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bbs_2_full -force run

ID: 1505240139 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 721 (683)
Sequences: 291 (216.4)
Seq/Len: 0.426
Nf(neff/√len): 8.3

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: 0.426).

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 > 50% 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
251_D256_G2.7680.98
255_D259_E2.5850.96
24_Y32_A2.4710.95
251_D255_D2.3200.92
219_Y227_G2.2380.90
253_N259_E1.7440.69
251_D259_E1.7390.68
77_C120_A1.6510.62
691_K710_L1.6370.61
402_L427_S1.5840.58
90_D101_L1.5550.55
262_T270_D1.5400.54
105_V110_D1.5300.54
296_D301_G1.5280.54
15_S18_M1.5240.53
90_D95_G1.5220.53
185_D189_R1.5030.52
505_E509_R1.4920.51
621_I648_Y1.4780.50
183_S191_F1.4690.49
161_D251_D1.4670.49
100_L306_I1.4660.49
182_G206_I1.4610.49
223_N236_W1.4540.48
3_Q37_A1.4520.48
18_M75_V1.4460.47
558_T564_A1.4410.47
93_L136_A1.4320.46
92_L102_A1.4290.46
8_L28_H1.4160.45
461_V484_Y1.4160.45
102_A136_A1.4080.45
26_G29_P1.4000.44
65_D83_L1.3980.44
92_L138_I1.3930.44
6_F31_L1.3920.43
654_L679_I1.3820.43
564_A580_L1.3770.42
455_L600_V1.3730.42
402_L535_F1.3700.42
675_V678_A1.3690.42
34_A37_A1.3660.42
170_D178_E1.3650.42
90_D264_W1.3640.41
21_V295_G1.3530.41
607_H610_L1.3500.40
270_D355_Y1.3490.40
93_L102_A1.3450.40
312_G348_L1.3400.40
289_I352_L1.3380.40
43_H81_G1.3250.39
226_V289_I1.3140.38
673_K685_L1.3070.37
570_S586_F1.3040.37
26_G81_G1.3010.37
221_L227_G1.2960.37
164_H184_E1.2940.37
611_S614_M1.2940.37
188_I222_S1.2890.36
156_W199_E1.2870.36
184_E269_V1.2870.36
220_A224_G1.2870.36
124_V252_L1.2860.36
217_F239_K1.2850.36
82_V87_L1.2850.36
515_N519_L1.2810.36
685_L688_G1.2770.35
291_G306_I1.2730.35
379_A383_H1.2710.35
18_M67_S1.2680.35
423_F426_E1.2680.35
71_I75_V1.2670.35
103_Y108_N1.2630.34
217_F234_R1.2600.34
146_G151_G1.2580.34
157_T191_F1.2520.34
163_V179_L1.2510.34
270_D454_D1.2490.34
514_L642_N1.2470.33
664_N672_L1.2460.33
680_Q684_H1.2460.33
156_W202_E1.2400.33
651_N655_L1.2390.33
688_G699_R1.2370.33
269_V401_E1.2340.33
613_D636_D1.2320.32
18_M22_G1.2290.32
452_P483_M1.2280.32
158_V182_G1.2280.32
495_P559_D1.2270.32
251_D263_G1.2260.32
11_R44_N1.2240.32
123_I219_Y1.2240.32
238_I402_L1.2240.32
519_L567_I1.2210.32
5_V13_K1.2200.32
227_G236_W1.2150.31
506_R509_R1.2150.31
26_G33_A1.2140.31
13_K32_A1.2140.31
40_V72_N1.2130.31
179_L202_E1.2120.31
673_K703_R1.2110.31
4_P26_G1.2100.31
202_E234_R1.2090.31
223_N240_S1.2070.31
10_L34_A1.2050.31
100_L147_F1.2050.31
340_E344_K1.2030.31
644_Y679_I1.2030.31
137_I149_H1.2000.30
560_D569_Q1.1970.30
4_P35_T1.1930.30
25_D35_T1.1910.30
296_D345_K1.1910.30
17_R29_P1.1890.30
14_I21_V1.1880.30
