OPENSEQ.org
E coli UvrD

ID: 1515937872 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 720 (642)
Sequences: 8832 (5782.1)
Seq/Len: 13.757
Nf(neff/√len): 228.2

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: 13.757).

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
56_S215_T4.6321.00
333_V573_V4.4691.00
559_L602_G4.3651.00
575_M612_L3.9741.00
15_R19_A3.7811.00
568_P608_Q3.7781.00
336_R339_T3.7351.00
201_L231_A3.6591.00
372_M554_V3.6331.00
336_R571_F3.1861.00
577_E631_R3.1441.00
345_G569_Q3.1311.00
572_I602_G3.0991.00
16_E275_E3.0401.00
569_Q609_K3.0211.00
13_K16_E3.0091.00
10_L18_V2.9781.00
349_E568_P2.9071.00
568_P607_M2.9011.00
230_Y270_D2.8911.00
348_A552_D2.8851.00
11_N283_Y2.8811.00
341_Q347_L2.8651.00
195_R198_E2.7961.00
198_E202_N2.7931.00
287_S291_S2.7561.00
346_A552_D2.7091.00
20_A25_L2.7071.00
176_A179_E2.6891.00
86_W214_F2.6291.00
337_I350_C2.5751.00
336_R611_T2.5111.00
94_A196_A2.4011.00
234_R270_D2.3931.00
334_V370_A2.3671.00
347_L373_P2.2771.00
355_R595_E2.2751.00
338_K370_A2.2441.00
481_T516_T2.2421.00
407_F411_V2.2281.00
126_L180_A2.2261.00
354_Y556_L2.2261.00
200_W207_L2.2031.00
53_S56_S2.1941.00
147_N190_A2.1911.00
571_F611_T2.1901.00
569_Q611_T2.1871.00
88_G93_L2.1681.00
187_V195_R2.1251.00
101_H209_H2.1001.00
352_I367_L2.0871.00
193_L228_I2.0791.00
25_L277_I2.0741.00
41_H77_L2.0501.00
320_L614_Y2.0481.00
180_A183_R2.0431.00
262_E266_R2.0311.00
299_N635_E2.0291.00
346_A349_E2.0261.00
160_Q175_Q2.0141.00
329_E613_T2.0131.00
557_M567_F1.9941.00
207_L211_R1.9921.00
482_D513_V1.9881.00
114_L186_L1.9861.00
345_G350_C1.9861.00
104_D206_I1.9851.00
101_H210_Y1.9851.00
204_P207_L1.9831.00
335_N370_A1.9751.00
323_A332_F1.9711.00
5_Y8_D1.9631.00
559_L580_F1.9491.00
363_L573_V1.9491.00
603_V610_L1.9421.00
43_I59_A1.9361.00
332_F613_T1.9341.00
491_R506_I1.9301.00
341_Q350_C1.9161.00
572_I612_L1.9061.00
340_W571_F1.8961.00
179_E183_R1.8951.00
102_H187_V1.8771.00
231_A234_R1.8661.00
155_R158_H1.8641.00
519_F533_A1.8641.00
37_R41_H1.8581.00
208_Q212_E1.8551.00
129_A176_A1.8281.00
13_K281_Q1.8221.00
250_D303_R1.8181.00
345_G608_Q1.8091.00
483_R487_D1.8041.00
201_L235_L1.8011.00
403_D406_A1.7881.00
387_E508_N1.7621.00
180_A184_A1.7381.00
153_G228_I1.7171.00
27_V244_M1.7131.00
197_H232_W1.7081.00
366_A370_A1.7021.00
340_W350_C1.7011.00
340_W569_Q1.6951.00
322_C614_Y1.6891.00
178_Q181_C1.6881.00
175_Q179_E1.6801.00
295_A637_P1.6781.00
227_N260_Q1.6701.00
176_A180_A1.6501.00
58_M217_I1.6501.00
331_R370_A1.6491.00
467_A487_D1.6441.00
397_L410_V1.6391.00
25_L244_M1.6341.00
281_Q309_W1.6331.00
333_V363_L1.6191.00
126_L173_V1.6131.00
122_L180_A1.6131.00
129_A180_A1.6111.00
125_R180_A1.6101.00
72_H76_Q1.6101.00
123_L143_M1.6101.00
629_P633_I1.6091.00
354_Y360_S1.6071.00
149_Q159_I1.6061.00
478_H520_S1.5981.00
69_E73_R1.5961.00
296_L603_V1.5951.00
292_A318_I1.5911.00
219_V233_I1.5881.00
97_L196_A1.5851.00
340_W609_K1.5841.00
575_M599_A1.5841.00
319_S336_R1.5821.00
489_G492_T1.5821.00
46_L216_N1.5741.00
268_L276_T1.5731.00
292_A603_V1.5671.00
241_G273_G1.5611.00
19_A45_W1.5581.00
492_T495_E1.5581.00
319_S609_K1.5571.00
97_L210_Y1.5441.00
200_W235_L1.5421.00
130_M176_A1.5391.00
390_D409_R1.5371.00
157_H175_Q1.5271.00
334_V366_A1.5221.00
123_L173_V1.5181.00
490_L494_Y1.5181.00
43_I74_I1.5131.00
333_V571_F1.5111.00
210_Y214_F1.5061.00
391_A509_L1.5061.00
91_H192_L1.5051.00
407_F441_C1.4981.00
222_F230_Y1.4971.00
331_R366_A1.4881.00
412_N416_R1.4821.00
126_L176_A1.4721.00
126_L130_M1.4641.00
516_T534_F1.4631.00
