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NRAMP_1000

ID: 1501613013 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 406 (390)
Sequences: 4399 (2574.3)
Seq/Len: 11.279
Nf(neff/√len): 130.4

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: 11.279).

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
67_A75_K6.5421.00
175_D178_A4.5901.00
76_R371_M3.3471.00
372_K379_V3.2751.00
274_A277_P2.9811.00
370_N384_K2.8321.00
382_G385_A2.5261.00
363_L391_L2.5131.00
369_Q380_V2.4711.00
56_A60_R2.4381.00
347_P350_T2.4121.00
53_V390_A2.3961.00
366_F387_L2.3751.00
179_L251_T2.3091.00
61_Q369_Q2.3071.00
363_L395_A2.3021.00
77_L367_L2.2051.00
50_L390_A2.0861.00
97_Q101_Y2.0851.00
176_F179_L2.0831.00
64_L378_D2.0621.00
399_V403_A2.0471.00
380_V384_K2.0181.00
216_Y309_L1.9691.00
370_N380_V1.9611.00
41_L247_T1.9311.00
247_T251_T1.9261.00
276_E280_G1.9201.00
159_F163_G1.9131.00
371_M374_Y1.9121.00
31_L35_A1.9101.00
93_S97_Q1.8951.00
52_V236_G1.8931.00
79_P90_F1.8811.00
240_F244_V1.8791.00
363_L367_L1.8451.00
277_P282_T1.7751.00
368_L374_Y1.7691.00
346_V349_A1.7581.00
68_R71_D1.7541.00
56_A232_N1.7321.00
277_P285_R1.7251.00
388_W392_L1.7201.00
277_P280_G1.6901.00
88_T93_S1.6671.00
286_I290_F1.6371.00
160_F290_F1.6311.00
67_A72_V1.6261.00
79_P91_V1.6171.00
184_F247_T1.6121.00
176_F180_L1.6071.00
114_V131_A1.6061.00
28_S200_G1.5861.00
14_W238_S1.5791.00
123_P126_L1.5711.00
61_Q72_V1.5701.00
362_Y391_L1.5581.00
90_F94_V1.5341.00
181_G185_G1.5301.00
79_P88_T1.5221.00
45_P183_L1.5161.00
148_R152_R1.5101.00
400_A404_A1.5071.00
57_A380_V1.4811.00
59_G231_K1.4761.00
6_Y233_F1.4751.00
178_A182_G1.4621.00
392_L396_I1.4591.00
276_E281_L1.4491.00
174_V179_L1.4451.00
158_L298_T1.4441.00
177_K181_G1.4351.00
191_T276_E1.4301.00
225_R377_E1.4171.00
278_L281_L1.3920.99
183_L247_T1.3630.99
60_R380_V1.3610.99
106_A109_K1.3610.99
271_A274_A1.3550.99
367_L371_M1.3540.99
17_S21_L1.3520.99
340_A344_F1.3470.99
177_K180_L1.3340.99
181_G187_H1.3260.99
32_A197_L1.3140.99
339_F343_P1.3130.99
57_A387_L1.3050.99
58_I62_T1.3010.99
283_L287_V1.2630.99
304_M308_G1.2600.99
367_L388_W1.2580.99
134_A297_F1.2530.99
63_L231_K1.2520.99
366_F391_L1.2460.98
19_I302_L1.2460.98
190_G193_E1.2440.98
70_Y310_V1.2430.98
131_A293_L1.2370.98
110_D299_T1.2370.98
370_N388_W1.2350.98
191_T350_T1.2240.98
63_L224_G1.2230.98
27_G272_A1.2220.98
366_F370_N1.2200.98
322_G325_K1.2170.98
170_V173_G1.2150.98
20_T242_P1.2130.98
48_M243_F1.2110.98
45_P243_F1.2100.98
29_T246_A1.2070.98
277_P281_L1.2060.98
228_L232_N1.2010.98
190_G349_A1.1940.98
369_Q375_L1.1930.98
122_L130_V1.1890.98
157_M294_S1.1870.98
191_T347_P1.1850.98
359_P395_A1.1810.98
38_Y256_N1.1810.98
391_L395_A1.1800.98
22_G25_S1.1790.98
200_G352_S1.1740.98
13_G17_S1.1690.97
128_L342_L1.1660.97
147_L220_A1.1620.97
166_F248_S1.1610.97
20_T209_N1.1560.97
98_F357_M1.1510.97
169_V248_S1.1500.97
380_V383_P1.1460.97
32_A201_Q1.1390.97
44_N250_V1.1300.97
102_S106_A1.1140.96
125_V343_P1.1090.96
64_L228_L1.1080.96
149_T152_R1.1070.96
23_A296_C1.1060.96
39_K189_P1.1030.96
65_T374_Y1.1010.96
152_R155_K1.0990.96
229_R233_F1.0990.96
204_A207_G1.0920.96
39_K187_H1.0900.96
190_G346_V1.0820.96
340_A343_P1.0810.95
188_I194_G1.0790.95
55_F70_Y1.0760.95
36_F197_L1.0730.95
335_A339_F1.0720.95
126_L129_L1.0720.95
72_V75_K1.0720.95
326_A330_L1.0700.95
273_H285_R1.0700.95
54_V362_Y1.0590.95
389_N392_L1.0570.95
130_V133_T1.0540.95
286_I289_S1.0480.94
317_F321_G1.0460.94
102_S105_T1.0420.94
158_L162_V1.0370.94
67_A71_D1.0350.94
396_I399_V1.0340.94
72_V368_L1.0300.94
241_L245_L1.0270.94
172_T256_N1.0230.93
74_R92_S1.0170.93
2_R6_Y1.0160.93
267_G271_A1.0140.93
99_P106_A1.0110.93
168_V252_I1.0100.93
38_Y175_D1.0090.93
196_T352_S1.0070.93
257_T260_A1.0070.93
59_G66_H1.0060.93
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  
4wgvA20.90391000.173Contact Map
3dh4A40.913898.50.87Contact Map
3giaA10.9163980.889Contact Map
2xq2A10.9138980.889Contact Map
3l1lA10.884297.80.892Contact Map
2jlnA10.928697.20.904Contact Map
4djkA20.879396.20.916Contact Map
4us3A10.916394.90.923Contact Map
2a65A10.940994.10.926Contact Map
4xp4A1092.10.931Contact 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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