37_A635_R1.1870.30
114_R120_A1.1870.30
518_F644_Y1.1840.29
4_P24_Y1.1830.29
313_E317_Y1.1830.29
14_I17_R1.1830.29
390_S412_I1.1810.29
214_G232_T1.1770.29
94_V226_V1.1760.29
688_G698_C1.1720.29
480_R622_R1.1700.29
119_G179_L1.1690.28
672_L686_R1.1690.28
217_F229_Y1.1640.28
115_E120_A1.1620.28
19_V23_R1.1600.28
182_G192_K1.1570.28
688_G701_A1.1570.28
4_P32_A1.1560.28
34_A76_S1.1550.28
113_Y157_T1.1550.28
194_D268_K1.1520.27
263_G267_G1.1520.27
251_D261_I1.1480.27
28_H44_N1.1470.27
180_L213_Y1.1470.27
221_L229_Y1.1470.27
314_I706_N1.1470.27
234_R237_R1.1450.27
4_P9_K1.1450.27
417_I425_G1.1440.27
217_F221_L1.1440.27
591_E598_V1.1440.27
92_L110_D1.1430.27
44_N67_S1.1430.27
151_G155_F1.1410.27
21_V80_A1.1400.27
455_L501_F1.1380.27
379_A385_T1.1380.27
285_F305_L1.1360.27
4_P25_D1.1350.26
21_V29_P1.1340.26
5_V32_A1.1330.26
76_S138_I1.1320.26
4_P12_H1.1310.26
33_A67_S1.1310.26
261_I455_L1.1310.26
159_T183_S1.1290.26
252_L255_D1.1280.26
90_D96_T1.1270.26
21_V34_A1.1270.26
179_L194_D1.1270.26
443_I447_P1.1240.26
18_M44_N1.1220.26
191_F220_A1.1220.26
71_I94_V1.1210.26
170_D352_L1.1200.26
103_Y164_H1.1200.26
108_N341_L1.1200.26
76_S80_A1.1180.26
229_Y234_R1.1180.26
682_A686_R1.1160.25
421_G425_G1.1150.25
673_K686_R1.1150.25
100_L145_Q1.1150.25
26_G75_V1.1120.25
175_G178_E1.1120.25
268_K291_G1.1110.25
514_L545_Y1.1110.25
668_L679_I1.1090.25
236_W348_L1.1080.25
600_V618_S1.1080.25
11_R20_A1.1070.25
7_T16_P1.1070.25
701_A713_I1.1070.25
167_A173_G1.1060.25
5_V11_R1.1060.25
214_G245_M1.1060.25
19_V338_I1.1050.25
587_P628_A1.1050.25
250_F305_L1.1040.25
670_G684_H1.1040.25
21_V33_A1.1020.25
688_G695_I1.1020.25
420_E468_Q1.1010.25
170_D175_G1.1000.25
694_V706_N1.1000.25
4_P39_K1.0990.24
261_I294_E1.0990.24
238_I268_K1.0990.24
159_T162_N1.0960.24
5_V21_V1.0950.24
29_P33_A1.0950.24
37_A74_T1.0940.24
226_V256_G1.0910.24
515_N537_S1.0910.24
143_A153_D1.0910.24
219_Y351_E1.0900.24
95_G108_N1.0880.24
153_D156_W1.0880.24
576_A633_L1.0860.24
146_G412_I1.0860.24
137_I287_S1.0850.24
13_K24_Y1.0840.24
424_A482_S1.0840.24
9_K17_R1.0820.24
622_R660_I1.0810.23
255_D289_I1.0800.23
679_I701_A1.0800.23
41_F71_I1.0750.23
11_R71_I1.0740.23
20_A74_T1.0740.23
34_A42_I1.0730.23
103_Y240_S1.0730.23
679_I686_R1.0730.23
634_M683_G1.0720.23
70_N73_Q1.0710.23
10_L13_K1.0710.23
68_L80_A1.0710.23
247_I250_F1.0710.23
405_S408_N1.0710.23
629_E651_N1.0710.23
144_L309_S1.0700.23
74_T82_V1.0690.23
139_G272_R1.0690.23
217_F272_R1.0690.23
604_H647_L1.0690.23
255_D263_G1.0680.23
462_G479_P1.0660.23
178_E182_G1.0650.23
520_L544_L1.0650.23
36_Q68_L1.0640.23
8_L31_L1.0640.23
4_P43_H1.0630.23
137_I633_L1.0630.23
204_E287_S1.0630.23
21_V65_D1.0600.22
306_I309_S1.0590.22
