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OPENSEQ.org

a1078

ID: 1415240553 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 481 (473)
Sequences: 628 (527.1)
Seq/Len: 1.328
Nf(neff/√len): 24.2

Jackhmmer Results: (2014_04_16)
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: 1.328).

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
348_A391_Y2.4281.00
384_M410_M2.3680.99
238_R295_D2.3230.99
289_N366_H2.2230.99
12_L16_S2.0000.97
297_R309_S1.9020.96
352_D389_Q1.8670.96
256_Q289_N1.8490.95
190_V221_G1.8310.95
289_N317_E1.8100.95
319_E323_L1.7940.94
247_I298_L1.7810.94
311_Y349_E1.7750.94
164_I195_A1.7390.93
431_I435_D1.7190.92
208_L212_G1.7050.92
311_Y332_G1.7040.92
165_V194_T1.6770.91
7_L15_A1.6730.91
152_G169_I1.6400.90
320_A361_G1.6210.89
395_G407_G1.6150.89
25_V58_I1.6030.89
237_L253_R1.5640.87
309_S334_D1.5550.86
8_S14_T1.5480.86
255_I290_Q1.5320.85
252_S313_Q1.5160.84
259_G318_D1.5160.84
253_R290_Q1.5160.84
290_Q372_G1.5120.84
3_L10_A1.5090.84
218_A273_F1.5070.84
204_E207_W1.5020.84
278_D281_G1.5010.84
267_S271_D1.4540.81
30_D34_D1.4540.81
265_S268_S1.4490.81
7_L16_S1.4360.80
12_L19_V1.4340.80
6_T16_S1.4280.79
189_P295_D1.4170.79
32_R51_W1.4170.79
265_S298_L1.4110.78
12_L17_S1.4000.77
36_N40_Q1.3990.77
6_T14_T1.3980.77
233_K258_G1.3930.77
134_V419_L1.3910.77
153_S179_G1.3840.76
58_I62_L1.3780.76
318_D361_G1.3770.76
205_T208_L1.3590.74
208_L471_E1.3580.74
250_G295_D1.3560.74
421_I424_A1.3510.74
180_S313_Q1.3400.73
8_S18_A1.3400.73
168_Q191_Y1.3390.73
318_D366_H1.3380.73
15_A20_F1.3350.73
268_S287_P1.3330.72
268_S367_S1.3320.72
75_V78_S1.3170.71
173_W252_S1.3160.71
328_M363_S1.3150.71
37_W41_Q1.3110.71
192_G232_A1.2910.69
366_H417_S1.2900.69
24_L27_N1.2800.68
12_L18_A1.2780.68
55_G59_Q1.2770.68
169_I192_G1.2700.67
364_Y368_T1.2690.67
204_E208_L1.2650.67
82_A86_D1.2610.66
264_E269_L1.2530.66
270_W274_V1.2480.65
295_D313_Q1.2420.65
249_L367_S1.2400.64
152_G168_Q1.2400.64
176_G212_G1.2340.64
207_W271_D1.2280.63
103_I184_G1.2260.63
166_A193_V1.2250.63
10_A19_V1.2250.63
333_V450_I1.2230.63
155_V450_I1.2220.63
397_I405_L1.2210.63
6_T9_I1.2140.62
184_G272_A1.2090.61
31_L34_D1.2090.61
252_S293_G1.2080.61
8_S12_L1.2050.61
258_G318_D1.2040.61
310_L450_I1.1990.60
363_S381_G1.1970.60
281_G284_E1.1910.60
13_A240_T1.1910.60
289_N365_A1.1880.59
431_I440_H1.1870.59
207_W357_G1.1800.59
34_D44_I1.1800.59
194_T297_R1.1800.59
57_E215_Q1.1790.59
353_T381_G1.1780.58
8_S15_A1.1770.58
206_K210_W1.1740.58
6_T11_L1.1730.58
8_S16_S1.1730.58
159_L206_K1.1700.58
24_L29_D1.1680.57
8_S13_A1.1670.57
268_S271_D1.1670.57
30_D33_T1.1660.57
269_L287_P1.1630.57
207_W210_W1.1630.57
173_W236_G1.1620.57
13_A16_S1.1550.56
308_V333_V1.1530.56
12_L20_F1.1530.56
293_G313_Q1.1530.56
179_G382_H1.1530.56
312_G331_A1.1510.56
187_S375_Q1.1500.56
