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tgac c term1

ID: 1506634845 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 527 (521)
Sequences: 10315 (8014.1)
Seq/Len: 19.798
Nf(neff/√len): 351.1

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: 19.798).

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
230_A380_P3.6711.00
261_A361_A3.0771.00
26_R30_A2.8431.00
27_L34_A2.7971.00
102_A245_V2.7541.00
182_H266_S2.7091.00
3_E250_S2.6741.00
181_L357_V2.6711.00
158_S167_S2.6471.00
248_R251_D2.6441.00
222_D233_D2.6421.00
228_F308_A2.6151.00
247_K257_D2.5931.00
19_D23_A2.5891.00
227_S343_S2.5841.00
260_L365_R2.5791.00
24_L341_I2.5451.00
98_T241_A2.5411.00
286_E326_A2.5101.00
368_T395_A2.5061.00
369_V392_P2.4991.00
117_Q194_D2.4981.00
465_D505_D2.4911.00
230_A377_A2.4851.00
4_P264_R2.4821.00
461_R505_D2.4591.00
302_H403_L2.4171.00
403_L421_E2.4111.00
124_M153_A2.3751.00
80_V88_M2.3481.00
264_R421_E2.3071.00
37_E63_R2.2871.00
20_D23_A2.2841.00
69_D72_R2.2651.00
99_A197_L2.2631.00
363_A370_P2.2471.00
251_D254_A2.2471.00
29_L368_T2.2321.00
121_F187_S2.1971.00
360_A404_A2.1711.00
242_G354_L2.1681.00
494_A500_L2.1451.00
187_S193_C2.1161.00
247_K255_A2.0781.00
341_I355_A2.0711.00
368_T397_A2.0371.00
50_D55_A2.0341.00
117_Q291_R2.0211.00
443_L500_L2.0051.00
390_E396_R2.0041.00
186_Q190_A2.0021.00
172_T175_S2.0001.00
7_I357_V1.9871.00
33_D224_R1.9621.00
495_R499_A1.9541.00
321_A338_V1.9531.00
231_A376_E1.9451.00
244_L357_V1.9441.00
371_A395_A1.9411.00
238_S348_T1.9241.00
497_R501_L1.9201.00
7_I361_A1.8951.00
154_S169_T1.8931.00
383_P386_A1.8861.00
14_F355_A1.8841.00
337_V390_E1.8831.00
185_C263_V1.8781.00
474_D477_C1.8741.00
266_S418_V1.8591.00
95_L122_V1.8471.00
11_G98_T1.8391.00
55_A58_K1.8391.00
114_R162_G1.8381.00
267_A292_A1.8191.00
443_L494_A1.8151.00
343_S373_L1.8131.00
222_D226_K1.8131.00
44_D47_A1.8051.00
465_D501_L1.8041.00
179_V416_A1.7921.00
372_N375_A1.7851.00
105_Q260_L1.7811.00
456_Q459_K1.7781.00
229_S375_A1.7391.00
3_E6_A1.7361.00
343_S372_N1.7351.00
305_Y369_V1.7291.00
337_V392_P1.7261.00
367_R402_R1.7041.00
18_A27_L1.6851.00
456_Q460_L1.6741.00
402_R422_R1.6711.00
164_H287_A1.6601.00
478_S482_T1.6541.00
95_L157_L1.6511.00
337_V396_R1.6481.00
229_S376_E1.6091.00
460_L479_L1.6081.00
398_W402_R1.6041.00
242_G358_L1.5931.00
179_V414_T1.5891.00
9_G105_Q1.5831.00
400_D422_R1.5761.00
22_E105_Q1.5671.00
181_L418_V1.5621.00
155_G412_S1.5611.00
23_A26_R1.5581.00
244_L354_L1.5541.00
496_D499_A1.5511.00
27_L32_T1.5511.00
220_A226_K1.5461.00
490_A507_L1.5421.00
444_V480_A1.5421.00
357_V420_L1.5341.00
345_L355_A1.5331.00
474_D478_S1.5271.00
182_H192_E1.5231.00
14_F242_G1.5211.00
461_R501_L1.5211.00
306_V324_L1.5201.00
152_V277_L1.5121.00
35_T65_G1.5101.00
12_C21_P1.5071.00
360_A364_L1.5051.00
299_E302_H1.5041.00
463_H467_H1.5031.00
111_E484_T1.5021.00
99_A243_V1.5021.00
221_P233_D1.4971.00
29_L395_A1.4911.00
448_R486_F1.4891.00
253_L423_A1.4811.00
186_Q295_L1.4801.00
197_L245_V1.4771.00
447_G453_L1.4751.00
461_R465_D1.4731.00
288_V292_A1.4711.00
36_R68_E1.4701.00
181_L246_V1.4681.00
181_L198_V1.4641.00
33_D374_H1.4551.00
305_Y360_A1.4541.00
