OPENSEQ.org
gremlin_3nmz_chainA

ID: 1517448877 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 458 (398)
Sequences: 3427 (2151.7)
Seq/Len: 8.611
Nf(neff/√len): 107.9

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: 8.611).

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
75_L105_A2.8691.00
130_E133_R2.8631.00
269_N313_N2.8611.00
185_M190_G2.7631.00
57_S108_N2.6111.00
66_M71_C2.6101.00
264_A310_A2.5441.00
118_R122_E2.5351.00
271_S313_N2.4651.00
311_L357_I2.4621.00
407_S447_N2.3941.00
57_S66_M2.3721.00
176_S185_M2.1951.00
375_L380_C2.1901.00
176_S226_N2.1751.00
267_L310_A2.1361.00
271_S282_L2.0421.00
312_W356_G2.0341.00
221_G266_V2.0201.00
360_N405_N1.9891.00
128_L133_R1.9761.00
128_L131_Q1.9751.00
417_L422_A1.9501.00
362_S375_L1.9481.00
282_L287_S1.9391.00
362_S405_N1.9311.00
280_K284_E1.8801.00
336_V380_C1.8691.00
373_Q377_E1.8681.00
313_N360_N1.8041.00
106_L171_V1.7951.00
172_L223_A1.7901.00
228_T269_N1.7791.00
415_E419_D1.7681.00
385_L422_A1.7611.00
325_I331_A1.7441.00
72_L106_L1.7391.00
183_H187_E1.7051.00
76_I123_I1.6591.00
77_Q80_H1.5801.00
400_C426_L1.5781.00
335_L357_I1.5731.00
39_S42_G1.5451.00
76_I125_V1.5391.00
426_L444_A1.5291.00
53_L105_A1.5251.00
53_L56_M1.5181.00
226_N269_N1.5041.00
397_S436_M1.5021.00
416_A420_M1.5011.00
304_L350_I1.4911.00
421_G424_S1.4831.00
315_S325_I1.4650.99
304_L307_V1.4570.99
103_S171_V1.4470.99
393_L396_V1.4460.99
46_K49_M1.4210.99
356_G398_N1.4140.99
265_S306_S1.4130.99
271_S310_A1.4090.99
309_S353_S1.3820.99
430_I442_A1.3640.99
184_A188_L1.3530.99
169_V223_A1.3530.99
257_E300_K1.3410.99
78_L98_A1.3400.99
418_W423_V1.3350.99
384_L399_A1.3350.99
101_R104_A1.3310.99
405_N447_N1.3290.99
224_L270_L1.3230.99
416_A419_D1.3190.99
216_L259_L1.3170.99
429_L437_I1.3150.99
323_A326_C1.3140.99
260_Q298_V1.3080.99
304_L341_Y1.3050.99
308_L357_I1.3030.99
323_A327_A1.3000.99
37_L40_M1.2930.98
121_R181_H1.2810.98
374_I378_N1.2810.98
424_S428_N1.2730.98
355_G387_H1.2690.98
385_L426_L1.2660.98
32_E35_Y1.2650.98
50_S75_L1.2560.98
217_R254_S1.2470.98
311_L361_V1.2450.98
107_H167_P1.2400.98
48_D51_R1.2280.98
38_L74_L1.2200.98
351_I354_G1.2190.98
379_N382_Q1.2110.97
376_R381_L1.2100.97
106_L175_L1.2090.97
312_W353_S1.2040.97
110_I174_K1.2020.97
315_S360_N1.2010.97
310_A314_L1.1990.97
248_L266_V1.1880.97
249_V285_V1.1860.97
174_K360_N1.1850.97
67_R116_D1.1810.97
359_R401_G1.1790.97
257_E302_S1.1660.97
355_G402_T1.1660.97
316_A360_N1.1600.96
107_H170_C1.1560.96
36_S40_M1.1500.96
267_L282_L1.1440.96
104_A170_C1.1360.96
116_D120_R1.1340.96
400_C429_L1.1330.96
29_T32_E1.1300.96
353_S356_G1.1270.96
176_S182_R1.1260.95
306_S353_S1.1250.95
195_A249_V1.1240.95
358_L402_T1.1240.95
42_G74_L1.1210.95
50_S57_S1.1210.95
384_L402_T1.1190.95
400_C444_A1.1180.95
169_V384_L1.1180.95
291_L310_A1.1160.95
40_M52_T1.1080.95
400_C441_S1.1070.95
288_V326_C1.1020.95
309_S352_E1.1020.95
125_V171_V1.1010.95
404_W430_I1.0960.95
194_I220_A1.0940.94
111_H174_K1.0930.94
173_M222_M1.0870.94
55_A58_S1.0870.94
268_R313_N1.0870.94
35_Y39_S1.0860.94
358_L428_N1.0820.94
403_L444_A1.0810.94
222_M226_N1.0800.94
175_L178_D1.0770.94
222_M262_V1.0760.94
287_S315_S1.0750.94
27_L30_K1.0720.94
390_S432_S1.0720.94
76_I79_L1.0680.94
315_S357_I1.0660.93
387_H395_I1.0650.93
110_I120_R1.0640.93
268_R309_S1.0620.93
120_R125_V1.0580.93
268_R306_S1.0570.93
238_L244_C1.0560.93
38_L49_M1.0530.93
172_L271_S1.0520.93
240_S243_G1.0460.93
173_M176_S1.0460.93
227_L311_L1.0420.92
80_H131_Q1.0410.92
262_V265_S1.0410.92
322_K330_G1.0410.92
225_T262_V1.0370.92
352_E395_I1.0360.92
277_N412_K1.0320.92
110_I309_S1.0320.92
78_L102_A1.0320.92
194_I198_L1.0300.92
400_C427_K1.0290.92
385_L421_G1.0290.92
77_Q224_L1.0290.92
351_I358_L1.0270.92
115_D119_G1.0260.92
378_N382_Q1.0260.92
376_R406_L1.0260.92
281_T285_V1.0250.92
116_D119_G1.0240.92
54_L101_R1.0210.91
102_A425_M1.0190.91
355_G448_L1.0190.91
398_N401_G1.0170.91
296_L308_L1.0170.91
260_Q351_I1.0140.91
305_K350_I1.0110.91
393_L434_H1.0090.91
327_A377_E1.0040.90
360_N401_G1.0040.90
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  
3nmzA20.88651000.303Contact Map
4rxhB101000.396Contact Map
4uaeA10.80791000.401Contact Map
4uafB10.82751000.404Contact Map
4uadA10.811000.406Contact Map
4rv1A60.8691000.408Contact Map
3l6xA10.83621000.414Contact Map
2jdqA20.86681000.417Contact Map
3opbA20.89521000.424Contact Map
1xm9A10.81441000.43Contact 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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