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1PW4

ID: 1507586679 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 451 (406)
Sequences: 66419 (41009.2)
Seq/Len: 163.594
Nf(neff/√len): 2035.3

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: 163.594).

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
117_S121_V4.2461.00
101_L132_F3.5141.00
108_F125_L3.3281.00
110_G190_Y3.2671.00
103_A196_A3.0481.00
300_A354_I2.8751.00
154_G313_D2.8141.00
98_G135_M2.7581.00
105_V125_L2.7381.00
118_S121_V2.7121.00
120_A124_V2.7021.00
74_A127_F2.6631.00
91_P146_H2.6221.00
262_V394_G2.6081.00
152_E155_G2.5951.00
286_A289_K2.5891.00
266_L398_A2.5771.00
82_M135_M2.4021.00
375_A383_A2.3771.00
105_V128_L2.3621.00
60_S63_D2.2911.00
26_R152_E2.2631.00
105_V132_F2.2331.00
119_I123_F2.1941.00
87_D381_G2.1851.00
337_V352_C2.1581.00
78_S131_W2.0961.00
148_W156_I2.0961.00
304_G358_F2.0361.00
246_Q250_P2.0321.00
116_T121_V2.0081.00
59_F119_I1.9991.00
258_A390_F1.9961.00
96_P204_F1.9821.00
183_N187_A1.9501.00
70_G127_F1.9361.00
330_L359_L1.9361.00
270_G403_V1.9181.00
107_L193_A1.8831.00
201_L205_A1.8771.00
247_Y379_A1.8551.00
86_S139_P1.8411.00
347_T351_I1.8401.00
92_R96_P1.8241.00
116_T125_L1.8151.00
376_P379_A1.7871.00
34_F163_A1.7861.00
84_S88_R1.7681.00
417_M421_G1.7621.00
96_P200_A1.7541.00
109_M125_L1.7461.00
334_A352_C1.7431.00
103_A200_A1.7411.00
70_G123_F1.7301.00
63_D119_I1.7271.00
149_S152_E1.7181.00
78_S134_G1.7101.00
67_A122_M1.7041.00
100_I200_A1.6981.00
85_V94_F1.6831.00
109_M122_M1.6761.00
53_Y56_E1.6721.00
90_N93_V1.6531.00
334_A359_L1.6501.00
310_W314_K1.6211.00
327_F362_G1.5851.00
184_D187_A1.5801.00
103_A193_A1.5561.00
121_V125_L1.5421.00
334_A356_I1.5321.00
93_V97_A1.5101.00
289_K292_W1.5101.00
59_F63_D1.4951.00
297_Y357_G1.4731.00
51_M64_L1.4531.00
41_Y164_H1.4391.00
55_V64_L1.4391.00
83_G87_D1.4211.00
97_A101_L1.4171.00
280_K290_S1.4030.99
203_A207_M1.4030.99
319_N373_E1.4000.99
105_V129_C1.3920.99
144_M160_W1.3820.99
202_F206_M1.3630.99
190_Y194_F1.3630.99
120_A123_F1.3610.99
345_N348_V1.3580.99
107_L111_F1.3500.99
285_F289_K1.3480.99
178_G187_A1.3470.99
309_G313_D1.3440.99
308_C362_G1.3400.99
180_A288_D1.3350.99
29_I147_W1.3280.99
74_A78_S1.3270.99
78_S81_I1.3260.99
247_Y250_P1.3210.99
269_Y395_G1.3150.99
104_A108_F1.3030.99
89_S94_F1.3000.99
93_V209_D1.2950.99
50_A179_M1.2900.99
267_L423_S1.2820.99
73_I396_S1.2760.99
71_I133_Q1.2760.99
87_D382_T1.2730.99
278_Y283_K1.2720.99
76_G396_S1.2620.99
347_T350_M1.2610.99
255_W259_I1.2610.99
61_R408_D1.2500.99
300_A304_G1.2490.99
307_L310_W1.2480.99
101_L105_V1.2480.99
155_G310_W1.2440.98
249_L255_W1.2380.98
36_G136_G1.2320.98
394_G398_A1.2280.98
311_M315_V1.2250.98
86_S91_P1.2240.98
145_V153_R1.2230.98
332_T420_I1.2120.98
108_F111_F1.2060.98
90_N94_F1.2040.98
69_S396_S1.2010.98
194_F198_L1.1980.98
155_G313_D1.1890.98
187_A190_Y1.1830.98
85_V89_S1.1810.98
371_A387_T1.1810.98
65_G274_W1.1780.98
280_K287_L1.1770.98
150_Q153_R1.1760.98
81_I84_S1.1760.98
27_W31_L1.1760.98
103_A197_I1.1730.98
36_G95_L1.1720.98
329_T333_I1.1610.97
55_V61_R1.1610.97
332_T424_I1.1610.97
35_F199_V1.1590.97
106_M192_P1.1550.97
331_V359_L1.1510.97
264_V363_P1.1490.97
146_H380_A1.1450.97
28_Q206_M1.1410.97
124_V128_L1.1400.97
62_G408_D1.1390.97
108_F121_V1.1370.97
332_T427_V1.1260.97
327_F363_P1.1250.97
93_V96_P1.1210.97
270_G419_M1.1120.96
42_L171_P1.1100.96
96_P100_I1.1090.96
25_L28_Q1.1070.96
351_I354_I1.1020.96
98_G132_F1.1000.96
155_G159_V1.0990.96
54_L185_W1.0970.96
405_Y409_F1.0970.96
92_R209_D1.0960.96
334_A355_V1.0950.96
109_M189_L1.0760.95
153_R373_E1.0750.95
332_T336_I1.0740.95
263_F422_G1.0690.95
177_L181_W1.0680.95
279_L349_D1.0680.95
303_P307_L1.0680.95
43_V46_N1.0670.95
107_L190_Y1.0640.95
74_A130_G1.0630.95
36_G99_L1.0630.95
111_F190_Y1.0620.95
50_A188_A1.0620.95
89_S93_V1.0530.95
336_I420_I1.0490.94
30_F148_W1.0480.94
304_G307_L1.0340.94
252_K256_Y1.0330.94
50_A54_L1.0300.94
174_L177_L1.0270.94
68_L273_D1.0260.94
140_C160_W1.0240.93
38_A167_G1.0220.93
99_L200_A1.0210.93
91_P209_D1.0200.93
44_R75_Y1.0190.93
67_A119_I1.0190.93
97_A100_I1.0160.93
79_K388_G1.0150.93
278_Y282_V1.0150.93
406_T410_F1.0120.93
38_A170_I1.0110.93
279_L285_F1.0110.93
404_G408_D1.0090.93
201_L204_F1.0040.93
318_G321_G1.0040.93
91_P142_R1.0010.92
274_W404_G1.0010.92
193_A197_I1.0010.92
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  
1pw4A10.95571000.218Contact Map
4j05A20.83151000.32Contact Map
3wdoA10.88911000.341Contact Map
4pypA10.88911000.351Contact Map
3o7qA10.8471000.352Contact Map
2gfpA20.82261000.363Contact Map
4zw9A101000.377Contact Map
4ldsA20.88691000.385Contact Map
4gc0A10.92681000.391Contact Map
4xnjA101000.395Contact 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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