OPENSEQ.org
KNL1_vertebrates -force run

ID: 1516979462 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 451 (449)
Sequences: 112 (54)
Seq/Len: 0.249
Nf(neff/√len): 2.5

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: 0.249).

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 > 50% 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
50_Q96_M1.7980.56
366_P425_A1.7100.50
279_V320_Y1.7050.50
368_Y440_N1.6780.48
89_N352_R1.5690.41
302_D442_V1.5460.40
16_L26_P1.5450.40
26_P319_Q1.4990.37
154_E265_Y1.4990.37
17_L24_Q1.4970.37
420_S423_D1.4910.36
187_E221_E1.4800.36
245_S267_S1.4660.35
139_Q408_L1.4650.35
44_E431_V1.4580.35
15_I440_N1.4320.33
176_L353_L1.3950.31
81_Q358_I1.3950.31
241_L339_K1.3940.31
434_E440_N1.3930.31
262_T315_K1.3790.30
312_L351_C1.3740.30
28_Q326_S1.3690.30
83_K163_D1.3690.30
28_Q138_V1.3650.29
74_L93_W1.3650.29
88_I346_L1.3590.29
347_V394_E1.3590.29
17_L21_I1.3570.29
9_T12_E1.3550.29
109_I422_D1.3500.29
9_T32_P1.3420.28
265_Y303_E1.3400.28
103_E312_L1.3320.28
16_L28_Q1.3310.28
69_Q287_R1.3210.27
156_D346_L1.3210.27
83_K176_L1.3200.27
424_I445_I1.3200.27
385_S393_F1.3200.27
38_N286_N1.3180.27
100_S165_C1.3180.27
341_L357_E1.3120.27
341_L364_W1.3120.27
19_V24_Q1.3120.27
395_I428_L1.3050.26
2_K16_L1.3040.26
357_E364_W1.2950.26
8_I13_F1.2880.25
217_E222_Q1.2880.25
408_L416_I1.2850.25
62_Q399_L1.2720.25
438_L442_V1.2710.25
271_T382_L1.2680.24
163_D353_L1.2670.24
144_E337_V1.2480.24
83_K124_V1.2470.23
114_I126_T1.2430.23
70_K252_V1.2410.23
295_V420_S1.2380.23
426_T432_P1.2380.23
17_L22_L1.2350.23
227_I256_D1.2340.23
118_F327_W1.2320.23
22_L31_L1.2300.23
163_D443_K1.2250.22
89_N416_I1.2240.22
122_T125_F1.2220.22
46_L152_I1.2210.22
383_L404_P1.2180.22
99_C442_V1.2160.22
152_I322_E1.2090.22
366_P373_I1.2070.22
227_I274_F1.2040.22
23_I108_G1.2020.21
408_L438_L1.2020.21
158_I272_I1.2000.21
103_E351_C1.1940.21
48_L323_E1.1910.21
405_S408_L1.1820.21
97_R398_F1.1810.21
19_V112_N1.1810.21
3_L50_Q1.1790.20
368_Y373_I1.1790.20
265_Y319_Q1.1770.20
178_D183_N1.1770.20
383_L403_Y1.1750.20
158_I192_T1.1740.20
390_F416_I1.1740.20
10_I65_E1.1720.20
2_K12_E1.1710.20
52_V145_R1.1710.20
164_N372_N1.1710.20
83_K443_K1.1710.20
251_V317_I1.1700.20
431_V437_Y1.1690.20
73_E99_C1.1670.20
121_M163_D1.1670.20
70_K342_Q1.1650.20
52_V430_K1.1630.20
254_W258_Q1.1620.20
131_V268_I1.1620.20
232_K427_I1.1590.20
392_K449_L1.1580.20
331_C340_I1.1530.19
87_D422_D1.1530.19
412_I446_Y1.1460.19
259_A269_E1.1430.19
2_K26_P1.1410.19
126_T169_V1.1410.19
230_M234_T1.1390.19
89_N165_C1.1370.19
81_Q200_E1.1360.19
110_Y366_P1.1340.19
202_L345_S1.1340.19
153_D441_V1.1310.19
292_I347_V1.1290.18
232_K235_N1.1270.18
43_P291_K1.1270.18
230_M353_L1.1270.18
54_R208_E1.1260.18
138_V326_S1.1220.18
4_K154_E1.1210.18
186_E440_N1.1180.18
205_E315_K1.1180.18
123_K199_L1.1180.18
238_E434_E1.1170.18
