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OPENSEQ.org

AraC GapRand FL 0it

ID: 1497556640 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 501 (501)
Sequences: 987 (987)
Seq/Len: 1.970
Nf(neff/√len): 44.1

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: 1.970).

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
443_P447_R1.7390.97
213_H217_N1.6940.96
265_H298_E1.6900.96
406_K411_T1.6540.95
321_A337_N1.6470.95
267_S271_G1.6290.95
275_N295_G1.5990.94
345_Y349_H1.5540.93
163_Q262_H1.5460.92
275_N320_E1.5430.92
262_H320_E1.5290.92
217_N275_N1.5110.91
271_G302_S1.5040.91
99_L108_F1.4890.90
94_A157_V1.4870.90
435_F443_P1.4790.90
137_R140_G1.4380.88
262_H321_A1.4360.88
264_P298_E1.4360.88
389_L393_V1.4350.88
431_F435_F1.4330.88
262_H267_S1.4240.88
158_K167_E1.4220.88
114_A274_I1.4210.88
274_I395_S1.4170.87
271_G298_E1.4120.87
275_N298_E1.4070.87
275_N358_N1.4010.87
267_S298_E1.3980.86
150_T153_G1.3890.86
429_L432_S1.3820.85
267_S274_I1.3790.85
295_G302_S1.3700.85
265_H275_N1.3470.83
275_N337_N1.3420.83
151_I252_F1.3360.83
220_S248_N1.3290.82
122_N298_E1.3290.82
444_S447_R1.3190.82
424_G435_F1.3170.82
265_H426_D1.3120.81
163_Q275_N1.3080.81
108_F115_G1.3060.81
220_S263_Q1.3010.80
320_E337_N1.3010.80
445_E448_A1.2970.80
432_S442_S1.2960.80
108_F117_T1.2910.80
271_G295_G1.2900.80
262_H275_N1.2900.80
263_Q271_G1.2840.79
134_F164_G1.2790.79
121_A129_G1.2790.79
257_A274_I1.2770.79
424_G443_P1.2750.79
199_W203_W1.2720.78
377_S380_R1.2700.78
442_S447_R1.2690.78
430_Y443_P1.2630.78
97_D111_H1.2630.78
443_P446_F1.2570.77
441_A448_A1.2550.77
335_M426_D1.2540.77
115_G132_D1.2520.77
249_T252_F1.2490.77
407_L417_A1.2470.76
158_K220_S1.2470.76
432_S435_F1.2450.76
114_A395_S1.2440.76
102_P108_F1.2410.76
188_R205_Y1.2370.76
262_H337_N1.2350.75
263_Q295_G1.2330.75
435_F447_R1.2320.75
262_H358_N1.2320.75
217_N264_P1.2310.75
135_I313_L1.2260.75
99_L117_T1.2250.75
163_Q298_E1.2230.74
396_W400_Q1.2220.74
427_D430_Y1.2220.74
163_Q265_H1.2200.74
115_G119_I1.2160.74
442_S446_F1.2140.74
416_I446_F1.2140.74
113_V117_T1.2100.73
168_F179_P1.2090.73
399_D434_V1.2070.73
141_M144_G1.2070.73
117_T132_D1.2040.73
432_S443_P1.2020.73
379_S383_H1.1990.72
177_L180_P1.1950.72
430_Y435_F1.1950.72
431_F443_P1.1930.72
248_N268_D1.1890.71
119_I135_I1.1840.71
167_E220_S1.1840.71
114_A122_N1.1790.70
429_L442_S1.1760.70
267_S337_N1.1750.70
99_L113_V1.1720.70
99_L118_P1.1700.70
424_G431_F1.1670.69
262_H274_I1.1650.69
440_G443_P1.1610.69
163_Q175_I1.1600.69
158_K165_R1.1570.68
391_I426_D1.1570.68
424_G430_Y1.1560.68
163_Q358_N1.1540.68
108_F118_P1.1540.68
115_G118_P1.1520.68
165_R262_H1.1480.68
275_N321_A1.1470.67
97_D104_Y1.1450.67
98_P108_F1.1440.67
195_E248_N1.1430.67
430_Y447_R1.1430.67
439_T446_F1.1430.67
267_S395_S1.1410.67
122_N151_I1.1400.67
208_P212_W1.1400.67
122_N275_N1.1380.67
305_L308_N1.1370.66
99_L115_G1.1360.66
199_W206_F1.1330.66
113_V118_P1.1330.66
310_L314_L1.1330.66
199_W208_P1.1320.66
108_F113_V1.1320.66
150_T155_G1.1280.66
265_H335_M1.1270.65
108_F132_D1.1270.65
99_L132_D1.1260.65
172_P266_F1.1210.65
342_A364_V1.1160.64
263_Q267_S1.1160.64
267_S275_N1.1110.64
103_G112_L1.1110.64
428_Q444_S1.1070.63
