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BlaR1 -force run

ID: 1505788046 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 605 (588)
Sequences: 114 (95.6)
Seq/Len: 0.194
Nf(neff/√len): 3.9

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: 0.194).

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
416_A462_L2.8970.93
487_V495_G1.9880.60
529_S549_I1.9300.56
573_V590_A1.8540.52
494_D593_I1.7890.48
14_L467_G1.7680.46
39_T553_L1.7050.43
153_V177_L1.6610.40
147_K346_S1.6490.39
375_S420_G1.6170.38
124_V299_F1.5770.35
405_A494_D1.5770.35
418_E522_N1.5580.34
501_P588_E1.5380.33
280_I398_S1.5310.33
413_A526_V1.5140.32
225_D384_N1.4980.31
177_L384_N1.4750.30
31_K43_H1.4410.28
120_A299_F1.4360.28
418_E574_H1.4320.28
405_A456_T1.4250.28
47_S255_E1.4180.27
440_E453_S1.4110.27
238_V561_Y1.4070.27
162_F302_S1.4010.26
39_T444_D1.3940.26
231_F234_L1.3940.26
235_L567_N1.3880.26
438_Y456_T1.3760.25
162_F166_K1.3680.25
242_N478_I1.3670.25
33_L320_S1.3520.24
516_F523_I1.3500.24
527_K563_E1.3420.24
48_V405_A1.3370.24
108_S575_I1.3340.23
246_W256_M1.3240.23
390_Y398_S1.3230.23
512_Y570_F1.3210.23
157_E528_D1.3160.23
29_L327_S1.3120.23
314_V588_E1.3110.23
190_G194_P1.3090.22
494_D555_A1.3060.22
129_V173_Q1.2950.22
442_N593_I1.2940.22
444_D502_L1.2910.22
417_L459_F1.2900.22
405_A502_L1.2890.22
248_L252_A1.2880.22
123_A478_I1.2860.21
214_L510_K1.2840.21
419_S516_F1.2720.21
244_L528_D1.2620.21
255_E403_A1.2610.20
183_I197_I1.2570.20
299_F419_S1.2550.20
24_F64_L1.2540.20
237_I589_I1.2530.20
402_F574_H1.2500.20
416_A471_L1.2500.20
393_Y540_L1.2470.20
432_D559_I1.2460.20
169_I172_H1.2460.20
198_L405_A1.2400.20
183_I398_S1.2340.19
442_N495_G1.2300.19
150_L178_S1.2280.19
54_L57_P1.2240.19
138_Y416_A1.2240.19
186_P199_P1.2220.19
194_P467_G1.2190.19
49_I432_D1.2160.19
50_S248_L1.2150.19
541_S561_Y1.2150.19
9_F592_S1.2110.19
132_M201_D1.2110.19
146_I440_E1.2100.19
174_K421_I1.2090.19
306_I552_E1.2080.19
500_S503_E1.2080.19
59_I98_H1.2060.18
438_Y541_S1.2050.18
255_E442_N1.2000.18
532_L558_F1.1910.18
101_W491_Y1.1880.18
329_L432_D1.1860.18
231_F346_S1.1830.18
242_N484_D1.1830.18
31_K270_K1.1820.18
132_M282_K1.1800.18
206_S390_Y1.1790.17
210_M244_L1.1770.17
543_K560_G1.1750.17
543_K571_F1.1750.17
560_G571_F1.1750.17
24_F50_S1.1680.17
457_W543_K1.1660.17
457_W560_G1.1660.17
457_W571_F1.1660.17
432_D443_Q1.1650.17
450_A459_F1.1640.17
13_F84_Q1.1640.17
27_I205_F1.1640.17
340_A516_F1.1610.17
481_G543_K1.1600.17
481_G560_G1.1600.17
481_G571_F1.1600.17
100_N354_T1.1590.17
401_R503_E1.1570.17
279_V422_I1.1530.17
416_A513_D1.1530.17
480_Y556_G1.1530.17
530_I539_V1.1510.17
457_W481_G1.1500.16
384_N567_N1.1480.16
487_V494_D1.1480.16
424_K525_T1.1450.16
406_S441_W1.1400.16
467_G551_G1.1400.16
282_K511_F1.1390.16
102_V580_R1.1380.16
38_I256_M1.1370.16
192_I538_R1.1370.16
180_S308_R1.1350.16
19_L312_T1.1330.16
39_T502_L1.1330.16
196_I214_L1.1330.16
208_D511_F1.1310.16
371_F492_W1.1310.16
180_S197_I1.1310.16
63_F172_H1.1290.16
196_I463_D1.1290.16
197_I374_F1.1280.16
43_H460_Q1.1240.16
210_M432_D1.1220.16
43_H202_I1.1200.16
544_T560_G1.1200.16
544_T571_F1.1200.16
49_I288_Q1.1190.16
345_V559_I1.1180.15
186_P518_F1.1170.15
36_T580_R1.1130.15
478_I590_A1.1130.15
247_Y516_F1.1130.15
250_K413_A1.1120.15
258_I346_S1.1110.15
296_A399_T1.1110.15
330_V577_G1.1100.15
543_K557_W1.1090.15
557_W560_G1.1090.15
557_W571_F1.1090.15
32_K306_I1.1090.15
522_N574_H1.1090.15
385_S405_A1.1070.15
457_W544_T1.1070.15
394_N540_L1.1070.15
59_I530_I1.1060.15
169_I297_S1.1060.15
