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serinc

ID: 1507038524 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 465 (457)
Sequences: 843 (451)
Seq/Len: 1.845
Nf(neff/√len): 21.1

Jackhmmer Results: (2016_04)
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: 1.845).

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
229_Y246_S3.4871.00
243_F247_I3.4581.00
192_L196_W3.0441.00
226_T230_I2.7211.00
223_T227_L2.5371.00
247_I251_F2.3921.00
258_I450_G2.2151.00
246_S250_I2.1880.99
343_I346_N1.9820.99
219_I223_T1.9370.98
220_L281_L1.8870.98
119_S402_L1.8490.98
248_N442_S1.8330.97
241_N294_N1.8250.97
196_W209_A1.8200.97
221_S280_T1.8150.97
432_E435_M1.8060.97
294_N435_M1.7980.97
314_T318_A1.7810.97
395_Y401_H1.7740.97
218_Y256_S1.7680.97
294_N432_E1.7310.96
451_W456_P1.6750.95
311_G315_T1.6610.95
48_V448_I1.6520.95
136_Q193_A1.6440.94
258_I261_L1.6420.94
271_S275_Q1.6040.93
272_G275_Q1.6040.93
255_I450_G1.5750.92
209_A213_V1.5670.92
224_G228_L1.5530.92
15_M20_T1.5510.92
109_F162_F1.5490.92
18_G22_A1.5460.92
17_C23_S1.5400.91
6_G9_S1.5380.91
20_T23_S1.5370.91
355_S358_S1.5320.91
413_M418_W1.5230.91
255_I446_V1.5200.91
17_C20_T1.5130.90
126_K130_D1.5130.90
15_M18_G1.5110.90
15_M22_A1.5070.90
140_W143_K1.5050.90
222_L226_T1.5040.90
6_G11_A1.5030.90
455_A462_R1.5030.90
240_I243_F1.4960.90
342_C345_Y1.4850.89
32_C37_S1.4780.89
342_C346_N1.4780.89
354_V357_I1.4710.89
286_L289_S1.4460.88
451_W455_A1.4400.87
9_S13_C1.4400.87
287_T439_I1.4360.87
410_Y418_W1.4300.87
157_I162_F1.4250.86
367_L370_A1.4170.86
18_G23_S1.4090.86
246_S249_L1.4080.86
17_C22_A1.4070.86
39_R132_R1.4000.85
15_M19_G1.3860.84
227_L230_I1.3850.84
244_F435_M1.3840.84
436_W443_W1.3820.84
95_C170_G1.3790.84
451_W462_R1.3750.84
455_A464_F1.3750.84
250_I254_A1.3670.83
192_L209_A1.3500.82
245_I259_S1.3500.82
133_S392_G1.3390.81
6_G10_A1.3300.81
173_G409_L1.3300.81
373_D378_T1.3290.81
116_A405_V1.3280.81
22_A25_C1.3190.80
117_L146_I1.3110.80
35_A38_S1.3070.79
12_Q15_M1.3060.79
222_L250_I1.2960.78
329_D333_I1.2950.78
144_F335_G1.2930.78
22_A40_F1.2900.78
441_S445_G1.2830.77
248_N287_T1.2820.77
420_K444_L1.2810.77
199_S228_L1.2760.77
452_S459_L1.2740.77
48_V335_G1.2730.77
123_L126_K1.2660.76
238_C299_C1.2580.75
453_L456_P1.2500.75
350_S354_V1.2480.75
224_G284_V1.2390.74
149_G454_A1.2310.73
179_L183_V1.2260.73
216_L447_F1.2260.73
41_M45_I1.2240.73
12_Q18_G1.2190.72
289_S438_K1.2170.72
22_A42_Y1.2070.71
14_A17_C1.2000.70
158_P335_G1.1970.70
116_A223_T1.1950.70
149_G153_G1.1850.69
366_V369_E1.1820.69
165_A169_V1.1760.68