122_V199_G1.4541.00
187_S192_E1.4461.00
286_E290_R1.4401.00
188_L248_R1.4361.00
471_A474_D1.4351.00
260_L361_A1.4241.00
337_V369_V1.4231.00
95_L243_V1.4181.00
367_R422_R1.4161.00
119_G166_P1.4151.00
375_A391_L1.4121.00
445_L457_A1.4101.00
226_K231_A1.4091.00
105_Q258_S1.4020.99
95_L153_A1.3970.99
168_I183_L1.3920.99
450_G488_R1.3910.99
99_A157_L1.3850.99
98_T243_V1.3820.99
477_C481_G1.3780.99
269_N415_N1.3730.99
28_L362_L1.3630.99
103_L245_V1.3560.99
405_G417_H1.3550.99
10_A358_L1.3540.99
26_R29_L1.3490.99
123_G176_S1.3400.99
367_R400_D1.3390.99
5_I246_V1.3370.99
384_W391_L1.3370.99
199_G243_V1.3340.99
364_L420_L1.3280.99
10_A21_P1.3270.99
449_T488_R1.3220.99
5_I185_C1.3150.99
170_I183_L1.3110.99
249_L262_V1.3060.99
332_R335_P1.3050.99
291_R295_L1.3010.99
18_A23_A1.3000.99
328_Y405_G1.2990.99
325_G387_L1.2960.99
186_Q189_R1.2960.99
100_W104_E1.2860.99
267_A288_V1.2820.99
119_G193_C1.2770.99
226_K233_D1.2770.99
19_D68_E1.2720.99
103_L161_L1.2690.99
109_V112_R1.2600.99
41_D71_D1.2590.99
179_V268_V1.2580.99
37_E62_R1.2520.99
60_T214_S1.2490.99
195_T245_V1.2470.99
362_L366_H1.2440.98
35_T63_R1.2430.98
258_S365_R1.2400.98
240_G348_T1.2390.98
449_T452_A1.2390.98
379_H382_I1.2300.98
65_G238_S1.2200.98
229_S377_A1.2190.98
314_R381_D1.2130.98
448_R487_A1.2130.98
443_L472_L1.2100.98
200_S354_L1.2100.98
476_A479_L1.2080.98
181_L263_V1.2080.98
492_V503_A1.1990.98
77_F100_W1.1970.98
26_R32_T1.1850.98
193_C196_A1.1830.98
457_A490_A1.1820.98
39_P42_R1.1760.98
298_V302_H1.1720.98
194_D251_D1.1670.97
182_H186_Q1.1620.97
321_A382_I1.1610.97
25_W370_P1.1520.97
99_A161_L1.1520.97
98_T101_E1.1480.97
102_A197_L1.1460.97
94_L241_A1.1440.97
109_V484_T1.1420.97
127_S150_G1.1400.97
445_L460_L1.1370.97
16_G34_A1.1370.97
455_A459_K1.1360.97
102_A243_V1.1350.97
392_P396_R1.1300.97
194_D248_R1.1280.97
458_A462_A1.1250.97
184_A196_A1.1250.97
499_A503_A1.1230.97
375_A378_P1.1220.97
442_P491_A1.1190.96
237_W349_Q1.1170.96
275_A279_A1.1150.96
298_V403_L1.1120.96
443_L479_L1.1110.96
155_G167_S1.1090.96
378_P384_W1.1030.96
265_A295_L1.0950.96
122_V243_V1.0900.96
378_P391_L1.0880.96
470_L475_L1.0790.95
501_L505_D1.0790.95
11_G102_A1.0770.95
103_L113_L1.0730.95
197_L243_V1.0730.95
268_V416_A1.0700.95
441_L444_V1.0690.95
118_T195_T1.0660.95
455_A458_A1.0620.95
13_R101_E1.0590.95
14_F358_L1.0540.95
121_F193_C1.0470.94
124_M150_G1.0460.94
77_F486_F1.0450.94
279_A315_L1.0440.94
31_G371_A1.0410.94
303_V403_L1.0380.94
360_A406_V1.0330.94
125_M350_A1.0250.93
293_L328_Y1.0240.93
441_L473_A1.0230.93
447_G452_A1.0230.93
461_R508_A1.0200.93
293_L303_V1.0120.93
505_D509_Q1.0110.93
38_V210_F1.0100.93
95_L199_G1.0050.93
25_W366_H1.0040.93
185_C189_R1.0010.92
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  
2vz8A20.95261000.062Contact Map
4na1A20.97531000.074Contact Map
4tktA10.96581000.093Contact Map
4kc5A40.98861000.102Contact Map
4zdnA101000.102Contact Map
4opeA40.98291000.103Contact Map
4qyrA10.95831000.104Contact Map
4mz0A20.97721000.105Contact Map
2qo3A20.97911000.114Contact Map
2hg4A60.95451000.115Contact 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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