189_F446_D1.1060.15
59_I138_Y1.1040.15
253_K370_F1.1040.15
390_Y412_S1.1030.15
481_G544_T1.1030.15
324_K452_S1.1010.15
39_T43_H1.0980.15
48_V255_E1.0980.15
457_W557_W1.0980.15
48_V198_L1.0970.15
407_T457_W1.0960.15
93_E296_A1.0950.15
9_F449_S1.0930.15
481_G557_W1.0930.15
183_I267_T1.0920.15
478_I516_F1.0910.15
314_V366_D1.0900.15
415_L474_Y1.0900.15
449_S462_L1.0890.15
299_F473_H1.0860.14
431_W450_A1.0840.14
46_I169_I1.0830.14
20_L192_I1.0810.14
296_A484_D1.0810.14
401_R500_S1.0810.14
26_I107_L1.0800.14
141_L296_A1.0800.14
482_N545_G1.0800.14
153_V281_L1.0790.14
37_Q493_L1.0780.14
474_Y518_F1.0780.14
180_S183_I1.0780.14
427_S525_T1.0780.14
36_T316_F1.0750.14
121_F528_D1.0730.14
63_F478_I1.0710.14
548_V553_L1.0700.14
29_L222_K1.0690.14
23_F426_D1.0680.14
255_E495_G1.0670.14
482_N497_L1.0670.14
190_G260_C1.0650.14
273_H281_L1.0650.14
242_N325_A1.0640.14
281_L453_S1.0620.14
15_V173_Q1.0610.14
166_K390_Y1.0590.14
211_K364_Y1.0590.14
234_L443_Q1.0590.14
135_A192_I1.0580.14
229_N432_D1.0580.14
91_T137_L1.0570.14
407_T543_K1.0560.14
407_T560_G1.0560.14
407_T571_F1.0560.14
441_W543_K1.0560.14
441_W560_G1.0560.14
441_W571_F1.0560.14
53_A398_S1.0540.14
58_F194_P1.0540.14
197_I398_S1.0540.14
455_T586_A1.0530.14
46_I221_C1.0520.14
148_K222_K1.0510.13
158_L374_F1.0510.13
245_V396_K1.0510.13
239_Y411_F1.0490.13
242_N509_K1.0490.13
161_L281_L1.0470.13
380_F586_A1.0470.13
544_T557_W1.0470.13
431_W540_L1.0470.13
129_V518_F1.0450.13
316_F442_N1.0450.13
242_N372_D1.0450.13
34_L299_F1.0440.13
47_S494_D1.0440.13
441_W457_W1.0420.13
379_G501_P1.0420.13
338_I520_Q1.0410.13
383_F415_L1.0410.13
213_V245_V1.0400.13
183_I432_D1.0400.13
393_Y405_A1.0390.13
496_S555_A1.0390.13
407_T481_G1.0380.13
296_A566_D1.0370.13
441_W481_G1.0370.13
421_I466_I1.0360.13
24_F550_N1.0360.13
458_Y558_F1.0350.13
153_V590_A1.0340.13
106_S244_L1.0320.13
198_L268_L1.0310.13
252_A487_V1.0310.13
252_A589_I1.0300.13
20_L162_F1.0290.13
54_L563_E1.0290.13
380_F455_T1.0290.13
280_I466_I1.0290.13
512_Y584_S1.0290.13
336_G585_S1.0280.13
48_V319_A1.0270.13
58_F343_P1.0270.13
153_V201_D1.0270.13
179_R223_R1.0270.13
296_A443_Q1.0250.13
122_F228_I1.0230.13
178_S280_I1.0230.13
234_L284_T1.0220.13
316_F584_S1.0210.13
442_N494_D1.0210.13
34_L87_S1.0200.13
244_L337_A1.0200.13
305_H514_N1.0200.13
186_P460_Q1.0180.13
92_T177_L1.0180.13
258_I528_D1.0180.13
281_L335_L1.0180.13
37_Q364_Y1.0170.13
49_I337_A1.0160.13
316_F490_D1.0160.13
68_H137_L1.0150.13
170_R385_S1.0150.13
39_T226_M1.0140.12
301_S306_I1.0140.12
485_F578_E1.0140.12
364_Y438_Y1.0130.12
381_V586_A1.0130.12
38_I190_G1.0120.12
52_L559_I1.0120.12
183_I209_E1.0120.12
54_L239_Y1.0110.12
33_L584_S1.0100.12
165_C451_M1.0100.12
401_R441_W1.0100.12
104_D371_F1.0090.12
205_F520_Q1.0090.12
213_V225_D1.0090.12
327_S554_H1.0090.12
31_K415_L1.0070.12
207_A332_T1.0070.12
441_W544_T1.0060.12
18_I296_A1.0050.12
406_S543_K1.0050.12
406_S560_G1.0050.12
406_S571_F1.0050.12
382_L547_S1.0050.12
45_Y201_D1.0030.12
402_F470_H1.0030.12
119_S168_E1.0020.12
24_F279_V1.0000.12
225_D276_Y1.0000.12
43_H466_I1.0000.12
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  
1nrfA10.4051000.83Contact Map
4iedA40.40331000.842Contact Map
1xkzA40.40991000.842Contact Map
4s2pA20.39671000.843Contact Map
2iwbA10.40331000.846Contact Map
1k38A20.38681000.847Contact Map
4zdxA101000.852Contact Map
4oh0A10.39671000.852Contact Map
4jf5A10.39671000.854Contact Map
2x02A20.40171000.855Contact 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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