112_A405_V1.1750.68
241_N397_W1.1740.68
365_R369_E1.1710.68
18_G26_C1.1700.68
329_D332_N1.1700.68
133_S277_S1.1670.67
26_C30_P1.1670.67
399_M418_W1.1660.67
113_C154_A1.1650.67
210_L214_T1.1620.67
190_H277_S1.1600.67
13_C22_A1.1590.67
18_G28_A1.1580.67
240_I244_F1.1570.66
145_L148_F1.1560.66
252_C280_T1.1550.66
345_Y348_I1.1520.66
171_L180_V1.1520.66
333_I337_V1.1500.66
49_G111_M1.1480.66
315_T318_A1.1470.65
14_A20_T1.1430.65
175_L399_M1.1410.65
118_M186_V1.1390.65
13_C23_S1.1360.64
459_L464_F1.1360.64
313_A316_T1.1350.64
119_S350_S1.1260.63
38_S133_S1.1240.63
313_A322_H1.1200.63
343_I347_C1.1200.63
8_C12_Q1.1180.63
16_C20_T1.1150.62
233_T342_C1.1130.62
286_L445_G1.1120.62
114_F173_G1.1090.62
17_C37_S1.1090.62
250_I257_V1.1090.62
275_Q282_Y1.1080.62
52_L118_M1.1070.61
265_Q455_A1.1060.61
409_L412_M1.1020.61
14_A461_N1.0980.60
168_W217_C1.0760.58
214_T457_I1.0750.58
364_K367_L1.0750.58
39_R389_E1.0730.58
116_A119_S1.0720.58
386_T411_V1.0720.58
126_K285_Y1.0700.58
181_Q274_L1.0700.58
29_C35_A1.0670.57
448_I454_A1.0630.57
271_S293_N1.0620.57
456_P462_R1.0620.57
169_V199_S1.0580.56
361_N370_A1.0580.56
276_S286_L1.0550.56
95_C412_M1.0510.55
318_A321_T1.0510.55
127_S298_E1.0510.55
40_F135_I1.0510.55
21_A26_C1.0500.55
45_I144_F1.0500.55
268_L463_D1.0460.55
249_L254_A1.0450.55
232_F430_G1.0440.55
267_R457_I1.0430.55
365_R370_A1.0420.54
283_T446_V1.0420.54
452_S462_R1.0420.54
25_C385_S1.0410.54
295_P432_E1.0410.54
129_R276_S1.0380.54
459_L462_R1.0370.54
14_A23_S1.0330.54
83_L87_S1.0330.54
136_Q432_E1.0320.53
295_P438_K1.0320.53
10_A13_C1.0310.53
167_M431_N1.0300.53
45_I147_C1.0270.53
183_V453_L1.0260.53
195_N199_S1.0260.53
229_Y236_T1.0260.53
227_L231_Y1.0220.52
215_L219_I1.0220.52
311_G318_A1.0210.52
176_A346_N1.0210.52
186_V446_V1.0200.52
210_L265_Q1.0190.52
14_A32_C1.0190.52
223_T276_S1.0180.52
188_F192_L1.0150.52
98_A193_A1.0140.51
332_N339_W1.0120.51
129_R398_S1.0120.51
287_T442_S1.0090.51
243_F250_I1.0060.51
451_W464_F1.0060.51
24_M30_P1.0050.50
260_I373_D1.0010.50
193_A274_L1.0010.50
16_C24_M1.0010.50
110_G150_A1.0010.50
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  
4ymkA209.80.983Contact Map
3j1rA210.05598.70.983Contact Map
4zw9A104.50.985Contact Map
4he8A20.19144.10.985Contact Map
3dl8E20.13764.10.985Contact Map
4k5yA30.49253.90.986Contact Map
4pypA10.64092.80.987Contact Map
4mzzA20.06882.40.987Contact Map
3rkoA20.19572.10.987Contact Map
4bgnA20.410820.988Contact 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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