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T0840 -force run

ID: 1404412421 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 669 (659)
Sequences: 66 (39.4)
Seq/Len: 0.100
Nf(neff/√len): 1.5

HHblits Results: (2013_03)
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: 0.100).

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
503_P521_M1.9040.37
258_L296_Y1.8650.35
529_M648_V1.6330.25
524_G540_W1.6110.24
297_P343_V1.6010.24
60_G543_D1.5700.23
19_D634_S1.5400.22
451_Q572_F1.5280.21
286_P589_V1.5210.21
157_A321_Q1.5050.21
356_I380_Q1.4890.20
431_V498_V1.4820.20
635_L661_E1.4700.19
152_C155_C1.4620.19
62_D228_V1.4620.19
359_G380_Q1.4610.19
158_S283_K1.4370.18
162_T517_A1.4210.18
327_V445_M1.4210.18
237_V267_E1.4160.18
565_L632_N1.4120.18
49_F465_S1.4050.17
225_I507_H1.4020.17
563_T566_T1.3980.17
17_D247_V1.3910.17
50_V229_H1.3900.17
347_F650_G1.3880.17
227_Y243_Q1.3870.17
33_V420_L1.3830.17
255_H476_V1.3830.17
227_Y558_P1.3820.17
175_F568_C1.3650.16
228_V265_E1.3620.16
510_T659_F1.3550.16
195_S243_Q1.3540.16
242_V456_R1.3540.16
415_D438_T1.3520.16
50_V546_P1.3500.16
508_F520_F1.3380.16
273_E302_A1.3350.16
182_D326_G1.3320.15
63_L126_L1.3270.15
223_Y563_T1.3260.15
245_A426_V1.3240.15
195_S227_Y1.3170.15
112_S124_H1.3150.15
194_V439_V1.3130.15
359_G363_C1.3110.15
285_V452_V1.3060.15
49_F144_A1.3040.15
237_V431_V1.2980.15
49_F491_S1.2980.15
124_H241_T1.2950.14
157_A487_L1.2940.14
363_C385_C1.2930.14
177_V499_P1.2870.14
226_E236_F1.2850.14
56_L565_L1.2830.14
176_Y323_V1.2820.14
439_V546_P1.2680.14
175_F451_Q1.2680.14
356_I359_G1.2630.14
608_P611_D1.2610.14
428_A593_P1.2610.14
156_V350_D1.2600.14
517_A520_F1.2570.14
167_V589_V1.2550.14
220_L321_Q1.2520.13
6_Q26_S1.2500.13
224_S255_H1.2480.13
194_V546_P1.2460.13
503_P510_T1.2460.13
243_Q558_P1.2440.13
300_Q353_D1.2430.13
504_G520_F1.2410.13
229_H309_A1.2400.13
98_T182_D1.2400.13
56_L178_A1.2320.13
445_M543_D1.2320.13
476_V491_S1.2290.13
78_G228_V1.2290.13
308_G561_G1.2280.13
329_V660_M1.2270.13
356_I404_P1.2240.13
215_V225_I1.2240.13
115_S164_V1.2230.13
149_P173_S1.2230.13
193_S590_G1.2230.13
62_D655_R1.2210.13
22_Y502_G1.2200.13
451_Q488_L1.2200.13
25_P566_T1.2170.13
126_L285_V1.2170.13
98_T343_V1.2150.13
400_C404_P1.2130.13
176_Y553_H1.2120.13
297_P329_V1.2090.12
39_Y617_E1.2070.12
37_V66_V1.2070.12
323_V633_V1.2060.12
563_T569_G1.2060.12
223_Y257_R1.2040.12
311_L440_A1.2010.12
137_A290_P1.2000.12
561_G569_G1.1990.12
103_L637_V1.1960.12
325_F633_V1.1950.12
324_L328_F1.1940.12
157_A178_A1.1910.12
273_E427_T1.1910.12
302_A427_T1.1910.12
502_G520_F1.1900.12
237_V521_M1.1890.12
50_V431_V1.1870.12
475_P480_V1.1840.12
22_Y504_G1.1830.12
104_D347_F1.1820.12
359_G650_G1.1820.12
504_G508_F1.1800.12
439_V445_M1.1790.12
147_N552_F1.1780.12
338_V343_V1.1780.12