386_S393_F1.1160.18
100_S427_I1.1150.18
242_D435_N1.1150.18
393_F404_P1.1150.18
26_P351_C1.1120.18
91_N243_Q1.1110.18
16_L103_E1.1100.18
124_V220_K1.1100.18
159_L194_T1.1090.18
14_F262_T1.1080.18
385_S424_I1.1080.18
152_I221_E1.1070.18
196_E216_L1.1070.18
13_F16_L1.1060.18
304_D322_E1.1060.18
37_I71_I1.1050.18
88_I103_E1.1030.18
97_R299_S1.1030.18
62_Q320_Y1.1020.17
163_D340_I1.1010.17
18_Q209_F1.1010.17
97_R329_K1.1000.17
54_R118_F1.0970.17
171_I302_D1.0930.17
253_E321_I1.0930.17
342_Q354_L1.0930.17
43_P100_S1.0920.17
23_I32_P1.0910.17
83_K121_M1.0900.17
256_D353_L1.0900.17
135_G450_L1.0870.17
403_Y429_S1.0860.17
427_I449_L1.0850.17
267_S367_N1.0840.17
426_T434_E1.0830.17
266_D382_L1.0820.17
187_E216_L1.0820.17
346_L350_H1.0820.17
319_Q398_F1.0810.17
404_P429_S1.0800.17
260_V344_F1.0800.17
204_T395_I1.0760.17
105_Q222_Q1.0760.17
78_A227_I1.0740.16
8_I12_E1.0720.16
192_T272_I1.0720.16
393_F403_Y1.0680.16
12_E23_I1.0650.16
124_V163_D1.0650.16
155_M397_L1.0640.16
258_Q271_T1.0640.16
287_R319_Q1.0630.16
385_S392_K1.0620.16
2_K9_T1.0620.16
170_E196_E1.0590.16
8_I23_I1.0580.16
203_K210_Q1.0570.16
89_N338_P1.0570.16
174_K183_N1.0560.16
57_I73_E1.0540.16
368_Y418_N1.0530.16
422_D439_K1.0490.16
303_E339_K1.0490.16
1_E17_L1.0470.16
46_L75_K1.0470.16
298_Q315_K1.0470.16
100_S222_Q1.0450.15
290_R445_I1.0450.15
247_S262_T1.0450.15
25_K88_I1.0450.15
57_I244_L1.0430.15
367_N419_T1.0430.15
176_L375_V1.0420.15
58_Q286_N1.0410.15
175_N182_D1.0400.15
138_V256_D1.0390.15
1_E19_V1.0380.15
52_V80_N1.0370.15
384_F393_F1.0350.15
329_K336_Q1.0350.15
372_N427_I1.0350.15
105_Q139_Q1.0310.15
28_Q256_D1.0310.15
121_M234_T1.0290.15
379_E414_N1.0290.15
429_S437_Y1.0280.15
358_I445_I1.0270.15
97_R100_S1.0260.15
154_E448_D1.0250.15
160_K397_L1.0240.15
56_K122_T1.0230.15
180_E387_S1.0210.15
142_Q324_K1.0210.15
391_A400_S1.0210.15
263_F371_M1.0200.15
65_E164_N1.0190.15
40_P374_D1.0190.15
142_Q177_E1.0190.15
102_E336_Q1.0190.15
312_L317_I1.0160.15
86_A96_M1.0160.15
38_N220_K1.0150.14
50_Q222_Q1.0140.14
155_M412_I1.0140.14
2_K19_V1.0130.14
345_S361_L1.0130.14
86_A315_K1.0130.14
56_K394_E1.0110.14
279_V368_Y1.0100.14
208_E408_L1.0100.14
88_I169_V1.0100.14
152_I241_L1.0090.14
58_Q176_L1.0090.14
163_D176_L1.0080.14
438_L449_L1.0080.14
76_L427_I1.0080.14
171_I220_K1.0080.14
438_L451_Q1.0060.14
72_E147_K1.0050.14
71_I149_Q1.0040.14
78_A84_L1.0010.14
230_M380_L1.0000.14
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  
4nfaA10.45011000.562Contact Map
1l8dA20.230691.50.976Contact Map
1i84S20.035591.30.976Contact Map
3hnwA20.279490.90.976Contact Map
2dfsA20.40889.80.976Contact Map
1fxkC10.228481.70.979Contact Map
3q8tA20.1996730.981Contact Map
3ojaB10.396972.90.981Contact Map
2zdiC10.257266.90.981Contact Map
2dawA10.250665.30.982Contact 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 0.0306 seconds.