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P38105

ID: 1507886928 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 339 (337)
Sequences: 74179 (45238.6)
Seq/Len: 220.116
Nf(neff/√len): 2464.3

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: 220.116).

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
32_K137_D3.1451.00
30_K66_D3.0731.00
32_K64_V2.9721.00
315_H318_D2.9611.00
28_R66_D2.7421.00
163_T188_N2.6681.00
7_E15_V2.5741.00
76_R79_E2.5601.00
79_E130_K2.5241.00
27_V128_A2.5241.00
80_R131_I2.5151.00
136_A139_Y2.5001.00
181_K208_D2.4301.00
138_Q310_T2.4031.00
30_K64_V2.3751.00
19_I120_Y2.3271.00
311_F322_L2.3231.00
30_K120_Y2.3191.00
164_V180_L2.2561.00
309_H322_L2.2241.00
310_T336_T2.2211.00
61_F116_G2.2151.00
221_I224_E2.2051.00
200_E204_E2.2021.00
7_E13_A2.1951.00
61_F83_V2.1711.00
199_L203_K2.1701.00
188_N209_W2.1561.00
294_D298_K2.1421.00
24_A70_E2.1351.00
169_A191_V2.1231.00
5_L15_V2.0991.00
74_S125_A2.0571.00
23_S26_E2.0551.00
80_R137_D2.0411.00
177_V207_A2.0381.00
159_T162_D2.0291.00
62_F137_D2.0001.00
134_A297_S1.9841.00
321_S325_Q1.9791.00
312_D315_H1.9681.00
28_R122_V1.9671.00
24_A71_G1.9661.00
66_D120_Y1.9381.00
25_G71_G1.9221.00
45_R324_E1.9161.00
200_E203_K1.8661.00
165_L192_A1.8161.00
165_L229_P1.8061.00
199_L210_A1.7901.00
322_L327_Q1.7701.00
146_F175_T1.7681.00
21_T67_A1.7671.00
131_I137_D1.7481.00
230_T250_S1.7371.00
318_D321_S1.7351.00
254_R278_S1.7331.00
196_D200_E1.7141.00
190_I229_P1.7131.00
318_D322_L1.7081.00
311_F319_A1.6831.00
193_D199_L1.6601.00
201_K204_E1.6391.00
254_R280_F1.6371.00
28_R120_Y1.6291.00
4_I316_V1.6261.00
67_A77_V1.6211.00
131_I140_A1.6131.00
75_A130_K1.6051.00
182_G300_L1.5911.00
249_A255_I1.5851.00
167_Y245_A1.5761.00
162_D254_R1.5751.00
64_V80_R1.5631.00
188_N208_D1.5591.00
26_E124_P1.5581.00
68_V77_V1.5581.00
75_A79_E1.5411.00
196_D212_N1.5201.00
25_G124_P1.5161.00
138_Q336_T1.5101.00
117_F320_I1.5091.00
28_R67_A1.5051.00
31_V61_F1.4991.00
69_G72_V1.4841.00
26_E122_V1.4731.00
2_K16_E1.4731.00
249_A277_L1.4691.00
232_I249_A1.4611.00
249_A253_A1.4501.00
216_T221_I1.4501.00
80_R133_E1.4491.00
212_N215_Q1.4381.00
317_A321_S1.4341.00
33_L138_Q1.4261.00
156_G231_L1.4241.00
22_P122_V1.4221.00
92_C95_C1.4161.00
196_D215_Q1.4131.00
232_I245_A1.3960.99
217_P220_E1.3950.99
3_S17_R1.3910.99
308_T322_L1.3900.99
27_V75_A1.3680.99
44_Y320_I1.3580.99
65_I75_A1.3530.99
294_D297_S1.3530.99
176_I233_I1.3480.99
32_K80_R1.3460.99
92_C103_C1.3380.99
2_K314_Q1.3380.99
2_K119_E1.3380.99
64_V137_D1.3340.99
22_P28_R1.3260.99
163_T190_I1.3250.99
154_G291_I1.3120.99
167_Y192_A1.3050.99
177_V191_V1.3000.99
194_R213_N1.2950.99
33_L336_T1.2940.99
31_V121_A1.2720.99
4_I14_I1.2690.99
196_D199_L1.2630.99
95_C103_C1.2490.99
154_G288_K1.2430.98
220_E224_E1.2360.98
89_C92_C1.2270.98
19_I28_R1.2170.98
313_F337_F1.1870.98
75_A128_A1.1860.98
25_G125_A1.1750.98
163_T230_T1.1640.97
199_L212_N1.1570.97
8_K11_Q1.1500.97
291_I294_D1.1500.97
312_D336_T1.1450.97
143_I296_L1.1370.97
29_V63_G1.1320.97
139_Y304_E1.1220.97
89_C95_C1.1080.96
66_D77_V1.1070.96
33_L137_D1.1000.96
295_W300_L1.0950.96
203_K210_A1.0950.96
316_V335_L1.0740.95
36_I319_A1.0720.95
123_V128_A1.0720.95
162_D230_T1.0700.95
4_I313_F1.0700.95
22_P26_E1.0660.95
89_C103_C1.0660.95
139_Y302_K1.0640.95
178_Q302_K1.0620.95
151_N288_K1.0610.95
204_E305_K1.0590.95
149_A176_I1.0560.95
234_D237_C1.0560.95
158_P186_V1.0540.95
236_A241_I1.0510.94
217_P221_I1.0480.94
247_T271_G1.0430.94
201_K330_C1.0410.94
191_V207_A1.0390.94
219_G247_T1.0330.94
29_V81_V1.0320.94
5_L17_R1.0320.94
44_Y324_E1.0240.93
286_A290_P1.0210.93
321_S324_E1.0080.93
34_A117_F1.0040.93
302_K305_K1.0020.92
158_P162_D1.0000.92
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  
4ilkA20.98821000.043Contact Map
4ej6A10.98531000.071Contact Map
2dq4A20.98531000.074Contact Map
4oh1A10.97051000.089Contact Map
3ukoA20.98821000.09Contact Map
3m6iA20.98821000.093Contact Map
4gkvA40.97941000.093Contact Map
4uejA201000.095Contact Map
1e3jA10.99121000.1Contact Map
4cpdA40.98231000.1Contact 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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