1.7250.89
41_Y73_A1.6960.88
264_T270_T1.6810.88
301_E304_Q1.6800.88
236_G272_Q1.6400.86
314_R323_Y1.6270.85
317_D320_R1.6160.85
342_E345_R1.5920.83
314_R318_K1.5790.83
220_H226_N1.5700.82
289_E314_R1.5690.82
102_A106_N1.5570.82
146_D149_E1.5560.81
39_G93_A1.5410.81
10_L15_K1.5330.80
272_Q275_E1.4970.78
6_V104_I1.4910.77
11_P14_G1.4810.77
265_S269_R1.4710.76
319_Y330_E1.4610.75
358_M362_L1.4560.75
269_R273_T1.4540.75
304_Q311_F1.4180.72
43_R55_F1.4120.72
226_N323_Y1.4110.72
12_A15_K1.4060.71
145_R352_I1.3960.71
264_T269_R1.3940.71
310_E321_Y1.3930.70
237_L241_G1.3900.70
242_R275_E1.3840.70
289_E292_A1.3780.69
220_H300_Y1.3710.69
13_R28_F1.3700.69
298_M303_I1.3620.68
9_G14_G1.3510.67
200_R337_E1.3470.67
89_A118_V1.3390.66
38_V55_F1.3370.66
300_Y318_K1.3270.65
178_Y243_E1.3260.65
24_R28_F1.3230.65
94_T100_R1.3210.64
9_G12_A1.3060.63
60_E64_K1.3020.63
154_F318_K1.2990.63
33_T41_Y1.2880.62
10_L14_G1.2860.61
232_G318_K1.2830.61
36_F39_G1.2800.61
288_N296_E1.2800.61
220_H318_K1.2780.61
94_T161_Y1.2740.60
14_G26_L1.2740.60
358_M384_L1.2690.60
156_R159_E1.2680.60
65_I68_Q1.2670.60
9_G13_R1.2660.60
16_T200_R1.2660.60
201_I352_I1.2620.59
264_T274_A1.2580.59
159_E162_E1.2530.58
31_V319_Y1.2510.58
8_V15_K1.2500.58
8_V12_A1.2410.57
10_L13_R1.2410.57
55_F141_D1.2400.57
144_N244_F1.2390.57
217_L358_M1.2390.57
289_E300_Y1.2340.57
123_V183_D1.2330.57
220_H355_Q1.2310.56
8_V11_P1.2290.56
59_N161_Y1.2280.56
57_P164_S1.2190.55
13_R158_I1.2170.55
318_K359_R1.2160.55
77_V89_A1.2140.55
220_H314_R1.2140.55
39_G66_R1.2140.55
74_L77_V1.2090.54
90_V116_F1.2080.54
335_R354_H1.2000.54
274_A352_I1.2000.54
362_L384_L1.1970.53
222_E381_H1.1930.53
4_L81_L1.1930.53
333_V341_M1.1900.53
221_G273_T1.1890.52
300_Y323_Y1.1880.52
233_G356_A1.1830.52
144_N352_I1.1830.52
5_I162_E1.1820.52
233_G318_K1.1820.52
340_I345_R1.1800.52
207_N340_I1.1790.52
247_H250_Q1.1790.52
128_I132_I1.1780.51
5_I188_Y1.1780.51
80_F235_P1.1760.51
234_D268_K1.1760.51
404_A407_T1.1730.51
266_Q288_N1.1730.51
146_D307_Y1.1700.51
93_A117_F1.1690.51
203_Y229_G1.1630.50
330_E333_V1.1590.50
16_T190_V1.1530.49
22_L205_L1.1510.49
351_V365_F1.1500.49
203_Y207_N1.1410.48
406_N412_P1.1380.48
37_N43_R1.1370.48
13_R162_E1.1370.48
153_D157_R1.1370.48
38_V290_I1.1360.48
20_K33_T1.1330.47
300_Y359_R1.1330.47
344_E364_Y1.1320.47
25_Y28_F1.1320.47
220_H289_E1.1320.47
300_Y355_Q1.1310.47
292_A352_I1.1310.47
37_N96_T1.1230.46
197_I332_L1.1230.46
226_N300_Y1.1220.46
25_Y29_I1.1200.46
192_R204_Y1.1190.46
42_R55_F1.1180.46
209_H213_R1.1170.46
264_T267_M1.1130.45
122_C128_I1.1120.45
390_A393_C1.1090.45
70_A100_R1.1080.45
246_K276_A1.1070.45
93_A157_R1.1070.45
243_E247_H1.1050.45
42_R66_R1.1040.45
95_N157_R1.1010.44
318_K321_Y1.0980.44
319_Y332_L1.0960.44
139_S286_V1.0960.44
90_V104_I1.0960.44
55_F66_R1.0920.43
91_F365_F1.0860.43
166_E301_E1.0840.43
396_E409_R1.0830.43
141_D153_D1.0830.43
54_F100_R1.0830.43
226_N380_L1.0800.42
304_Q312_A1.0800.42
41_Y69_C1.0790.42
204_Y290_I1.0760.42
39_G59_N1.0750.42
318_K356_A1.0680.41
195_D205_L1.0590.40
122_C141_D1.0570.40
362_L395_V1.0570.40
120_S124_D1.0540.40
39_G140_P1.0500.40
163_N307_Y1.0500.40
66_R93_A1.0480.39
232_G314_R1.0460.39
226_N355_Q1.0450.39
356_A360_C1.0440.39
238_S245_S1.0420.39
195_D214_S1.0420.39
37_N42_R1.0380.39
311_F315_D1.0360.38
354_H361_L1.0360.38
226_N314_R1.0320.38
80_F183_D1.0300.38
220_H233_G1.0280.38
328_S331_D1.0280.38
9_G16_T1.0270.38
402_V407_T1.0250.37
283_Q352_I1.0250.37
41_Y77_V1.0240.37
88_V317_D1.0220.37
273_T298_M1.0210.37
273_T303_I1.0210.37
6_V115_T1.0210.37
295_C300_Y1.0190.37
220_H295_C1.0170.37
241_G269_R1.0160.37
289_E323_Y1.0150.36
202_V331_D1.0140.36
30_G41_Y1.0140.36
54_F59_N1.0130.36
219_R223_S1.0130.36
298_M351_V1.0120.36
55_F142_Y1.0120.36
195_D319_Y1.0120.36
39_G100_R1.0120.36
238_S294_V1.0110.36
277_L325_K1.0110.36
312_A316_Q1.0110.36
26_L226_N1.0110.36
353_C358_M1.0090.36
288_N332_L1.0060.36
221_G335_R1.0050.36
300_Y303_I1.0030.35
97_T388_P1.0030.35
217_L313_L1.0030.35
79_K84_E1.0030.35
54_F94_T1.0030.35
367_D381_H1.0020.35
221_G354_H1.0010.35
362_L397_S1.0010.35
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: (06Sep14)
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  
1bifA111000.438Contact Map
2axnA10.97221000.445Contact Map
1fztA10.4561000.81Contact Map
2hhjA20.46761000.822Contact Map
3gp3A40.44211000.823Contact Map
4ij5A20.46761000.824Contact Map
1e58A10.47451000.824Contact Map
1h2eA10.4561000.825Contact Map
3f3kA20.50231000.826Contact Map
4gpzA20.4631000.827Contact 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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