201_H205_Y1.1060.63
435_F440_G1.1060.63
167_E248_N1.1060.63
179_P263_Q1.1050.63
163_Q267_S1.1050.63
132_D144_G1.1040.63
298_E335_M1.1030.63
457_V462_S1.1020.63
264_P268_D1.1020.63
252_F271_G1.1010.63
99_L102_P1.0980.62
115_G131_L1.0970.62
323_N333_P1.0960.62
364_V373_H1.0950.62
197_R265_H1.0940.62
140_G153_G1.0940.62
430_Y442_S1.0930.62
373_H378_P1.0910.62
407_L428_Q1.0910.62
222_F228_A1.0910.62
110_A114_A1.0900.62
203_W206_F1.0880.61
165_R220_S1.0880.61
374_V378_P1.0860.61
302_S335_M1.0840.61
113_V131_L1.0820.61
220_S358_N1.0810.61
342_A399_D1.0810.61
122_N264_P1.0810.61
175_I426_D1.0800.61
409_L424_G1.0800.61
417_A428_Q1.0800.61
130_Y189_H1.0790.60
458_A461_L1.0790.60
95_Q100_L1.0780.60
401_R409_L1.0750.60
302_S391_I1.0750.60
405_A409_L1.0750.60
222_F387_Q1.0740.60
110_A118_P1.0740.60
377_S383_H1.0740.60
431_F447_R1.0730.60
113_V119_I1.0710.60
250_G303_E1.0700.60
386_R399_D1.0700.60
140_G150_T1.0690.59
436_K439_T1.0690.59
335_M391_I1.0690.59
154_Q157_V1.0690.59
267_S320_E1.0680.59
104_Y108_F1.0680.59
401_R424_G1.0670.59
265_H274_I1.0660.59
113_V132_D1.0620.59
379_S385_F1.0610.59
199_W212_W1.0590.58
407_L410_S1.0560.58
435_F442_S1.0550.58
408_L424_G1.0540.58
203_W208_P1.0540.58
434_V442_S1.0530.58
197_R220_S1.0520.58
427_D432_S1.0520.58
432_S447_R1.0520.58
116_L134_F1.0510.57
439_T448_A1.0500.57
108_F119_I1.0500.57
453_K457_V1.0490.57
380_R383_H1.0480.57
424_G447_R1.0460.57
170_C294_Q1.0460.57
102_P116_L1.0430.57
200_Y211_Y1.0420.56
212_W218_W1.0420.56
378_P384_L1.0420.56
118_P132_D1.0420.56
273_I309_L1.0410.56
377_S385_F1.0410.56
164_G295_G1.0390.56
137_R150_T1.0390.56
377_S384_L1.0390.56
411_T420_G1.0380.56
401_R405_A1.0360.56
131_L141_M1.0350.56
271_G293_G1.0350.56
272_Q298_E1.0340.56
99_L104_Y1.0340.56
98_P118_P1.0330.55
199_W216_L1.0310.55
405_A424_G1.0300.55
163_Q320_E1.0300.55
95_Q102_P1.0300.55
154_Q171_R1.0290.55
380_R384_L1.0270.55
151_I391_I1.0250.55
171_R174_D1.0250.55
95_Q103_G1.0230.54
348_D359_F1.0200.54
118_P131_L1.0200.54
213_H298_E1.0190.54
293_G306_A1.0180.54
217_N262_H1.0180.54
380_R385_F1.0180.54
137_R153_G1.0170.54
147_L151_I1.0150.54
293_G333_P1.0150.54
186_Y199_W1.0140.53
197_R213_H1.0140.53
412_T423_V1.0120.53
267_S321_A1.0120.53
132_D137_R1.0090.53
116_L136_D1.0070.53
348_D414_M1.0070.53
428_Q438_C1.0070.53
168_F176_L1.0060.53
182_E263_Q1.0060.53
453_K456_D1.0060.53
220_S275_N1.0060.53
86_L89_C1.0060.53
132_D140_G1.0060.53
386_R434_V1.0060.53
212_W216_L1.0050.52
175_I217_N1.0040.52
293_G319_M1.0040.52
115_G135_I1.0040.52
264_P426_D1.0040.52
254_P399_D1.0040.52
98_P117_T1.0030.52
117_T131_L1.0020.52
94_A295_G1.0020.52
179_P182_E1.0010.52
99_L109_N1.0010.52
254_P299_G1.0010.52
453_K462_S1.0000.52
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  
3gbgA10.51799.90.75Contact Map
2k9sA10.213699.80.798Contact Map
3oioA10.223699.80.803Contact Map
3oouA10.209699.80.803Contact Map
1bl0A10.231599.80.803Contact Map
3mn2A20.211699.80.804Contact Map
3w6vA10.221699.80.809Contact Map
3mklA20.221699.80.811Contact Map
3lsgA50.205699.80.815Contact Map
1d5yA40.311499.70.822Contact 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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