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OPENSEQ.org

c-Src full lenght

ID: 1468577524 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 536 (454)
Sequences: 633 (359.8)
Seq/Len: 1.394
Nf(neff/√len): 16.9

HHblits Results: (2016_02)
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: 1.394).

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
135_I140_V3.1261.00
232_Y238_D2.5751.00
272_L297_I2.4961.00
133_G136_P2.4861.00
467_P484_M2.3190.99
135_I138_N2.1890.99
173_G178_R2.0690.98
503_R508_E2.0450.98
270_L297_I2.0230.98
97_S104_S2.0110.98
152_Y179_E1.9760.97
158_R162_E1.9250.97
287_G297_I1.8720.96
509_R512_F1.8510.96
165_L180_S1.8480.96
113_I124_A1.8020.95
158_R161_S1.7760.94
136_P139_Y1.7700.94
370_A455_L1.7560.94
295_V298_K1.7540.94
412_R419_Y1.7540.94
482_Y485_P1.7520.94
380_V391_R1.7420.94
380_V393_A1.7420.94
133_G139_Y1.7370.94
109_E126_S1.7350.93
124_A135_I1.7200.93
158_R178_R1.7040.93
151_W158_R1.6860.92
346_K357_T1.6270.90
486_C492_E1.6260.90
277_G284_V1.6250.90
175_F178_R1.6240.90
176_L179_E1.6140.90
253_P258_L1.5990.89
389_D407_D1.5950.89
179_E185_G1.5360.86
165_L178_R1.5280.86
264_E333_S1.5210.86
173_G180_S1.5150.85
336_P339_I1.4760.83
123_L132_T1.4740.83
170_N180_S1.4680.83
349_L353_L1.4600.82
264_E276_L1.4480.82
279_G284_V1.4430.81
133_G140_V1.4400.81
161_S178_R1.4350.81
361_L366_L1.4310.81
331_V336_P1.4210.80
313_E317_M1.4190.80
158_R165_L1.4150.80
226_L230_V1.4140.80
394_N404_K1.4130.80
135_I139_Y1.4120.79
456_T463_R1.4080.79
394_N408_F1.4070.79
368_D372_Q1.4010.79
290_N293_T1.3970.78
174_T249_P1.3940.78
432_T436_A1.3880.78
224_N228_Q1.3780.77
267_R283_E1.3740.77
181_E188_C1.3690.76
407_D428_P1.3670.76
389_D394_N1.3640.76
521_D530_Y1.3600.76
158_R180_S1.3600.76
498_M502_W1.3480.75
326_V343_Y1.3270.73
103_L124_A1.3250.73
152_Y162_E1.3190.73
389_D408_F1.3180.73
265_I270_L1.3150.72
253_P257_G1.3120.72
445_K448_V1.3020.71
505_E508_E1.2970.71
301_K325_L1.2940.71
94_D106_K1.2920.70
388_R412_R1.2910.70
133_G138_N1.2850.70
462_G465_P1.2780.69
373_I405_V1.2730.69
430_K467_P1.2730.69
370_A458_L1.2690.68
317_M326_V1.2690.68
279_G282_G1.2650.68
263_W318_K1.2640.68
240_L265_I1.2630.68
502_W509_R1.2600.68
275_K283_E1.2570.67
313_E322_H1.2570.67
277_G296_A1.2520.67
269_S290_N1.2380.66
404_K407_D1.2340.65
394_N407_D1.2330.65
424_G427_F1.2280.65
404_K408_F1.2250.64
169_E192_S1.2240.64
456_T459_T1.2230.64
281_F284_V1.2170.64
171_P174_T1.2170.64
173_G177_V1.2140.63
103_L108_G1.2120.63
502_W512_F1.2120.63
276_L284_V1.2100.63
369_M405_V1.2080.63
439_Y480_R1.2080.63
429_I443_T1.2070.63
286_M294_R1.2070.63
477_Q480_R1.2040.62
500_Q518_F1.1990.62
118_E340_V1.1910.61
111_L126_S1.1900.61
477_Q482_Y1.1890.61
151_W162_E1.1850.61
136_P140_V1.1820.60
126_S129_T1.1780.60
255_T258_L1.1770.60