305_A419_G1.1770.12
96_T262_S1.1770.12
389_P428_A1.1770.12
329_V425_Q1.1730.12
104_D407_V1.1730.12
140_C451_Q1.1720.12
508_F590_G1.1720.12
110_L126_L1.1700.12
154_D448_R1.1680.12
195_S558_P1.1680.12
312_A590_G1.1650.12
205_G451_Q1.1620.11
431_V503_P1.1610.11
160_L164_V1.1600.11
100_V478_R1.1600.11
215_V639_N1.1600.11
468_S489_F1.1560.11
257_R563_T1.1560.11
343_V494_Q1.1550.11
200_K311_L1.1540.11
100_V178_A1.1520.11
400_C454_L1.1520.11
223_Y510_T1.1510.11
297_P494_Q1.1500.11
110_L540_W1.1490.11
140_C572_F1.1490.11
198_R590_G1.1490.11
60_G188_S1.1480.11
550_T589_V1.1480.11
32_L535_E1.1460.11
158_S451_Q1.1460.11
182_D426_V1.1430.11
380_Q386_P1.1430.11
41_G605_R1.1410.11
167_V213_L1.1410.11
60_G553_H1.1410.11
21_K599_K1.1400.11
135_L571_N1.1400.11
413_R451_Q1.1390.11
126_L595_R1.1380.11
515_L540_W1.1350.11
82_C193_S1.1350.11
259_A497_Q1.1350.11
50_V194_V1.1300.11
448_R469_L1.1300.11
175_F561_G1.1280.11
175_F572_F1.1280.11
77_P115_S1.1270.11
243_Q273_E1.1240.11
243_Q302_A1.1240.11
19_D579_L1.1230.11
98_T338_V1.1230.11
66_V634_S1.1230.11
110_L524_G1.1230.11
11_P635_L1.1230.11
104_D405_L1.1220.11
193_S225_I1.1220.11
180_S316_S1.1210.11
17_D630_P1.1200.11
267_E314_E1.1200.11
98_T494_Q1.1180.11
454_L498_V1.1180.11
152_C198_R1.1170.11
96_T178_A1.1160.11
656_G659_F1.1130.11
286_P315_L1.1110.10
140_C205_G1.1110.10
34_Q569_G1.1110.10
318_A637_V1.1100.10
193_S508_F1.1100.10
124_H242_V1.1090.10
30_G156_V1.1060.10
162_T178_A1.1050.10
74_A570_S1.1040.10
21_K601_S1.1040.10
633_V655_R1.1020.10
42_D642_P1.1010.10
275_V306_P1.1010.10
569_G594_C1.1000.10
155_C198_R1.0990.10
407_V633_V1.0990.10
283_K287_R1.0980.10
85_C561_G1.0950.10
72_G342_S1.0950.10
73_P342_S1.0950.10
191_P421_L1.0950.10
102_V254_L1.0950.10
233_T481_S1.0930.10
34_Q243_Q1.0910.10
287_R466_N1.0910.10
3_E26_S1.0910.10
69_L587_V1.0900.10
126_L546_P1.0890.10
503_P659_F1.0890.10
198_R216_L1.0890.10
343_V426_V1.0850.10
63_L242_V1.0850.10
152_C216_L1.0840.10
154_D161_G1.0840.10
103_L503_P1.0830.10
51_A265_E1.0820.10
205_G572_F1.0820.10
76_D567_L1.0820.10
220_L652_S1.0820.10
262_S476_V1.0790.10
593_P600_D1.0780.10
498_V533_Q1.0770.10
243_Q569_G1.0770.10
6_Q431_V1.0760.10
68_S176_Y1.0740.10
227_Y569_G1.0740.10
74_A423_P1.0730.10
492_G594_C1.0730.10
182_D655_R1.0730.10
225_I415_D1.0730.10
344_V467_F1.0710.10
213_L272_R1.0700.10
374_R380_Q1.0680.10
338_V486_H1.0680.10
314_E584_T1.0670.10
102_V196_I1.0660.10
33_V107_L1.0660.10
507_H547_P1.0660.10
363_C380_Q1.0620.10
159_P636_T1.0610.10
237_V314_E1.0610.10
439_V543_D1.0610.10
229_H538_G1.0600.10
141_L470_G1.0600.10
239_F273_E1.0590.10
239_F302_A1.0590.10
224_S245_A1.0590.10
255_H587_V1.0590.10
240_L413_R1.0570.10
103_L469_L1.0570.10
243_Q257_R1.0570.10
204_S425_Q1.0560.09
193_S216_L1.0560.09
159_P503_P1.0560.09
452_V497_Q1.0560.09