616_D686_R1.0590.22
22_G35_T1.0580.22
79_T82_V1.0580.22
503_I577_I1.0580.22
657_G660_I1.0580.22
103_Y140_G1.0570.22
194_D202_E1.0570.22
224_G227_G1.0560.22
44_N65_D1.0550.22
148_N160_G1.0540.22
92_L136_A1.0540.22
569_Q582_V1.0530.22
14_I19_V1.0520.22
28_H613_D1.0520.22
142_C159_T1.0510.22
21_V154_L1.0510.22
119_G223_N1.0510.22
682_A685_L1.0510.22
237_R282_K1.0500.22
25_D28_H1.0490.22
419_A456_H1.0490.22
32_A80_A1.0490.22
244_A259_E1.0480.22
16_P44_N1.0480.22
25_D29_P1.0460.22
523_D533_V1.0460.22
533_V541_G1.0460.22
104_D108_N1.0450.22
157_T183_S1.0440.22
688_G717_G1.0440.22
78_L467_T1.0440.22
105_V108_N1.0420.21
452_P461_V1.0410.21
627_Q630_D1.0410.21
96_T108_N1.0410.21
99_N115_E1.0410.21
164_H185_D1.0400.21
218_G221_L1.0400.21
268_K305_L1.0400.21
226_V261_I1.0400.21
259_E263_G1.0400.21
357_E427_S1.0400.21
193_E270_D1.0380.21
110_D139_G1.0360.21
705_N713_I1.0360.21
21_V66_V1.0350.21
106_Y109_S1.0340.21
559_D565_G1.0330.21
90_D108_N1.0320.21
240_S425_G1.0320.21
306_I428_H1.0310.21
23_R44_N1.0290.21
664_N679_I1.0290.21
117_A133_S1.0270.21
139_G146_G1.0270.21
14_I39_K1.0250.21
25_D31_L1.0250.21
481_F586_F1.0250.21
104_D204_E1.0240.21
8_L32_A1.0240.21
250_F336_D1.0240.21
9_K21_V1.0230.21
19_V33_A1.0230.21
458_K674_A1.0230.21
653_D656_N1.0220.21
673_K688_G1.0220.21
613_D683_G1.0210.20
241_K264_W1.0200.20
562_D601_D1.0200.20
25_D43_H1.0200.20
316_G340_E1.0180.20
4_P8_L1.0170.20
644_Y668_L1.0170.20
17_R42_I1.0170.20
95_G155_F1.0170.20
13_K73_Q1.0160.20
41_F76_S1.0150.20
157_T160_G1.0150.20
137_I147_F1.0140.20
17_R33_A1.0140.20
685_L695_I1.0140.20
575_F582_V1.0130.20
480_R690_P1.0120.20
559_D649_D1.0110.20
589_Y592_E1.0110.20
10_L412_I1.0110.20
28_H35_T1.0110.20
113_Y136_A1.0110.20
654_L668_L1.0110.20
21_V67_S1.0100.20
371_D415_V1.0090.20
671_S684_H1.0090.20
20_A36_Q1.0090.20
96_T449_K1.0090.20
100_L160_G1.0080.20
95_G100_L1.0080.20
684_H687_V1.0080.20
312_G316_G1.0060.20
687_V698_C1.0060.20
3_Q9_K1.0050.20
355_Y358_N1.0050.20
448_P452_P1.0050.20
239_K268_K1.0040.20
20_A266_N1.0040.20
20_A32_A1.0020.20
65_D80_A1.0020.20
380_N383_H1.0020.20
142_C156_W1.0010.20
43_H80_A1.0010.20
121_S207_T1.0000.19
269_V327_N1.0000.19
225_T237_R1.0000.19
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  
3odtA20.393999.40.935Contact Map
4g56B20.388399.40.937Contact Map
1gxrA20.402299.30.94Contact Map
4yvdA10.393999.20.941Contact Map
2hesX10.371799.20.941Contact Map
2pbiB20.400899.20.941Contact Map
4e54B10.395399.20.941Contact Map
4zoyA1099.20.941Contact Map
1r5mA10.373199.20.942Contact Map
4gqbB10.398199.20.942Contact 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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