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OPENSEQ.org

CENPN -force run

ID: 1493994672 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 494 (431)
Sequences: 322 (214.5)
Seq/Len: 0.747
Nf(neff/√len): 10.3

Jackhmmer Results: (2016_04)
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: 0.747).

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
450_G456_G2.3090.97
30_I33_A2.2410.97
453_V456_G2.0620.94
450_G453_V1.9670.92
196_I225_R1.8850.89
456_G472_P1.8210.87
450_G472_P1.8020.86
307_W454_F1.7070.82
54_A71_K1.5680.73
454_F484_G1.5190.70
261_I265_V1.4750.67
357_A464_G1.4580.65
51_P55_D1.4520.65
299_R311_A1.4390.64
366_G458_R1.4300.63
69_P76_L1.4220.62
115_D228_Y1.4010.61
195_R365_F1.4000.61
355_K359_T1.3860.59
105_G110_Q1.3840.59
191_L232_P1.3820.59
120_D184_S1.3750.59
28_A117_A1.3750.59
245_A248_P1.3700.58
246_T250_S1.3610.57
105_G180_H1.3480.56
307_W310_Y1.3460.56
448_F475_M1.3460.56
60_P71_K1.3300.55
318_S438_T1.3250.54
70_C74_E1.3180.54
96_R112_A1.3150.53
456_G460_L1.3120.53
453_V472_P1.3090.53
149_K245_A1.3050.53
454_F477_G1.3020.52
385_Q440_W1.2910.51
115_D230_A1.2900.51
318_S321_D1.2870.51
44_Y248_P1.2860.51
287_N291_L1.2860.51
373_D455_A1.2830.51
97_I102_W1.2790.50
327_P330_S1.2760.50
364_R462_E1.2760.50
472_P475_M1.2700.50
313_E316_K1.2680.49
461_V468_G1.2630.49
8_L12_S1.2610.49
50_S66_L1.2600.49
468_G473_G1.2570.49
10_V14_N1.2530.48
131_Y240_I1.2520.48
294_K452_H1.2510.48
200_E257_L1.2440.47
72_S75_E1.2430.47
165_F288_L1.2400.47
238_L357_A1.2370.47
96_R105_G1.2330.46
246_T249_I1.2300.46
100_G113_M1.2270.46
296_G311_A1.2260.46
131_Y242_R1.2250.46
182_H191_L1.2240.46
147_I247_G1.2210.45
51_P54_A1.2210.45
191_L230_A1.2200.45
20_A73_I1.2160.45
364_R477_G1.2150.45
345_R350_H1.2140.45
165_F225_R1.2090.44
111_L190_P1.2080.44
122_H160_F1.2040.44
307_W484_G1.2000.44
186_P189_F1.1980.43
283_L286_R1.1970.43
97_I106_L1.1950.43
363_A380_F1.1950.43
115_D195_R1.1930.43
132_K279_K1.1930.43
256_S290_A1.1860.42
469_E483_T1.1840.42
361_A461_V1.1800.42
107_T175_P1.1790.42
281_T295_R1.1790.42
195_R228_Y1.1770.42
296_G364_R1.1770.42
247_G441_T1.1760.42
366_G377_I1.1730.41
434_E446_I1.1710.41
169_L269_L1.1700.41
57_D60_P1.1690.41
55_D250_S1.1630.41
279_K466_V1.1620.40
66_L69_P1.1540.40
270_S281_T1.1520.40
306_G468_G1.1520.40
120_D182_H1.1510.40
150_A227_I1.1480.39
158_P175_P1.1430.39
296_G477_G1.1410.39
269_L283_L1.1410.39
76_L79_L1.1390.39
44_Y249_I1.1370.38
264_G287_N1.1340.38
229_L438_T1.1330.38
307_W361_A1.1320.38
165_F232_P1.1320.38
165_F270_S1.1310.38
364_R476_T1.1280.38
28_A33_A1.1280.38
115_D297_P1.1250.37
35_D65_D1.1170.37
186_P190_P1.1160.37
239_Y261_I1.1150.37
11_E14_N1.1140.37
102_W110_Q1.1140.37
53_R57_D1.1120.36
50_S71_K1.1090.36
441_T483_T1.1080.36
105_G108_L1.1070.36