204_P208_Q1.4611.00
282_N285_S1.4591.00
393_S409_R1.4561.00
45_W49_V1.4531.00
97_L200_W1.4501.00
596_R635_E1.4381.00
197_H231_A1.4311.00
599_A603_V1.4301.00
323_A613_T1.4281.00
336_R340_W1.4211.00
347_L350_C1.4191.00
203_K206_I1.4181.00
340_W345_G1.4131.00
208_Q211_R1.3980.99
7_L15_R1.3910.99
74_I87_V1.3890.99
375_R553_A1.3870.99
329_E574_G1.3860.99
44_A77_L1.3810.99
216_N242_K1.3800.99
338_K347_L1.3790.99
13_K280_E1.3790.99
47_M78_M1.3770.99
491_R510_E1.3700.99
217_I237_A1.3640.99
252_S255_G1.3590.99
345_G568_P1.3590.99
352_I363_L1.3580.99
337_I554_V1.3520.99
31_A294_N1.3510.99
158_H161_S1.3430.99
12_D15_R1.3430.99
366_A369_Q1.3360.99
93_L97_L1.3360.99
337_I347_L1.3280.99
207_L235_L1.3230.99
12_D16_E1.3200.99
367_L556_L1.3160.99
340_W611_T1.3160.99
98_L196_A1.3140.99
426_V437_L1.3130.99
17_A27_V1.3130.99
58_M214_F1.3100.99
337_I571_F1.3050.99
421_R425_V1.3050.99
266_R270_D1.2950.99
575_M580_F1.2880.99
396_R539_A1.2870.99
316_E609_K1.2840.99
150_K191_E1.2670.99
399_A532_Q1.2470.99
347_L372_M1.2460.98
569_Q608_Q1.2420.98
169_T172_K1.2320.98
530_P533_A1.2310.98
116_S119_Q1.2220.98
182_D195_R1.2210.98
178_Q182_D1.2200.98
108_P185_G1.2200.98
429_T440_A1.2140.98
196_A232_W1.2120.98
387_E505_R1.2090.98
193_L232_W1.2070.98
491_R495_E1.2040.98
172_K175_Q1.1990.98
419_G422_T1.1960.98
359_Q574_G1.1960.98
320_L641_V1.1910.98
391_A512_L1.1870.98
391_A481_T1.1840.98
636_L640_C1.1820.98
60_V93_L1.1750.98
104_D203_K1.1750.98
127_I132_L1.1660.97
576_E615_A1.1630.97
350_C569_Q1.1540.97
334_V554_V1.1530.97
354_Y573_V1.1520.97
571_F613_T1.1520.97
233_I243_V1.1500.97
154_L159_I1.1490.97
8_D15_R1.1480.97
375_R555_Q1.1450.97
6_L41_H1.1440.97
397_L407_F1.1390.97
197_H235_L1.1350.97
100_A213_R1.1280.97
86_W96_R1.1270.97
26_L276_T1.1270.97
325_N328_D1.1250.97
23_S242_K1.1240.97
321_Y332_F1.1210.97
16_E19_A1.1190.96
46_L52_C1.1190.96
326_E362_V1.1150.96
225_T263_N1.1150.96
361_R365_E1.1140.96
345_G349_E1.1070.96
42_R244_M1.1060.96
328_D331_R1.1050.96
350_C571_F1.1020.96
234_R271_F1.1010.96
156_P174_Y1.1010.96
396_R406_A1.1000.96
336_R609_K1.0990.96
96_R100_A1.0940.96
288_N318_I1.0910.96
566_E607_M1.0910.96
125_R408_E1.0890.96
196_A200_W1.0890.96
218_L244_M1.0880.96
374_Y556_L1.0870.96
330_A363_L1.0810.95
9_S41_H1.0740.95
478_H482_D1.0740.95
476_P479_V1.0720.95
293_A603_V1.0660.95
322_C616_E1.0630.95
123_L139_P1.0590.95
436_T439_Q1.0590.95
332_F336_R1.0580.95
28_L249_D1.0570.95
93_L210_Y1.0550.95
168_Q172_K1.0490.94
557_M562_A1.0480.94
402_N436_T1.0470.94
39_L218_L1.0460.94
398_I484_V1.0440.94
515_A534_F1.0440.94
105_A199_L1.0380.94
267_F274_A1.0310.94
391_A485_I1.0300.94
68_A72_H1.0300.94
95_H99_R1.0280.94
160_Q171_Q1.0280.94
293_A604_T1.0250.93
52_C56_S1.0230.93
266_R269_N1.0220.93
317_P642_E1.0220.93
227_N231_A1.0170.93
65_K69_E1.0150.93
150_K178_Q1.0140.93
20_A23_S1.0140.93
367_L554_V1.0130.93
194_L228_I1.0120.93
298_E307_K1.0100.93
268_L304_L1.0090.93
386_Q413_T1.0080.93
439_Q443_E1.0070.93
296_L599_A1.0070.93
288_N640_C1.0060.93
187_V192_L1.0050.93
200_W210_Y1.0050.93
381_R384_E1.0050.93
26_L245_I1.0030.93
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  
1pjrA10.85971000.094Contact Map
4c2tA40.89311000.094Contact Map
1uaaA20.87641000.274Contact Map
3lfuA10.87921000.287Contact Map
4c2uA20.89171000.298Contact Map
3u4qA10.90831000.321Contact Map
1w36B20.93331000.38Contact Map
3u4qB10.90971000.465Contact Map
4pj3A10.71000.633Contact Map
2xzlA10.56671000.706Contact 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.

Page generated in 0.0544 seconds.