139_Y158_R1.1770.60
102_D140_V1.1730.59
177_V180_S1.1730.59
354_K391_R1.1660.59
457_E462_G1.1600.58
289_W332_V1.1560.58
242_H245_T1.1530.57
125_H132_T1.1530.57
516_Q519_L1.1520.57
389_D404_K1.1470.57
175_F180_S1.1470.57
435_E449_W1.1420.56
457_E465_P1.1400.56
170_N176_L1.1390.56
442_F475_L1.1340.56
425_A429_I1.1340.56
322_H328_L1.1310.55
448_V457_E1.1220.54
288_T294_R1.1210.54
460_T487_P1.1200.54
96_E106_K1.1200.54
388_R392_A1.1190.54
204_H223_F1.1180.54
158_R190_S1.1170.54
279_G298_K1.1170.54
330_A456_T1.1160.54
162_E165_L1.1160.54
299_T343_Y1.1150.54
257_G327_Q1.1140.54
310_F313_E1.1120.53
524_T531_Q1.1120.53
265_I340_V1.1110.53
187_Y190_S1.1110.53
226_L233_Y1.1080.53
274_V286_M1.1030.52
457_E466_Y1.1010.52
348_S395_I1.1010.52
205_Y239_G1.0990.52
481_G487_P1.0990.52
124_A138_N1.0950.52
165_L173_G1.0940.52
91_A95_Y1.0920.51
472_R476_D1.0920.51
99_T290_N1.0910.51
321_R327_Q1.0880.51
373_I454_L1.0850.51
95_Y269_S1.0850.51
506_P509_R1.0840.51
233_Y395_I1.0810.50
435_E447_D1.0800.50
377_M390_L1.0790.50
310_F339_I1.0760.50
529_Q533_G1.0750.50
93_Y138_N1.0730.49
424_G429_I1.0730.49
435_E452_G1.0720.49
452_G462_G1.0710.49
182_T188_C1.0690.49
437_A450_S1.0670.49
388_R408_F1.0650.49
385_Y451_F1.0620.48
328_L336_P1.0620.48
388_R407_D1.0590.48
387_H394_N1.0580.48
298_K322_H1.0580.48
284_V298_K1.0550.48
473_E477_Q1.0540.48
165_L190_S1.0530.47
305_M317_M1.0520.47
452_G465_P1.0510.47
389_D428_P1.0510.47
264_E336_P1.0490.47
269_S376_G1.0490.47
377_M394_N1.0440.47
185_G188_C1.0430.46
310_F328_L1.0430.46
203_K208_R1.0430.46
162_E180_S1.0400.46
110_R143_S1.0390.46
377_M388_R1.0390.46
191_V241_C1.0380.46
281_F295_V1.0370.46
442_F467_P1.0360.46
165_L175_F1.0360.46
496_D500_Q1.0360.46
277_G313_E1.0350.46
298_K344_M1.0320.45
136_P190_S1.0320.45
244_L279_G1.0320.45
478_V481_G1.0290.45
216_Y225_S1.0270.45
314_A317_M1.0250.45
158_R173_G1.0240.44
431_W435_E1.0230.44
351_D423_Q1.0220.44
373_I395_I1.0190.44
166_L234_S1.0190.44
314_A331_V1.0180.44
377_M408_F1.0180.44
318_K330_A1.0170.44
151_W154_G1.0140.43
432_T469_M1.0140.43
254_Q258_L1.0130.43
277_G298_K1.0120.43
154_G505_E1.0100.43
298_K313_E1.0090.43
304_T314_A1.0090.43
296_A317_M1.0070.43
322_H342_E1.0070.43
429_I467_P1.0050.43
108_G133_G1.0040.42
166_L170_N1.0030.42
487_P502_W1.0020.42
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  
2h8hA10.82841000.375Contact Map
1fmkA10.81531000.405Contact Map
1qcfA10.83771000.416Contact Map
4xi2A10.77611000.446Contact Map
1opkA10.82281000.454Contact Map
1k9aA60.80781000.458Contact Map
4fl3A10.84331000.514Contact Map
2ozoA10.85261000.539Contact Map
3cblA10.65491000.564Contact Map
4rt7A101000.661Contact 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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