64_A244_Q1.1050.36
25_S51_P1.1040.36
107_T131_Y1.1040.36
488_N491_I1.1020.36
285_S295_R1.1010.36
6_S244_Q1.1010.36
321_D470_R1.1000.35
21_I106_L1.1000.35
165_F185_R1.1000.35
20_A40_P1.0930.35
196_I279_K1.0910.35
112_A180_H1.0910.35
77_H487_K1.0900.35
148_L246_T1.0900.35
170_Q228_Y1.0900.35
455_A458_R1.0890.35
361_A373_D1.0890.35
14_N17_V1.0890.35
446_I476_T1.0890.35
293_D300_S1.0890.35
184_S243_A1.0880.35
71_K245_A1.0880.35
185_R233_D1.0870.34
230_A235_S1.0870.34
118_Y122_H1.0860.34
458_R461_V1.0850.34
151_D244_Q1.0850.34
484_G491_I1.0850.34
331_R437_P1.0840.34
164_T168_S1.0830.34
115_D460_L1.0830.34
376_G473_G1.0800.34
266_P270_S1.0800.34
111_L123_P1.0780.34
285_S317_K1.0750.34
44_Y148_L1.0740.33
165_F177_I1.0740.33
162_P235_S1.0740.33
54_A57_D1.0710.33
102_W105_G1.0700.33
393_G437_P1.0700.33
263_N447_N1.0660.33
80_Y101_D1.0650.33
200_E254_S1.0650.33
147_I245_A1.0640.33
290_A351_E1.0640.33
117_A121_E1.0630.33
162_P167_Q1.0630.33
285_S482_T1.0620.33
235_S310_Y1.0620.33
149_K248_P1.0590.32
393_G453_V1.0580.32
110_Q113_M1.0560.32
165_F236_P1.0540.32
192_L286_R1.0530.32
290_A294_K1.0480.32
378_E473_G1.0470.31
148_L249_I1.0450.31
27_E215_S1.0440.31
484_G489_G1.0440.31
164_T458_R1.0410.31
185_R192_L1.0410.31
65_D244_Q1.0400.31
363_A452_H1.0400.31
456_G462_E1.0380.31
107_T325_P1.0380.31
310_Y475_M1.0350.31
115_D223_S1.0340.30
12_S132_K1.0330.30
229_L265_V1.0320.30
26_R30_I1.0320.30
229_L241_T1.0320.30
287_N310_Y1.0300.30
34_L37_L1.0290.30
246_T340_A1.0290.30
16_A286_R1.0290.30
460_L467_D1.0280.30
6_S35_D1.0260.30
113_M231_F1.0250.30
157_L320_L1.0240.30
217_N237_A1.0240.30
106_L310_Y1.0240.30
270_S296_G1.0230.30
20_A82_D1.0220.30
356_R360_V1.0220.30
299_R303_A1.0210.30
93_V162_P1.0200.29
79_L83_L1.0200.29
27_E76_L1.0190.29
332_E467_D1.0190.29
458_R464_G1.0180.29
200_E361_A1.0180.29
71_K147_I1.0170.29
246_T251_H1.0170.29
266_P269_L1.0170.29
162_P192_L1.0160.29
27_E73_I1.0150.29
455_A474_W1.0150.29
172_Q241_T1.0110.29
6_S76_L1.0110.29
95_S169_L1.0110.29
55_D74_E1.0100.29
311_A319_P1.0090.29
108_L115_D1.0080.29
94_V114_I1.0080.29
384_M485_V1.0060.28
134_Q167_Q1.0050.28
149_K246_T1.0050.28
95_S166_L1.0050.28
9_R304_G1.0040.28
244_Q252_G1.0040.28
100_G158_P1.0030.28
97_I108_L1.0030.28
165_F239_Y1.0020.28
150_A244_Q1.0010.28
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  
4je3B10.155999.90.803Contact Map
4c3eA160.0931120.98Contact Map
3j7yb10.2874110.98Contact Map
3q6aA80.09518.20.981Contact Map
2a8eA10.17217.30.981Contact Map
3hwuA10.12357.20.981Contact Map
4cs9A30.10326.80.982Contact Map
2pidA20.18226.80.982Contact Map
1h1jS10.0876.50.982Contact Map
3j39U10.125560.982Contact 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.

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