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Francisella tularensis large sub

ID: 1517304688 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 514 (432)
Sequences: 608 (284.3)
Seq/Len: 1.407
Nf(neff/√len): 13.7

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: 1.407).

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
97_N279_F5.6551.00
175_L301_V4.8281.00
242_F251_I4.0881.00
260_L294_G3.2731.00
291_Y332_C3.0831.00
177_L298_I2.8281.00
266_P280_N2.5591.00
205_I300_L2.3370.99
251_I383_A2.3000.99
96_V99_I2.2780.99
242_F383_A2.2760.99
201_H250_Y2.2430.99
252_G382_S2.1760.99
241_D373_S2.1710.99
134_K137_E2.1520.99
173_A304_M2.1040.98
116_Q120_Q2.0630.98
331_A342_T2.0030.98
303_N306_R2.0010.98
288_N343_K1.9940.98
257_D347_N1.9290.97
127_E169_E1.9160.97
212_F363_L1.8840.96
176_G204_F1.8810.96
184_T262_Q1.8760.96
110_Q292_L1.8620.96
132_D137_E1.8120.95
129_S171_Y1.7510.94
92_I96_V1.7110.93
244_N385_K1.6980.93
254_T296_A1.6820.92
403_N492_E1.6810.92
107_A179_N1.6690.92
442_I467_I1.6250.90
287_K290_S1.5700.88
110_Q294_G1.5640.88
447_T452_P1.5500.87
180_F189_W1.5250.86
140_Y272_Q1.4910.84
430_D433_S1.4760.84
265_N268_N1.4710.83
285_Y290_S1.4560.82
154_F193_M1.4520.82
316_Y454_P1.4460.82
160_V351_A1.4340.81
124_D228_E1.4230.80
380_V405_S1.4080.79
94_L279_F1.4010.79
117_E121_E1.3980.79
252_G364_I1.3970.79
198_K247_V1.3960.79
282_F290_S1.3910.78
193_M204_F1.3870.78
356_L360_N1.3800.78
258_F294_G1.3780.77
318_R490_Q1.3750.77
87_V90_K1.3750.77
213_F363_L1.3670.77
365_P382_S1.3610.76
245_L296_A1.3440.75
90_K98_S1.3400.75
413_I485_V1.3310.74
288_N332_C1.3300.74
450_Y463_R1.3220.73
450_Y457_M1.3210.73
143_E188_I1.3180.73
114_K298_I1.3060.72
90_K94_L1.3050.72
218_L485_V1.3030.72
97_N101_S1.2990.71
158_V420_V1.2870.70
141_D213_F1.2830.70
208_I212_F1.2780.69
88_I92_I1.2770.69
417_I483_I1.2760.69
238_E463_R1.2720.69
389_F444_E1.2660.68
478_W493_G1.2550.67
103_D118_V1.2530.67
166_Y201_H1.2480.67
157_K161_S1.2410.66
176_G297_S1.2390.66
435_Q439_S1.2280.65
163_F250_Y1.2260.65
175_L297_S1.2190.64
464_N486_I1.2170.64
359_A379_S1.2160.64
85_I107_A1.2140.64
265_N280_N1.2140.64
128_V172_G1.1980.62
178_Y202_A1.1900.61
106_R292_L1.1810.61
214_G236_Y1.1740.60
249_A401_I1.1720.60
430_D486_I1.1700.59
397_N469_V1.1690.59
228_E361_I1.1670.59
172_G314_F1.1620.59
359_A382_S1.1540.58
387_E435_Q1.1540.58
326_V366_F1.1520.58
389_F398_S1.1410.57
85_I382_S1.1320.56
99_I252_G1.1270.55
332_C347_N1.1260.55
180_F190_L1.1230.55
165_Q351_A1.1230.55
433_S486_I1.1230.55
448_T457_M1.1200.54
258_F299_H1.1140.54
371_G486_I1.1140.54
354_M357_S1.1130.54
130_I336_N1.1130.54
108_L206_A1.1100.53
99_I269_N1.1070.53
175_L207_S1.1070.53
236_Y498_M1.1030.53
133_V393_F1.0980.52
365_P417_I1.0950.52
314_F408_M1.0890.51
193_M200_S1.0880.51
180_F370_K1.0880.51
148_D195_M1.0870.51
113_L194_G1.0850.51
325_Y372_T1.0830.51
103_D290_S1.0810.51
93_D97_N1.0810.51
96_V100_I1.0720.50
260_L292_L1.0710.50
405_S492_E1.0680.49
471_T506_P1.0680.49
160_V424_K1.0660.49
163_F431_V1.0590.48
380_V498_M1.0570.48
417_I438_L1.0560.48
141_D148_D1.0560.48
447_T456_E1.0540.48
191_T383_A1.0500.47
163_F208_I1.0490.47
176_G193_M1.0480.47
114_K464_N1.0470.47
103_D187_I1.0460.47
100_I105_F1.0460.47
315_Q409_C1.0450.47
219_S383_A1.0450.47
187_I383_A1.0450.47
132_D208_I1.0450.47
300_L413_I1.0430.47
386_V402_A1.0420.47
100_I107_A1.0370.46
92_I275_L1.0360.46
130_I237_K1.0360.46
325_Y369_E1.0320.46
119_C420_V1.0320.46
215_V229_A1.0310.45
103_D289_E1.0310.45
319_G324_G1.0300.45
148_D238_E1.0300.45
128_V498_M1.0290.45
190_L251_I1.0290.45
166_Y325_Y1.0260.45
300_L382_S1.0260.45
449_V452_P1.0240.45
176_G295_P1.0220.45
151_S350_F1.0200.44
215_V220_E1.0190.44
94_L136_E1.0180.44
318_R492_E1.0170.44
474_G502_T1.0170.44
126_V305_M1.0150.44
119_C128_V1.0140.44
488_H504_L1.0140.44
492_E496_T1.0130.44
194_G198_K1.0090.43
129_S467_I1.0080.43
128_V314_F1.0070.43
320_V376_C1.0070.43
397_N499_T1.0050.43
307_S431_V1.0030.43
124_D486_I1.0030.43
294_G379_S1.0030.43
164_D351_A1.0000.42
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  
3j9oB60.8211000.167Contact Map
2jxfA10.042829.40.985Contact Map
3cuqA10.206210.30.988Contact Map
4flnA30.14017.90.988Contact Map
3jstA20.11097.30.989Contact Map
2ebbA10.10516.80.989Contact Map
3cuqB10.19266.40.989Contact Map
2v6uA20.11676.20.989Contact Map
3j7aJ10.16735.80.989Contact Map
4bpe310.16545.50.989Contact 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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