34_Q561_G1.0550.09
48_V625_T1.0550.09
193_S312_A1.0550.09
205_G413_R1.0540.09
488_L572_F1.0540.09
195_S273_E1.0520.09
195_S302_A1.0520.09
349_I565_L1.0520.09
53_R546_P1.0520.09
63_L456_R1.0510.09
127_E194_V1.0510.09
211_V249_D1.0500.09
299_L448_R1.0500.09
364_C386_P1.0500.09
236_F499_P1.0500.09
227_Y273_E1.0490.09
227_Y302_A1.0490.09
410_S580_V1.0490.09
230_S402_H1.0490.09
276_L448_R1.0490.09
347_F359_G1.0490.09
180_S230_S1.0480.09
285_V498_V1.0480.09
95_D283_K1.0460.09
27_F413_R1.0460.09
34_Q227_Y1.0460.09
71_T162_T1.0450.09
96_T275_V1.0450.09
193_S507_H1.0440.09
198_R312_A1.0440.09
608_P612_F1.0440.09
245_A343_V1.0430.09
315_L597_L1.0430.09
193_S198_R1.0430.09
56_L157_A1.0410.09
194_V454_L1.0410.09
69_L226_E1.0390.09
141_L237_V1.0390.09
375_G404_P1.0390.09
361_E372_L1.0380.09
431_V617_E1.0380.09
606_P612_F1.0380.09
323_V327_V1.0350.09
497_Q549_L1.0350.09
142_F557_G1.0340.09
510_T550_T1.0340.09
67_Q269_G1.0340.09
451_Q508_F1.0330.09
6_Q579_L1.0330.09
185_V397_N1.0330.09
277_D652_S1.0330.09
158_S287_R1.0320.09
220_L422_G1.0320.09
182_D215_V1.0320.09
227_Y257_R1.0320.09
29_A49_F1.0300.09
104_D189_F1.0300.09
50_V256_T1.0290.09
394_L407_V1.0280.09
52_I442_M1.0280.09
245_A297_P1.0270.09
240_L301_V1.0270.09
129_Q543_D1.0270.09
546_P623_L1.0260.09
193_S346_A1.0260.09
17_D156_V1.0240.09
34_Q124_H1.0240.09
18_F258_L1.0240.09
561_G594_C1.0240.09
290_P429_L1.0230.09
295_P343_V1.0230.09
176_Y633_V1.0230.09
155_C216_L1.0220.09
448_R572_F1.0220.09
489_F656_G1.0220.09
195_S569_G1.0210.09
568_C572_F1.0210.09
93_P266_P1.0210.09
154_D572_F1.0200.09
254_L658_S1.0200.09
6_Q11_P1.0200.09
35_A56_L1.0200.09
108_P510_T1.0200.09
146_H180_S1.0200.09
202_D329_V1.0180.09
82_C158_S1.0180.09
33_V543_D1.0170.09
34_Q195_S1.0170.09
244_P352_L1.0170.09
503_P550_T1.0160.09
381_S639_N1.0130.09
255_H331_G1.0130.09
297_P425_Q1.0110.09
224_S426_V1.0110.09
225_I547_P1.0110.09
173_S428_A1.0110.09
276_L360_V1.0100.09
353_D469_L1.0100.09
17_D649_D1.0090.09
82_C507_H1.0070.09
193_S572_F1.0070.09
286_P602_S1.0060.09
237_V503_P1.0060.09
300_Q549_L1.0060.09
425_Q594_C1.0060.09
112_S344_V1.0060.09
307_V600_D1.0050.09
166_V194_V1.0050.09
314_E417_F1.0050.09
176_Y219_H1.0040.09
476_V631_T1.0020.09
374_R386_P1.0020.09
49_F53_R1.0020.09
224_S331_G1.0010.09
284_L451_Q1.0010.09
154_D451_Q1.0010.09
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  
4qt8B20.94021000.438Contact Map
2uzxB20.79371000.52Contact Map
4fwwA10.76681000.537Contact Map
3okyA10.84161000.633Contact Map
3al9A20.71151000.64Contact Map
3ol2B10.7041000.664Contact Map
1olzA20.82811000.706Contact Map
4gz8A20.72051000.71Contact Map
3nvnB10.65321000.712Contact Map
3okyB10.69961000.716Contact 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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