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OPENSEQ.org

NRAMP -force run

ID: 1498853995 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 568 (501)
Sequences: 384 (172.9)
Seq/Len: 0.766
Nf(neff/√len): 7.7

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: 0.766).

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
461_T472_N2.8941.00
172_I180_I2.4270.98
131_L139_R2.1170.95
240_M312_V2.0720.94
109_L240_M2.0000.93
186_V420_I1.9970.93
425_L429_F1.9540.92
69_K291_E1.6690.80
84_Y265_M1.6650.80
152_M449_Q1.6350.78
286_K469_D1.6250.78
447_S494_F1.5830.75
264_I454_L1.5590.73
198_F232_S1.5520.73
102_F172_I1.5400.72
84_Y450_L1.5250.71
163_Q443_N1.5100.70
397_V471_A1.5080.70
269_M457_I1.5000.69
85_L315_V1.4970.69
165_V186_V1.4860.68
380_L451_P1.4750.67
363_L368_G1.4720.67
184_G471_A1.4690.67
436_T440_D1.4670.67
322_F444_V1.4480.65
154_E165_V1.4380.64
137_C150_W1.4380.64
534_G538_L1.4330.64
115_G307_S1.4230.63
516_V523_F1.4180.63
164_E419_A1.4130.62
54_K57_I1.4120.62
165_V452_F1.3830.60
150_W401_F1.3470.57
232_S496_V1.3360.56
464_R471_A1.3330.56
256_A404_L1.3230.55
176_S373_Y1.3170.54
180_I376_A1.3170.54
117_L209_A1.3170.54
85_L90_I1.3050.53
98_A322_F1.2920.52
151_L516_V1.2890.52
475_G519_L1.2860.52
157_I397_V1.2740.51
268_N272_H1.2740.51
132_H135_E1.2740.51
540_C543_T1.2690.50
199_L202_Y1.2620.50
325_K397_V1.2590.49
70_L206_K1.2590.49
226_Y233_Q1.2580.49
164_E386_S1.2540.49
179_R492_M1.2520.49
50_Y58_P1.2470.48
309_I326_T1.2460.48
153_V162_M1.2460.48
160_S262_A1.2410.48
55_I58_P1.2400.48
407_S410_A1.2340.47
267_H272_H1.2340.47
150_W451_P1.2290.47
379_I457_I1.2270.47
114_V483_L1.2250.47
378_G443_N1.2240.46
532_A536_S1.2190.46
533_L536_S1.2140.46
225_E371_A1.2120.45
81_S453_A1.2110.45
378_G446_Q1.2100.45
411_R416_R1.2080.45
302_I377_V1.2060.45
71_W80_M1.2060.45
94_L264_I1.2020.45
413_V488_C1.2020.45
355_D358_K1.1960.44
245_C248_C1.1950.44
70_L82_I1.1930.44
118_L270_Y1.1910.44
162_M310_I1.1910.44
318_F443_N1.1900.44
535_M538_L1.1900.44
444_V457_I1.1890.43
163_Q442_L1.1880.43
122_A252_Q1.1860.43
161_D416_R1.1840.43
483_L496_V1.1840.43
409_F463_L1.1810.43
272_H304_L1.1800.43
109_L231_P1.1800.43
131_L145_P1.1770.42
151_L219_A1.1770.42
401_F451_P1.1770.42
163_Q378_G1.1710.42
67_F238_K1.1690.42
424_L458_L1.1680.42
204_L210_F1.1660.41
517_A525_L1.1640.41
299_E392_Y1.1610.41
411_R419_A1.1610.41
310_I317_V1.1610.41
218_M264_I1.1580.41
461_T467_M1.1560.41
183_W218_M1.1540.40
521_F525_L1.1520.40
299_E375_W1.1520.40
91_E95_Q1.1510.40
94_L314_V1.1470.40
211_F375_W1.1460.40
143_K182_L1.1460.40
115_G375_W1.1450.40
375_W378_G1.1440.40
259_I399_E1.1430.40
102_F320_E1.1410.39
44_E48_A1.1410.39
519_L523_F1.1400.39
265_M389_T1.1350.39
162_M174_L1.1350.39
449_Q453_A1.1340.39
169_A281_V1.1340.39
503_G509_V1.1340.39
220_L284_N1.1330.39
143_K377_V1.1320.39
264_I310_I1.1310.39
161_D391_T1.1300.38
121_L137_C1.1280.38
44_E47_F1.1270.38
129_T137_C1.1250.38
238_K242_V1.1240.38
122_A424_L1.1240.38
479_A482_I1.1230.38
