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dbpa2

ID: 1502215302 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 457 (454)
Sequences: 1649 (997.2)
Seq/Len: 3.632
Nf(neff/√len): 46.8

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: 3.632).

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
58_G91_L3.8751.00
136_H141_T3.8351.00
128_A142_V3.5871.00
11_P63_Q3.5451.00
20_E97_F2.9071.00
134_L138_Q2.9061.00
128_A133_L2.8991.00
41_K203_L2.7951.00
29_V45_V2.7641.00
150_L171_I2.5601.00
75_L147_L2.5381.00
61_L74_A2.4631.00
134_L169_D2.3781.00
104_L123_P2.3501.00
309_S337_N2.2931.00
251_K274_D2.2421.00
14_Q63_Q2.2281.00
36_A205_I2.1231.00
138_Q169_D2.1021.00
10_L59_L2.0521.00
217_E340_L2.0261.00
12_P16_T1.9921.00
254_C272_H1.9801.00
37_I181_L1.9551.00
71_Q146_A1.9521.00
126_I142_V1.9431.00
169_D173_F1.9331.00
386_C390_G1.9311.00
40_G179_Q1.9181.00
134_L137_L1.9091.00
318_L343_S1.9011.00
67_A124_H1.8861.00
257_V296_V1.8721.00
399_D447_K1.8581.00
390_G397_P1.8531.00
390_G395_M1.8360.99
77_L133_L1.7920.99
387_I390_G1.7670.99
446_I451_C1.7480.99
385_L389_G1.7430.99
2_T6_T1.7320.99
381_E390_G1.7180.99
285_V289_N1.7160.99
217_E365_N1.6600.99
315_N329_I1.6490.99
16_T97_F1.6460.99
386_C389_G1.6420.99
218_Q329_I1.6380.99
112_F141_T1.6360.99
381_E386_C1.6290.98
215_P338_S1.6220.98
23_Y94_L1.6210.98
233_Q264_V1.6030.98
231_L344_F1.5950.98
390_G394_K1.5950.98
20_E96_R1.5940.98
258_C270_S1.5790.98
42_D178_R1.5690.98
382_M390_G1.5320.97
381_E384_T1.5270.97
73_Q124_H1.5170.97
315_N343_S1.5130.97
192_A204_A1.5120.97
242_S311_E1.5090.97
254_C270_S1.5010.97
66_D124_H1.4750.97
219_Q340_L1.4710.97
137_L147_L1.4690.97
236_L294_V1.4660.96
390_G393_A1.4640.96
91_L125_I1.4550.96
235_L342_I1.4530.96
61_L149_T1.4440.96
189_E193_A1.4350.96
427_V446_I1.4140.95
116_R141_T1.4090.95
384_T390_G1.4070.95
228_K317_E1.4040.95
248_C254_C1.4020.95
251_K272_H1.3950.95
381_E389_G1.3850.95
133_L142_V1.3840.95
221_Y367_Q1.3810.95
391_K397_P1.3800.95
357_S363_K1.3800.95
402_G406_G1.3620.94
168_D197_R1.3620.94
389_G395_M1.3570.94
72_T142_V1.3560.94
36_A203_L1.3510.94
42_D180_T1.3460.94
382_M385_L1.3440.94
237_S266_Q1.3420.93
229_I257_V1.3280.93
370_P400_V1.3170.93
401_L415_I1.3160.93
73_Q148_N1.3160.93
315_N341_A1.3150.93
110_Q136_H1.3080.92
381_E387_I1.3030.92
137_L144_L1.3020.92
383_A390_G1.2970.92
383_A386_C1.2860.91
32_A203_L1.2850.91
5_S19_N1.2720.91
269_L286_R1.2700.91
88_A105_T1.2680.91
382_M386_C1.2630.90
220_F366_W1.2630.90
23_Y55_A1.2610.90
147_L174_A1.2600.90
396_R399_D1.2570.90
116_R139_K1.2490.90
137_L173_F1.2460.90
361_Q370_P1.2430.89
66_D73_Q1.2410.89
235_L314_V1.2370.89
112_F116_R1.2350.89
389_G397_P1.2260.89
123_P126_I1.2200.88
219_Q367_Q1.2190.88
382_M387_I1.2180.88
78_C87_V1.2120.88
36_A39_A1.2100.88
61_L151_V1.2090.88
74_A149_T1.2090.88
4_F26_M1.2090.88
383_A388_D1.2040.87
382_M395_M1.2040.87
249_N312_L1.1990.87
287_F295_L1.1980.87
323_E326_V1.1980.87
381_E395_M1.1960.87
44_R195_S1.1930.87
243_S310_L1.1850.86
157_R160_D1.1700.85
18_L424_H1.1690.85
76_V91_L1.1670.85
42_D202_P1.1600.85
135_D139_K1.1600.85
218_Q315_N1.1560.84
386_C392_K1.1520.84
384_T387_I1.1510.84
383_A455_L1.1480.84
290_G337_N1.1450.84
239_H311_E1.1430.83
213_L216_I1.1370.83
382_M388_D1.1370.83
16_T20_E1.1290.82
296_V317_E1.1270.82
286_R291_S1.1240.82
400_V425_V1.1230.82
169_D172_R1.1230.82
387_I400_V1.1170.81
23_Y58_G1.1170.81
399_D402_G1.1120.81
269_L292_A1.1100.81
91_L103_I1.1100.81
418_I427_V1.1090.81
51_S106_L1.1040.80
387_I394_K1.1010.80
394_K397_P1.1000.80
266_Q294_V1.1000.80
146_A439_K1.0990.80
231_L369_P1.0970.80
223_T231_L1.0920.79
419_A448_G1.0890.79
395_M400_V1.0880.79
414_D433_V1.0870.79
244_C314_V1.0760.78
393_A449_K1.0760.78
235_L239_H1.0750.78
244_C294_V1.0720.78
387_I395_M1.0700.77
255_Q272_H1.0690.77
445_K450_T1.0670.77
416_G428_A1.0670.77
357_S360_L1.0650.77
439_K442_Q1.0640.77
382_M389_G1.0630.77
281_D284_L1.0600.76
32_A205_I1.0500.76
412_G415_I1.0500.76
351_Q354_N1.0490.75
385_L393_A1.0490.75
106_L141_T1.0480.75
69_L124_H1.0480.75
385_L388_D1.0460.75
403_A407_D1.0450.75
261_L294_V1.0430.75
391_K395_M1.0400.75
114_M117_D1.0400.75
107_C281_D1.0380.74
385_L395_M1.0340.74
77_L170_V1.0340.74
243_S287_F1.0340.74
143_S146_A1.0340.74
253_D317_E1.0310.74
1_M6_T1.0310.74
65_I124_H1.0250.73
402_G407_D1.0250.73
421_H426_Y1.0190.72
106_L136_H1.0170.72
311_E342_I1.0150.72
3_A6_T1.0140.72
176_A200_R1.0140.72
193_A196_G1.0130.72
24_L105_T1.0120.72
134_L173_F1.0100.71
234_R237_S1.0080.71
90_E93_R1.0050.71
159_L191_I1.0000.70
63_Q76_V1.0000.70
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  
3sqwA10.96061000.465Contact Map
3i5xA10.97161000.471Contact Map
4pxaA10.81841000.482Contact Map
2db3A40.80741000.487Contact Map
3fmpB20.44641000.501Contact Map
4ljyA10.84461000.503Contact Map
4nhoA10.80311000.505Contact Map
4d25A10.80961000.508Contact Map
4w7sA20.85121000.508Contact Map
4c9bA10.81181000.519Contact 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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