197_R216_Y1.1500.56
214_W466_A1.1470.55
364_Y373_Y1.1450.55
29_D32_R1.1420.55
9_I12_L1.1400.55
356_N359_V1.1400.55
155_V195_A1.1380.55
177_H364_Y1.1350.54
7_L20_F1.1330.54
318_D324_P1.1300.54
22_Q40_Q1.1250.53
375_Q378_Y1.1240.53
262_R278_D1.1240.53
304_F355_T1.1240.53
9_I15_A1.1230.53
420_A423_K1.1200.53
26_L29_D1.1190.53
327_K364_Y1.1190.53
24_L28_N1.1180.53
11_L20_F1.1160.52
255_I272_A1.1140.52
368_T371_D1.1140.52
172_W185_D1.1140.52
11_L15_A1.1130.52
197_R203_F1.1110.52
14_T18_A1.1110.52
252_S330_L1.1100.52
9_I13_A1.1080.52
164_I296_G1.1060.51
447_P450_I1.0980.51
83_L87_N1.0970.50
6_T10_A1.0950.50
5_K14_T1.0940.50
269_L300_L1.0920.50
181_L295_D1.0900.50
114_Q223_L1.0880.50
204_E212_G1.0880.50
236_G254_A1.0860.49
292_A318_D1.0860.49
395_G450_I1.0850.49
286_D368_T1.0840.49
384_M388_G1.0830.49
54_S57_E1.0790.49
38_L44_I1.0790.49
319_E324_P1.0790.49
128_W228_A1.0780.49
315_V381_G1.0740.48
136_A150_V1.0730.48
136_A239_V1.0730.48
12_L77_N1.0730.48
5_K11_L1.0730.48
426_P438_W1.0720.48
256_Q284_E1.0710.48
248_E297_R1.0700.48
34_D40_Q1.0700.48
180_S366_H1.0680.48
196_Q217_Q1.0670.47
7_L11_L1.0670.47
347_Y394_G1.0650.47
257_W317_E1.0630.47
4_R11_L1.0630.47
132_I380_L1.0610.47
259_G369_Y1.0590.47
273_F413_K1.0570.46
314_Y321_G1.0570.46
175_P383_A1.0560.46
20_F71_A1.0550.46
156_A163_W1.0540.46
247_I323_L1.0530.46
48_T51_W1.0480.46
34_D78_S1.0480.46
41_Q76_I1.0470.45
403_N440_H1.0450.45
137_E149_N1.0450.45
69_H72_Q1.0440.45
10_A16_S1.0430.45
252_S297_R1.0420.45
7_L17_S1.0420.45
181_L353_T1.0410.45
393_V454_V1.0400.45
257_W272_A1.0390.45
172_W180_S1.0360.44
98_T339_Y1.0350.44
189_P221_G1.0340.44
194_T217_Q1.0340.44
176_G330_L1.0340.44
389_Q413_K1.0340.44
83_L86_D1.0340.44
168_Q188_R1.0330.44
181_L252_S1.0330.44
262_R279_N1.0320.44
10_A63_S1.0320.44
182_I310_L1.0290.44
41_Q72_Q1.0290.44
12_L15_A1.0290.44
219_F236_G1.0280.44
205_T304_F1.0280.44
296_G421_I1.0260.43
464_A470_I1.0260.43
3_L6_T1.0240.43
374_Y385_G1.0210.43
31_L79_V1.0200.43
292_A316_G1.0190.43
420_A470_I1.0160.42
379_P385_G1.0150.42
224_D375_Q1.0150.42
465_G472_I1.0140.42
435_D451_N1.0130.42
24_L55_G1.0130.42
232_A253_R1.0120.42
262_R287_P1.0120.42
30_D40_Q1.0100.42
155_V166_A1.0090.42
192_G253_R1.0080.42
17_S58_I1.0060.41
39_N53_L1.0030.41
334_D345_Q1.0030.41
259_G292_A1.0020.41
411_V436_L1.0010.41
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  
2ynkA10.91481000.235Contact Map
2y2xA20.698592.50.946Contact Map
2y0hA10.679887.50.951Contact Map
3t24A30.681987.50.951Contact Map
3szvA10.681987.40.951Contact Map
4frtA20.690286.40.952Contact Map
3sybA10.731885.20.953Contact Map
2zfgA10.6611850.953Contact Map
1phoA10.6258800.955Contact Map
1ormA10.303579.10.956Contact 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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