109_L308_F1.1230.38
68_R73_F1.1220.38
129_T133_L1.1180.38
169_A186_V1.1180.38
249_R252_Q1.1160.37
178_G458_L1.1130.37
532_A535_M1.1080.37
159_G378_G1.1060.37
182_L242_V1.1060.37
118_L136_V1.1030.36
137_C401_F1.1020.36
482_I514_V1.1010.36
150_W168_S1.1000.36
213_F217_I1.0980.36
382_A442_L1.0980.36
219_A455_I1.0980.36
474_L478_I1.0970.36
172_I176_S1.0960.36
100_A375_W1.0960.36
531_I534_G1.0960.36
125_L199_L1.0950.36
73_F79_L1.0950.36
91_E314_V1.0940.36
204_L406_W1.0940.36
163_Q439_N1.0930.36
115_G443_N1.0920.35
81_S210_F1.0920.35
67_F241_F1.0900.35
378_G442_L1.0900.35
212_G420_I1.0890.35
174_L315_V1.0870.35
193_T262_A1.0870.35
106_W116_L1.0860.35
111_A124_R1.0860.35
443_N446_Q1.0850.35
388_M412_V1.0850.35
77_G310_I1.0850.35
439_N442_L1.0840.35
224_Y460_F1.0840.35
82_I317_V1.0830.35
85_L163_Q1.0810.35
209_A214_L1.0800.34
166_I313_F1.0760.34
385_S453_A1.0760.34
187_L516_V1.0750.34
112_T115_G1.0750.34
268_N273_S1.0720.34
199_L462_S1.0710.34
322_F354_V1.0690.34
148_I227_V1.0680.34
417_S483_L1.0680.34
49_T102_F1.0680.34
161_D415_T1.0680.34
136_V459_T1.0670.33
151_L485_L1.0660.33
523_F527_W1.0650.33
166_I420_I1.0640.33
245_C399_E1.0620.33
161_D411_R1.0600.33
136_V457_I1.0600.33
245_C397_V1.0600.33
106_W363_L1.0590.33
300_S329_Q1.0580.33
115_G218_M1.0580.33
503_G506_A1.0580.33
159_G446_Q1.0580.33
150_W171_A1.0580.33
509_V514_V1.0570.33
85_L263_V1.0520.32
475_G479_A1.0500.32
386_S467_M1.0500.32
518_Y525_L1.0490.32
274_A321_A1.0460.32
86_D89_N1.0450.32
146_R223_G1.0450.32
142_P178_G1.0440.32
263_V315_V1.0440.32
384_Q387_T1.0440.32
132_H455_I1.0430.32
48_A52_N1.0430.32
290_R464_R1.0410.32
124_R293_N1.0410.32
333_V338_S1.0400.31
381_A387_T1.0390.31
131_L136_V1.0390.31
267_H304_L1.0390.31
163_Q412_V1.0380.31
235_Q238_K1.0370.31
150_W398_M1.0360.31
382_A401_F1.0360.31
128_V389_T1.0360.31
132_H274_A1.0360.31
71_W74_T1.0350.31
254_E414_L1.0340.31
212_G517_A1.0330.31
170_I270_Y1.0310.31
518_Y524_Y1.0290.31
269_M458_L1.0270.30
193_T450_L1.0270.30
318_F446_Q1.0260.30
375_W443_N1.0240.30
418_I488_C1.0210.30
163_Q318_F1.0200.30
80_M189_T1.0190.30
166_I435_L1.0180.30
280_Q359_G1.0170.30
108_L487_I1.0140.30
455_I522_V1.0140.30
391_T394_G1.0120.29
412_V443_N1.0120.29
166_I413_V1.0110.29
78_F392_Y1.0100.29
515_S523_F1.0090.29
217_I513_V1.0070.29
109_L241_F1.0050.29
179_R431_D1.0040.29
266_P387_T1.0020.29
239_G279_R1.0020.29
115_G378_G1.0010.29
102_F356_I1.0010.29
281_V357_Y1.0010.29
177_V309_I1.0000.29
207_L211_F1.0000.29
68_R381_A1.0000.29
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  
4wgvA20.69011000.535Contact Map
3dh4A40.748296.80.967Contact Map
2jlnA10.7596.80.967Contact Map
4djkA20.716586.90.977Contact Map
3giaA10.723684.50.978Contact Map
2xq2A10.769480.50.979Contact Map
3l1lA10.695461.30.982Contact Map
4xp4A1030.40.985Contact Map
4lz6A10.71322.40.986Contact Map
1u5dA40.14797.80.989Contact 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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